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ToxLab Forms 3.1 User Guide Version A

1. 17 User Administration 20 Ser 3 sce RE ESUASESERUM STEAM puya qows EB DENS ERES 25 Project dERIBISCHHEIOM aaa sheet anne ee ed deri E beue 28 Compound D atastoreu Jul uyan bam nteraces hee medene sqa ede dd x 30 Application Configuration sse u md Races ded dena Rue ERE Rd C 37 Specifying the General Configuration 37 Specifying the Reports Configuration 42 Chapter4 Using the Method Development Mode 49 Working with Master Methods 52 Creating a New Master Method o c02 seuenvic cp eeydueecebeeece ee 53 Editing a Master Method 70 Creating a Method Template 139 Psponi e SRM Datar u u ssssasukaqawaqaqpaqasqaaqaqaqauqpuaqsaaaa 148 Working with Instrument Methods 149 Thermo Scientific ToxLab Forms 3 1 User Guide i Contents Chapter 5 Appendix A ToxLab Forms 3 1 User Guide Working with Development Batches 153 Creatine a Development Batch ss eue dde tor deuce aan 153 Editing Samples in a Development Batch 156 Acquiring Samples in a Development Batch 158 Using the Production Mode 161 Workine in Batch V
2. c 46 99 33 95 204 77 I 767 02 201 72 354 78 415 25 440 60 Relative Intensi Ln c m 50 100 150 200 250 300 350 450 miz 8 Select a filter from the Filter list 9 Click the peak in the chromatogram that represents the compound you want to add to the method 10 Right click and choose Add This Peak as New Compound from the shortcut menu 86 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 0 65 D B 7 Add this peak as new quan peak Add this peak as new compound Reset scaling Show graphics side by side 245 242 0 5 1 0 1 5 2 0 2 5 3 0 The ToxLab Forms application performs a library search for the selected compound The application uses the first match it finds as the compound name the base peak of the mass spectrum as the quan peak and the second and third largest ions as the confirming ions If the name of the first match is already in the library the Add New Compound dialog box opens Add new compound Mame of new compound Methylene Chloride Methylene Chloride HL 95508 BP 48 89 Relative Intensity x ient e 7207 79 00 ns Library results Methylene Chloride MAINLIB 338 MP 1 Ea HL 393 BP 49 00 t e m Relative Intensity amp eo e ho m 14 00 24 00 31 00 75 00 NL 939 BP 112 00 112 00 11 Optional In the Add New Compound dialog box do the following
3. Method View See Working with Master Methods on page 52 Create method Opens the Create Master Method dialog box where you can choose the process you want to use to begin your master method Open method Opens the Open Master Method dialog box where you can choose a master method to open 50 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Table 12 Method Development navigation pane functions Sheet 2 of 2 Function Export SRM data Recent Files Instrument View New instrument method Open instrument method Development Batch Select batch location New sample list Open Qual Browser Description Writes the selected reaction monitoring SRM table to the following file Thermo ToxLab Forms Methods wmethodname xm You can use the data in this file in the instrument method editor when you open the TSQ 2 1 application This command is available only when you have selected Enable Compound Datastore on the General page of the Application Configuration view See Application Configuration on page 37 Displays recently saved master methods See Working with Instrument Methods on page 149 Opens the Instrument View where you can specify instrument settings for your configured instruments If the instrument you want to use is not configured close the ToxLab Forms application configure the instrument and then reopen the ToxLab Forms
4. High Density Sample Report 2 Long High Density Sample Report 3 High Density Sample Report 3 Long Internal Standard Summary Report on Ratio Failure Report Manual Integration Report Method Report Negative Report Qualitative Peak Report Qualitative Summary Report Quantitation Report Quantitation Report 2 Quality Control Report Sample Report Sample Report Long Solvent Blank Report Example PDFs of standard report formats are located in the following folder C Thermo Shared ExampleReports 4 ToxLab Forms 3 1 User Guide Thermo Scientific Custom Report Types 1 Introduction Reporting Features AltCalibrationReport BatchReport BlankReport CalibrationDensityReport CalibrationReport CheckStandardReport CompoundCalibrationReport ConfirmationReport ConfirmationReport2 DCCReport HighDensitySampleReport1 Long HighDensitySampleReport2Long HighDensitySampleReport3Long HighDensitySampleReport4 HighDensitySampleReport5 QuantitationReport For additional information about custom and standard reports and a sample of each standard report type see Reports on page 251 Thermo Scientific ToxLab Forms 3 1 User Guide 5 LLL M Getting Started This chapter describes the basic ToxLab Forms workflow and the procedures for getting started with the ToxLab Forms application Contents ToxLab Forms Workflow Installing the ToxLab Forms Application Installing the QED
5. If you enter a name for a batch that already exists when you click Finish the Batch Save dialog box asks you to enter another name You cannot overwrite an existing batch name To save the batch Click Finish The ToxLab Forms application saves the batch and displays it in Batch View From Batch View you can submit the batch for acquisition processing or report generation See Submitting a Batch on page 174 To edit the calibration file Select the Modify Calibrations or Active Compounds by Group check box The ToxLab Forms application replaces the Finish button with a Next button Click Next The Calibration and Compound Selection page opens See Selecting Calibration Files and Compounds on page 194 Thermo Scientific Thermo Scientific 5 Using the Production Mode Working in Batch View To identify specific compounds or groups of compounds 1 Select the Modify Calibrations or Active Compounds by Group check box The ToxLab Forms application replaces the Finish button with a Next button 2 Click Next The Calibration and Compound Selection page opens See Selecting Calibration Files and Compounds on page 194 Figure 46 Finish page Batch Wizard x Almost finished creating your batch C Modify Calibrations or Active Compounds by Group Please make sure the Batch name you want ix typed into the box below Batch name Cancel gt y N
6. Select the sample you want to move Right click and choose Move Sample Up or Move Sample Down from the shortcut menu The ToxLab Forms application moves the selected sample up or down one row in the sample list Note This function is not available when Quick Mode is selected ToxLab Forms 3 1 User Guide 189 5 Using the Production Mode Working in Batch View To browse in a raw data file 1 Double click the Filename column or right click and choose Browse in Raw File from the shortcut menu A dialog box opens where you can select a raw data file to use for the sample You can also browse in multiple raw data files to create multiple samples 2 Locate the raw data file to use for the sample and click Open Note This function is not available when Quick Mode is selected Figure 45 Batch Specification page Batch Wizard Batch Template C Thermo Tox Lab Farms sTemplates B atches B atchT emplate3 btmp Master Method Method2067 mms Batch File C Thermo Tox Lab Forms PrapectssPrajectl S ubpropectl B atehessethod2U0b7 142010 csMethadz b 142010 c bts Calibration File C Thermo T o x Lab Te m Quick mode MI Filename Sample type Sample level SamplelD Sample name Yial position Injection volume Conversion Beg woes NL Ni ese F ms s ee Te Add sample T TN RN Insert sample TR RN f nn Oe mosse ho io Move sample up drugs UB Specimen B j b
7. You can use the Fill Down command for the Sample Name Sample ID Vial Position and Sample Level columns You can use the Copy Down command for the Sample Type Vial Position Injection Volume Dilution and Sample Level columns Follow these procedures To automatically enter sequential column values To automatically copy column values To use Copy Down or Fill Down for a range of samples 4 To automatically enter sequential column values 1 Enter a value for the first row of the fill down sequence This does not have to be the first sample row You can begin the fill down procedure from any row in the sequence 2 Select the cell whose value is the first in the fill down sequence Observe that this cell is selected Vial position Vial position selected Not selected You can repeatedly use the Fill Down command to create multiple sequences See Example 1 on page 311 3 Right click and choose Fill Down from the shortcut menu The application enters sequential column values starting with the value in the selected row and ending with the last row in the column Thermo Scientific ToxLab Forms 3 1 User Guide 309 B Using Copy Down and Fill Down Note If you use the Fill Down command for the Vial Position column and you have an autosampler configured the ToxLab Forms application knows the number of vial positions configured in your autosampler and numbers the positions accordingly See Example
8. 20 20 P m m 0 6 j RTimin RT min m z 151 01 185 07 226 072 151 01 132 07 104 81 Apex HT 0 54 m Apex HT 0 73 hs Follow these procedures To manually add a peak To remove a manually created peak To zoom in on a peak To change the displayed information for detected peaks To display the peak information window Guide Thermo Scientific Thermo Scientific S 5 Using the Production Mode Working in Data Review To manually add a peak 1 Right click the chromatogram plot and select Add Peak from the shortcut menu S If a peak is already detected the Add Peak command is not enabled Click to indicate the left and right base points for the peak The ToxLab Forms application places the peak delimiter tags at these locations and automatically updates the peak values area height and so forth in the result set progesterone RT 3 18 ste RT 3 20 la 711687 oe MH 69491 11 SH IHF k Relative Intensity Manually added 3 base points RT min To remove a manually created peak Right click the chromatogram plot and choose Remove Peak from the shortcut menu The ToxLab Forms application removes the manually added peak To zoom in on a peak In the chromatogram plot drag the cursor to delineate a rectangle around the peak The delineated area expands to fill the view to help you examine the peak limits for enhanced review and confirmation To
9. Batch Template from the application menu The Open Method dialog box opens where you can select a master method to use for your template Open Method Ed Select a Master Method for the Template Methad2D42 Method206 2 Select a master method and open the file The Batch Template Editor opens See Batch Template Editor on page 181 The editor uses the selected master method for the template Template method information En Project Subproject Method Select Method Assay Type Assay name 4 To open a batch template 1 Choose File gt Open gt Batch Template from the main menu The Open Batch Template dialog box opens Open Batch Template Select a batch template ta open BatchT emplatel BatchTemplate2 BatchT emplate3 pen TLF 3 0 Batch Templates Open TLF 3 0 Batch Templates nen TLF 2 5 Batch Templates 2 Select the set of batch templates you want to use The ToxLab Forms 3 1 application lets you use LabForms 2 5 batch templates 178 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Batch View 3 Select a batch template and open the file The Batch Template Editor opens See Batch Template Editor on page 181 To specify template information 1 From the Project list select a project name 2 From the Subproject list select a subproject name Tip If there are no projects or subprojects to choose go to the Project Administration
10. Indicates a manually integrated confirming peak Indicates that the ion ratio is out of range Actual ratio of the confirming ion response to the quan ion response Acceptable range for the confirming ion Mass of the confirming peak Response of the confirming peak Indicates a manually integrated confirming peak Indicates that the ion ratio is out of range Actual ratio of the confirming ion response to the quan ion response Acceptable range for the confirming ion Table 66 Internal Standard Report Active View values Column Std Response Minimum Response Maximum Response Sample Response Std RT Min RT Max RT Sample RT ToxLab Forms 3 1 User Guide Description Average of the internal standard s response as found in the calibration file Minimum response time as specified on the ISTD page in Method Development mode See ISTD on page 124 Maximum response time as specified on the ISTD page in Method Development mode See ISTD on page 124 Area found in the sample Average retention time as found in the calibration file Minimum retention time as specified on the ISTD page in Method Development mode See ISTD on page 124 Maximum retention time as specified on the ISTD page in Method Development mode See ISTD on page 124 Retention time found in the sample Thermo Scientific Thermo Scientific 5 Using the Production Mode Working in Report View Table 67
11. Peak height 96 Tailing factor Min peak height S N Peak S N cutoff 100 ToxLab Forms 3 1 User Guide Description A signal must be above the baseline percentage of the total peak height 10096 before integration is turned on or off This text box is active only when the Constrain Peak Width check box is selected Range 0 0 to 100 096 A factor that controls how the ToxLab Forms application integrates the tail of a peak This factor is the maximum ratio of the trailing edge to the leading side of a constrained peak This text box is active only when the Constrain the Peak Width check box is selected Range 0 5 through 9 0 For the valley detection approximation method to use the Nearest RT Peak Identification criteria this peak signal to noise value must be equaled or exceeded For component identification purposes the ToxLab Forms application ignores all chromatogram peaks that have signal to noise values that are less than the S N Threshold value Range 0 0 all peaks through 999 0 The peak edge is set to values below this signal to noise ratio This test assumes it has found an edge of a peak when the baseline adjusted height of the edge is less than the ratio of the baseline adjusted apex height and the peak S N cutoff ratio When the S N at the apex is 500 and the peak S N cutoff value is 200 the ToxLab Forms application defines the right and left edges of the peak when the S N reaches a value less than
12. i oS Filename cal std bl m 0 19 0 33 BITTE ES RTimin Name Status Accela 45 Running 176 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Batch View Figure 41 Devices page Acquisition Instrument Devices Dueues sasaqa 100 Accela 45 50 Status E m ro 60 Status Scanning a 2 50 Scan speed x 1 m m 40 First scan 1 c Last scan 345 30 Scan number 216 20 Stark time min 2 406167 10 Real time elapsed min 2 406250 0 Repeat count 0 RTimin Figure 42 Queues page Status x Acquisition Instrument Devices Queues E Batch Queue 1 batch Ready Wij BatchB 7 samples Active E cal std 5 Complete e D K H al_std_10 Complete ER IB cal std 2D Acquisition Complete E H cab std 50 Pending en B cal std 100 Pending 50 W unknown Pending B 40 W unknown Pending 30 Processing Queue Empty Ready 20 Reporting Queue Empty Ready is 0 5 1 0 1 5 2 0 RTimin Thermo Scientific ToxLab Forms 3 1 User Guide 177 5 Using the Production Mode Working in Batch View Using a Batch Template Batches are created as a routine operation and because the nature and types of batches are often similar in some cases specified by laboratory operating procedure you can define a batch template that supplies the basic structure of a batch To create a new batch template 1 Choose New
13. IS IS ACENAPHTHENE D10_ IS IS ACENAPHTHENE D10_ IS ACENAPHTHENE D10_ IS ToxLab Forms 3 1 User Guide A Reports sample Standard Reports Page 4 of 36 ISTD Units ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL 287 A Reports sample Standard Reports Method name Master method name Current calibration file Assay type Inj vol Instrument method Tune Breakdown method QAQC Limits Compound N Nitrosodimethylamine Pyridine RCRA 2 Picoline N Nitrosomethylethylamine APP9 Methyl methanesulfonate 2 fluorophenol sur N Nitrosodiethylamine APP9 Ethyl methanesulfonate phenol d5 sur Phenol CCC Aniline Bis 2 chloroethyl ether Pentachloroethane 2 chlorophenol 1 3 Dichlorobenzene 1 4 Dichlorobenzene CCC Benzyl alcohol 1 2 Dichlorobenzene 2 methylphenol Bis 2 chloroisopropyl ether N Nitrosopyrrolidine_APP9 3 Methylphenol amp 4 methylphenol Acetophenone N Nitroso di N propylamine SPCC o toluidine APP9 Hexachloroethane nitrobenzene d5 sur Nitrobenzene N Nitrosopiperidine Isophorone 2 Nitrophenol CCC 2 4 Dimethylphenol Bis 2 chloroethoxy methane 2 4 Dichlorophenol CCC 1 2 4 Trichlorob
14. Method Report Theo Conc 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 Level Min Recovery 96 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 Page number Max Recovery 96 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 Page 29 of 36 Max RPD 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00
15. The High ICIS peak detection algorithm is designed for MS data and has superior peak detection efficiency at low MS signal levels The Standard Genesis peak detection algorithm is provided for backward compatibility with Xcalibur 1 0 studies 2 To look for peaks only in a certain range of the entire chromatogram select the Limit the Retention Time Range check box and specify a retention time RT range 3 To indicate whether to select peaks by relative height or area and the percentage of the highest peak that will result in compound selection select the Enable Peak Threshold check box To consider a peak for a processing method the ToxLab Forms application uses the Enable Peak Threshold filter to determine which peaks meet the specified percentage of the largest peak 4 To display a specific number of the largest peaks by height or area select the Only Select Top Peaks check box and choose the number of peaks to display 140 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To choose a library Identity the peaks E 1 Use these libraries Limit library hits Totti Heverse search Index 1 In the Use these Libraries box select the libraries you want to search All libraries loaded on your instrument are displayed in the Use these Libraries box 2 To limit the number of hits returned when the system searches a spectrum against the selecte
16. lon coelution mir Enable peak threshold of largest peak Ey height L By area Window type Absolute Window 2 ce spectrum Unly select top peaks Calibrate the compounds Select the tap By height Be D RT E ternal L Ep ara Curve type pom Identify the peaks Origin Ignore Use these libraries Weighting MAINLIE Hespanse via Wualitative Peak Processing ISTO matching min Lirrut library hits Exclude matching quan peaks Erlen Merere Search Index s c T Exclusion window Z min These parameters may also be used for qualitative peak pr 144 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 39 Method Template Editor parameters Sheet 1 of 3 Parameter Find the peaks Sensitivity Limit the retention time range Enable peak threshold Only select top peaks Identify the peaks Use these libraries Limit library hits Best match method Handle confirming ions Include confirming ions Number of confirming ions Specify default ion ratio ranges Include compound peak spectrum as reference spectrum Calibrate the compounds Calibration method Curve type Description Defines how extensively the peak detector algorithm searches for low level peaks Min RT specifies the beginning of the range Max RT specifies the end of the range Specifies whether to select
17. 0 00 0 00 0 00 0 00 Thermo Scientific Method name Master method name Current calibration file Assay type Robustness Inj vol 1 000 Instrument method TargetsSplit Tune Breakdown method DFTPPSplit QAQC Method Validation Compound N Nitrosodimethylamine Pyridine RCRA 2 Picoline N Nitrosomethylethylamine APP9 Methyl methanesulfonate 2 fluorophenol sur N Nitrosodiethylamine APP9 Ethyl methanesulfonate phenol d5 sur Phenol CCC Aniline Bis 2 chloroethyl ether Pentachloroethane 2 chlorophenol 1 3 Dichlorobenzene 1 4 Dichlorobenzene CCC Benzyl_alcohol 1 2 Dichlorobenzene 2 methylphenol Bis 2 chloroisopropyl ether N Nitrosopyrrolidine APP9 3 Methylphenol amp 4 methylphenol Acetophenone N Nitroso di N propylamine SPCC o toluidine APP9 Hexachloroethane nitrobenzene d5 sur Nitrobenzene N Nitrosopiperidine Isophorone 2 Nitrophenol CCC 2 4 Dimethylphenol Bis 2 chloroethoxy methane 2 4 Dichlorophenol CCC 1 2 4 Trichlorobenzene Naphthalene p Chloroaniline 2 6 Dichlorophenol Hexachloropropene APP9 Hexachlorobutadiene CCC N Nitroso di N butylamine 4 Chloro 3 methylphenol CCC Safrole APP9 2 Methylnaphthalene Hexachlorocyclopentadiene SPCC 1 2 4 5 Tetrachlorobenzene 2 4 5 Trichlorophenol 2 4 6 Trichlorophenol CCC 2 fluorobiphenyl sur Isosafrole APP9 2 Chloronaphthalene Thermo Scientific EPAMethod8270B 8level EC25B 8level 322010 a calx EC25B 8level 322010 a EPAMethod8270B 8level lo
18. 184 186 188 180 192 m z To zoom in on an area 1 Drag the cursor to delineate a rectangle around an area The delineated area expands to fill the view 2 To restore the method default view right click the spectra plot and choose Reset Scaling from the shortcut menu ToxLab Forms 3 1 User Guide 215 5 Using the Production Mode Working in Data Review 216 ToxLab Forms 3 1 User Confirming lons The Confirming Ions page displays a graphical view of all qualifying confirming ions for the selected sample and compound and displays calculated ion ratios and ion ratio acceptance windows A red border indicates that an ion ratio is outside of its window Depending on the method option settings another ion view is available on the Ion Overlay page See lon Overlay on page 219 RT 0 87 APN_001 RT 0 87 APN_001 AR 1053 28 AH 396 35 SN 17 14am 100 100 g 90 a0 go 70 70 2 60 2 60 AR 118 65 c 7 AH 107 94 E F SH 17 Deine 40 40 30 30 20 20 10 10 0 0 1 2 0 6 0 8 1 0 1 2 RT min RT min m z 151 01 M m z 70 15 164 56 247 292 151 017192 07 2392 ote oe Uo eee 22 s Apex AT 0 87 Apex HT 0 87 A red border indicates that an ion ratio is outside of its window RT 0 54 APN_001 RT 0 73 APN 001 h amp c 540 76 MH 354 38 100 58 15 Zen 100 oe ee Lr Ar 197 09 AH 163 15 em Lr Relative Intensity I e Relative Intensity Eu c Eu m
19. 5 Optional Enter the users full name account number phone number and E mail address 6 To enable this user logon select the Enabled check box You can disable a user logon without deleting the user s information Follow the instructions Io edit user information on page 21 7 Do one of the following F rm e When all the user information is correct click the Save Changes icon E The ToxLab Forms application adds the new user to the User Listing table and the parameters in the User area are unavailable E To discard all information and not create a new user from the parameter values you entered click che Cancel Changes icon m All information is discarded and the parameters in the User area are unavailable To edit user information 1 In the User Listing table select a user User Listing Account Phone EL Username Hole Tien ber Email Address Enabled 1 IT Administrator UAUL WALL 2 3 ZETTTNICTTTNNNN Ei Bla E s S Technician Technician Note Clicking anywhere in the row selects the user The user information populates the parameter fields in the User area 2 Click the Edit User icon ToxLab Forms 3 1 User Guide 21 3 Using the Configuration Mode User Administration The parameters in the User area are enabled User Fole TA 408 123 4567 Password SITES Pi smithreithermofisher cord at rag John Smith Enabled 3 Edit any of the
20. 6 leo g eo 1 leo I A97 eV les onespen uojeg Jes jueuinJjsu OWEN qe1 Thermo Scientific ToxLab Forms 3 1 User Guide 210 A Reports sample Standard Reports luu 6d H00 S1 Iw Bd 00012Q1S juu 6d 00 S1 1u 6d 008 ALS wW 6d 00 S1 1u 6d 009 QALS juu 6d 0OL sI lw 6d 007 QLS w 6d 00 S1 1u 6d 002 ALS w 6d 00 S1 1u 6d 00L ALS w 6d oo L SI 1wW 6d o s qi1s w 6d 00 S1 1u 6d SZ QLS w 6d 00 S1 1u 6d OL ALS w 6d 00 S1 1u 6d OL ALS w 6d 00 S1 1u 6d OL ALS jueuiuo Jo e oDeg NV v LVL CV 966L S S WY 8E L0 21 9661 S S Wd v LS KV 966L v s Wd 9 Lr VV 966L v s Wd v L LV 966L v s Wd LC VV 966L v s Nd LV VV 966L v s Wd LE LY OL 966L v S Nd 2 L 01 966L v S Wd vc Vc 0V 966L v s Nd LC L 0V 966V v S 9JEQ allg junowy V palenbs J H 10284 asuodsay 4 GSY A sBe 4 uoneiqileo E Swen Sjdwes XeoX XNA alld HED xDBnup xBnuip x xniq pouje N ojeuJej v MOodoy uoneuqi e Punodwoy 6 le 9 Jeo 4 le 9 E92 G E95 r jeo Je g le Jeo jes Jeo 19497 LL xBnup OL xBnip 60 xDnup 90 xDnup 140 xBnup 90 xDnup co xDnup vo xDnup co xDnup zo xDnup LO xBnup OWEN 9114 pejeJ659 V l el LL OL 60 80 SO VO 0 cO qi eidures x xniq s wer jueuunJjsu JeusiJouuJ9u AloyeJoge7 J8usi JouuJ9U 271 ToxLab Forms 3 1 User Guide Thermo Scientific
21. All projects are created under a main Projects folder on the C drive C Thermo ToxLab Forms Projects 28 ToxLab Forms 3 1 User Guide Thermo Scientific S 3 Using the Configuration Mode Project Administration To create projects or subprojects 1 Select the top level project You can select the main Projects folder and create a new project under it or you can select one of your existing projects and create a subproject under it When you select a project folder the application enables the plus sign icon indicating that you can create a folder within the selected folder ag Project ag Project ag Projects Cllick the plus sign The ToxLab Forms application creates a new unnamed project folder under the selected project While the new project is still highlighted type a new name Project names can contain spaces and special characters except for the following special J P P P 8 characters V lt gt Note After you add a subproject to a project you cannot rename the project To save the new name press ENTER or click anywhere in the view To delete projects or subprojects Select the project or subproject you want to delete You can delete any project that contains no subprojects You can delete any subproject that contains no batches When the selected project or subproject is available for deletion the application enables the minus sign icon f N El Projec
22. Delete compound from Removes the selected compound from the current master method method 122 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Blank Use the Blank page to define acceptable levels of target compounds in blank samples The ToxLab Forms application makes the evaluation by comparing the calculated concentration for each compound in the sample to the maximum concentration defined on this page You can enter the maximum concentration as a percentage of a flag value or as a specified value On the Blank report the application flags the calculated values for target compounds that exceed these limits To specify the maximum concentration as a percentage 1 From the Method column list box choose one of the following methods of LOD of LOQ of LOR of Cutoff 2 In the Percentage column type a percentage value To specify the maximum concentration as an absolute value 1 From the Method column list box select Concentration 2 In the Max Conc column type an absolute value To specify no maximum concentration From the Method column list box select None Figure 27 Blank page asss ma I Groups Reports N HT Compound Method Percentage Max Conc 1 Methylene Chloride Mone w E Arsine of LOD bal 1 00 E Phenol 3 methul of LOG w 0 00 4 6H Purin 6 one 1 7 d of LOG Ww 1 00 E a Lhlaraaniline
23. For a detailed description of how to modify a master method see Editing a Master Method on page 70 Thermo Scientific ToxLab Forms 3 1 User Guide 69 4 Using the Method Development Mode Working with Master Methods Editing a Master Method You can open a master method to view or edit the compounds method instructions and reporting options in the method This section includes instructions for the following tasks Opening a Master Method Editing the General Page Editing the Compounds Page Editing the QAQC Page Editing the Groups Page Editing the Reports Page Opening a Master Method The ToxLab Forms application lets you open a master method that was created and saved in the ToxLab Forms 3 1 application or one that was created and saved in the ToxLab Forms 2 5 application Follow these procedures To open a saved master method To open a saved master method from the Recent Files list 4 To open a saved master method 1 Click Method Development from the dashboard or the navigation pane The Method Development navigation pane opens 2 In the Method View task pane click Open Method or choose File gt Open gt Master Method from the main menu The Open Master Method dialog box opens where you can select a master method 10 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Open Master Method Select a master
24. Ion range calc method 78 Ionization Acquisition List 81 Compound datastore 35 ISTD 113 ISTD matching min 147 Lab name 77 Laboratory Name 41 Lens Acquisition List 82 Compound datastore 36 Level 118 Limit library hits 145 Limit the retention time range 145 LOD Detection limit 119 Login 9 LOQ Quantitation limit 119 LOR Reporting limit 119 m z Detection 97 Manual Flags 236 Manual injection 60 Max Amt Diff 121 Max Conc 124 Max recovery ISTD page 125 Max RF Diff 122 Max RSD Calibration page 121 Max RT min ISTD page 125 Method Matrix Blank page 124 Thermo Scientific Solvent Blank page 126 Min peak height S N Genesis 100 ICIS 104 Min peak width 104 Min recovery ISTD page 125 Min RT min 125 Modify Calibrations or Active Compounds by Group 193 Multiplet resolution 104 Name the master method 60 New instrument method 51 New sample list 51 Noise method 104 Number of Scans to Subtract 74 Number of scans to subtract 78 Only select top peaks 145 Open instrument method 51 Open method 50 Open Qual Browser 51 Operand 314 Operator 314 Or conditions 314 Origin Calibration 113 Method Template Editor 146 Overwrite 60 Password logon screen 9 user administration 23 Path 60 Peak height 96 Genesis 100 ICIS 104 Peak noise factor 103 Peak S N cutoff 100 Percentage 124 Phone Number 23 Polarity Acquisition List 82 Compound datastore 36 Precursor Mass Acquisition List 82 Compound dat
25. Shade row when sample is outside of evaluation criteria 197 Show chromatogram on Quantitation Report 137 Showing 235 Smoothing Genesis 99 ICIS 103 Specify default ion ratio ranges 145 Standard type 113 Starting vialnumber 186 Status 236 Stepoff value 78 Tailing factor Genesis 100 ICIS 104 Technology selection 40 Template Layout 186 Theoretical amount 237 Threshold Lower Limit 127 Total batch rows 186 Total response 236 Trace Detection 96 Tune file lifetime 138 ULOL Linearity limit 120 Units 113 Upper Limit 126 127 Use alternate calibration report format 137 Use an existing raw data file 60 Use as RT Reference 84 Use autosampler 60 Use Method Forge 54 Use the default template 60 Use these libraries 145 User Security 40 Username 9 23 Valley rise 101 Valley S N 101 Vial position 60 View width Detection 95 Weighting Calibration 113 Method Template Editor 146 Window Acquisition List 82 Compound datastore 36 Detection 95 322 ToxLab Forms 3 1 User Guide password administrator 8 Password parameter logon screen 9 user administration 23 Path parameter 60 Peak detection settings Calibration Curve page 214 Confirming Ions page 216 Ion Overlay page 219 Spectra page 215 Peak height parameter Genesis 100 ICIS 104 Peak noise factor parameter 103 Peak S N cutoff parameter 100 Percentage parameter 124 Phone Number parameter 23 Polarity parameter Acquisition List 82 Compound datastore 36 Precursor Mass parame
26. The Tooltip does not list compounds that are not found in Specimen sample types EE Statue Flags Filename Sample type Sample level Sample IL ES M ee ee A level 100402140750 Flag Details E A 3 Dichlorobenzene e 4 461 lon Ratio of 135 57 is not between 35 and 35 3 1 4 Dichlarobenzene d4 4 442 Feak area 13341547 35 ts out of bounds SD Minimum Recovery 0 000 and ISTO Max Recovery 0 000 J 147 5pex Retention Time 4 442 ts out of bounds ISTO Min RT 0 250 and ISTO Max AT 0 250 Ww kJ ToxLab Forms 3 1 User Guide 201 5 Using the Production Mode Working in Data Review Figure 48 Samples List pane Method Batchl1b8UB Steroid Method Instrument Thermo Scientific Instrument Status Flags Filename sample type u NS duis L omment e ued 1 Q A Beroids02 Specimen Sample 2 Q amp seno specimen Sample Bt JE LEE O a O steroids05 Specimen S amplels 20 0 LUTTER IU SIE AMETE ale Height Area AT RT Calc Amt Theo Amt ln IS Amt ES Mewa Sumo amen a as waf 43m Dm emo Wi GENOA am al NA 238 060 En Mewa nmo zum am al waj oma nam Wes SERIE am al Na 347 060 ens Cells in the Samples list that should not have a value such as theoretical concentration for an Specimen sample are shaded and empty Cells that should have a value but none exists report N A not available Results for compounds that are not detected display N F
27. a To use a compound other than the compound already in the library scroll to the spectrum for that compound and select the compound name in the header of the spectr um pane Thermo Scientific ToxLab Forms 3 1 User Guide 87 4 Using the Method Development Mode Working with Master Methods Select Pyrazine 1 4 dioxide MAINLIB RSI 740 SE 410 MP 1 compound NL 999 BP 112 00 112 00 Ge cC te B e E a m m 50 m Hm qi iE hi 62 00 80 00 36 00 c b Inthe Type of Compound to Add list select a compound type c Click OK 12 Repeat these steps for each compound you want to add to the method For a detailed description of all parameters on the Detection page see Editing the Compounds Page on page 79 To change the compound reference spectrum 1 In the raw file chromatogram pane select a peak The ToxLab Forms application displays the spectrum for the selected peak in the spectrum pane 2 In the raw file spectrum pane right click and choose Use This Spectrum for Compound Reference Spectrum from the shortcut menu 3 Choose either Update Spectrum Only or Update Spectrum and Ion Ratios The ToxLab Forms application replaces the spectrum in the Spectrum page of the quan peak pane with this spectrum If you choose to update the spectrum and the ion ratios the application also replaces the ion ratios for the confirming peaks You can see the updated ion ratios on the Ratios page fo
28. k drugs 5 Specimen 3 be k Move sample down Browse in raw File Fill down 190 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Batch View Table 45 Batch Specification parameters Sheet 1 of 2 Parameter Description Batch Template Displays the path names of the batch template master method Master Method batch file and calibration file used to create this batch Batch File Calibration File Adds a new Unknown sample to the end of the sample list This function is not available when Quick Mode is selected Removes the selected sample This function is not available when Quick Mode is selected Quick mode Limits the columns of information in the Batch Specification page to the following Sample Type Sample ID Injection Volume e Conversion Factor In Quick Mode the shortcut menu and add remove sample icons are unavailable Back Returns you to the Batch Template Selection page where you can choose a different batch template master method or starting vial position Next Takes you to the Finish page where you can submit the batch for acquisition or processing See Submitting the Batch on page 192 Cancel Immediately exits the Batch Wizard and does not save the batch There is no confirming message Shortcut Menu Add sample Adds a single empty row to the sample list Insert sample Inserts a new Specimen sample above the selected row Inse
29. ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ISTD Name 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS IS IS IS IS IS 1 4 DICHLOROBENZENE D4 1 4 DICHLOROBENZENE D4 1 4 DICHLOROBENZENE D4 1 4 DICHLOROBENZENE D4 1 4 DICHLOROBENZENE D4 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS IS IS IS IS 1 4 DICHLOROBENZENE D4 1 4 DICHLOROBENZENE D4 1 4 DICHLOROBENZENE D4 1 4 DICHLOROBENZENE D4 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS IS IS 1 4 DICHLOROBENZENE D4 IS EN _ E _ fl _ _ E _ fl _ fl _ E _ E _ E _ fl ef 1 4 DICHLOROBENZENE D4 NAPHTHALENE D8 IS 1 4 DICHLOROBENZENE D4 IS NAPHTHALENE D amp _ IS 1 4 DICHLOROBENZENE DA IS NAPHTHALENE D amp IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D amp IS NAPHTHALENE D amp IS NAPHTHALENE D amp IS NAPHTHALENE D8 IS NAPHTHALENE D amp IS NAPHTHALENE D amp IS NAPHTHALENE D8 IS NAPHTHALENE D amp IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS ACENAPHTHENE D40 IS ACENAPHTHENE D40 IS ACENAPHTHENE D40 IS ACENAPHTHENE D40 IS IS
30. on page 145 2 From the Peaks pane select a peak in the sample Peak AT min RSI MP entry mm in lim sim ss ram sine k 5 p0 32 p Ar En DENEN CNN PN m BE The ToxLab Forms application displays the selected peak in the Qual Peak pane RT S D hiec 165586431 45 MH 1534222753 r78 SH IHF Relative Intensity 6 00 RT min The ToxLab Forms application displays the spectra data for the peak and the reference spectra for the identified library compound in the Spectra pane Thermo Scientific ToxLab Forms 3 1 User Guide 221 5 Using the Production Mode Working in Data Review Qual Library Ca C Relative Intensity cri e m Qual Data Ca C cn m 156 07 250 99 327 07 216 472 19 Relative Intensity m The ToxLab Forms application locates the selected peak in the navigation chromatogram 5 01 4 63 4 08 4 06 gg 6 09 6 99 734 u 8 57 874 9 88 235 2 93 3 54 ar i a u nu dll Mr TR ETAT iM LA A m IR ls A JUL I 3 4 5 6 r 8 a 10 RT min 4 To remove a peak 1 Select a peak in the Peaks pane 2 Right click and choose Remove Selected Peak from the shortcut menu The ToxLab Forms application removes the selected peak from the peaks list Note There is no undo for this action but you can manually add a peak to redefine a removed peak See Chromatogram Navigation Pane on page 223 Figure 49 Peaks pane Sim c Full ms 35 00 500 00 ws Peak AT min SI RS
31. software The application focuses on toxology markets creating the workflows that laboratories use In a single software package the ToxLab Forms application supports a focused workflow for specific non bioanalytical laboratory use instrument control and method development functionality The ToxLab Forms application is the primary application for the ISQ single quadrupole and the TSQ Quantum XLS triple quadrupole mass spectrometers The ToxLab Forms application can export SRM data in xml format so that other applications can import the files into their databases The ToxLab Forms application can import the following file types Sample lists in csv or xml format Processing pmd and instrument meth method files from the Xcalibur data system Compounds from xml files that use the datastore format Batches or methods from the LabForms 2 5 application or later versions The ToxLab Forms application checks the accuracy and precision of data against systems that have previously been certified against a standard processing program such as the Statistical Analysis System SAS Thermo Scientific ToxLab Forms 3 1 User Guide 1 1 Introduction About the ToxLab Forms Application 2 Supported File Types The ToxLab Forms application supports the following file types Comma separated values csv A textual representation of value fields that are denoted as separated from a stream of alpha numeric values that may be associ
32. v Stepoff value Set chromatogram reference sample one x Set Reference sample Table 14 General parameters Sheet 1 of 2 Parameter Description Lab name The laboratory name to be displayed on the top of each printed saved or exported report Default ThermoFisher Laboratory To specify this default laboratory name see Specifying the a ral Cant a a saoe 27 General Lonfiguration on pag Cy Assay type The name for the analysis type to be targeted by the method The assay type associates the method with the analysis of a compound or specific class of compounds for example an assay type of PAH might be used for the analysis of Polynuclear Aromatic Hydrocarbons The ToxLab Forms application uses this assay type in the batch template s ToxLab Forms 3 1 User Guide 77 4 Using the Method Development Mode Working with Master Methods Table 14 General parameters Sheet 2 of 2 Parameter Injection volume Ion range calc method Instrument method Edit Update Qualitative peak processing template Background subtraction range option Number of scans to subtract Stepoff value Set chromatogram reference sample Set Reference sample Notes ToxLab Forms 3 1 User Guide Description The system use the injection volume in uL for sample injection Certain autosamplers such as the AI AS 3000 use the injection volume specifi
33. 1 User Guide 15 MEN E Using the Configuration Mode This chapter discusses the configuration tasks assigned to the IT Administrator and Manager roles Contents e User Administration Project Administration Compound Datastore Application Configuration If your role is that of an IT Administrator or Manager you are responsible for the following Handling the databases Applying roles to users Understanding security users and groups Creating local users and network groups Creating projects and subprojects Maintaining compounds in the compounds datastore To access the Configuration mode Click Configuration from the dashboard or the navigation pane The Configuration navigation pane opens Thermo Scientific ToxLab Forms 3 1 User Guide 17 3 Using the Configuration Mode Figure 2 Configuration navigation pane i Configuration User Administration Project Administration Compound Datastore L Import Compounds L Mew Compound Datastore Load Compound Datastore zd Save Compound Datastore al Save As Compound Datastore Recent Files Application Configuration Production Method Development v Configuration Table 4 Configuration navigation pane functions Sheet 1 of 2 User Administration Opens the User Administration view where you can add remove or edit user accounts and permissions See User Administration on page 20 This task pane is available only wh
34. 100 00 15 69 23 54 19 91 m z 488 20 Composite RT 1 85 cal 1 100 is 100 a0 a0 2 a a0 70 m m 5 8D E 50 50 40 40 3n an 20 20 1 185 10 2 00 1 80 1 55 2 00 R Tiimi R Tiimi Amount Target Range Ratio Cal 6 000 4 800 7 200 5 581 ng mL 100 00 22 33 33 49 27 53 11 43 17 14 14 09 Page 1 of 1 Thermo Scientific Sample Report Long Data File cal_1 Method Drug_A_Drug_A Drug_A Cali File Drug_A calx Sample ID cal 1 6 ng mL Diln Factor 1 00 Comments 100 90 30 7O 6o so E 40 30 20 10 1 86 1 87 1 88 188 1 89 1 86 1 88 1 90 m z 380 20 m z 479 20 100 100 90 9n 2 a 2 a m m a0 p a 50 50 an ap an an 20 20 10 104 185 188 ir um 11 19 20 2m 1 80 1 85 2 00 1 80 RTimin RT min lon Response Int_Std 1 93 m z 380 20 678044 1 93 m z 479 20 134976 m z 371 20 m z 473 20 15 100 100 90 90 m m 70 m a0 a0 sp 50 E oan E an 30 30 20 20 10 im 18 18 2m cm lJ 188 D D 1 0 1 85 2 00 R Tiimi RT min lon Response Drug_A 1 95 m z 371 20 227568 1 94 m z 473 20 62641 1 94 m z 488 20 32066 Report Generated 3 31 2010 7 03 16AM Thermo Scientific Sample Report Long 1 93 1 92 1 94 1 26 ERT rmin 1 85 2 00 RTimin Amount 15 000 ng mL m z 488 20 13 a lt amp c c c Cc Cc Relative Intensity Ea Ex en a ha 19 201 28 1 85 2 0 R Tiimi Amount Cal 6
35. 2 on page 311 To automatically copy column values 1 Select the cell whose value you want to copy to all cells below it Observe that this cell is selected Vial position Vial position 2 Right click and choose Copy Down from the shortcut menu selected Not selected The value is copied to all rows below the selected row To use Copy Down or Fill Down for a range of samples 1 To select a range of sample values do one of the following Drag your cursor to select a contiguous group of sample values Or Hold down the SHIFT key to select a contiguous group of sample values 2 Right click and choose the appropriate command from the shortcut menu The column values are copied or entered sequentially starting with the value in the first selected row and ending with the last selected row Filename Sample ID Sample n Filename Sample S ample Sample 01 samples S ample1Uz Samples Samplel U3 Add samol S ample1 04 alius Sample Insert sample Insert copy sample Submit selected samples Submit batch 310 ToxLab Forms 3 1 User Guide Thermo Scientific B Using Copy Down and Fill Down Example 1 You can repeatedly use the Fill Down command to create multiple sequences Vial position Example 2 The ToxLab Forms application knows the number of vial positions configured in your autosampler and numbers the positions accordingly Vial position BA ABE Thermo Scientific Tox
36. 200 Range 50 0 to 10000 0 Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 20 Detect parameters for Standard Genesis Sheet 3 of 3 Parameter Valley rise 96 Valley S N background scans Report noise as Description The peak trace can rise above the baseline by this percentage after passing through a minimum before or after the peak This method drops a vertical line from the apex of the valley between unresolved peaks to the baseline The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak When the trace exceeds rise percentage the ToxLab Forms application applies valley detection peak integration criteria This test is applied to both the left and right edges of the peak The rise percentage criteria is useful for integrating peaks with long tails Range 0 1 to 500 0 Specifies a value to evaluate the valley bottom Using this parameter ensures that the surrounding measurements are higher Range 1 0 to 100 0 Default 2 0 Number of background scans performed by the ToxLab Forms application Determines if the noise used in calculating S N values is calculated using an RMS calculation or peak to peak resolution threshold Options are RMS or Peak to Peak ToxLab Forms 3 1 User Guide 101 4 Using the Method Development Mode Working with Master Methods
37. 4 Production mode 230 sample PDFs 256 viewing landscape in PDF 256 Reports page editing 130 Reports page Master Method View 130 Reset scaling command 111 Response parameter 237 Response via parameter Calibration 113 Method Template Editor 146 Retention Time parameter 237 RMS parameter 105 Role parameter 23 RT parameter Acquisition List 82 Calibration 113 Calibration levels 115 Calibration page 121 Thermo Scientific Index R Compound datastore 36 Hydrolysis page 127 Identification 83 ISTD page 124 Limits page 119 Matrix Blank page 123 QC Check page 122 QC levels page 118 Solvent Blank page 126 S S N threshold parameter 99 Sample comment parameter 60 Sample Concentration parameter 237 Sample file parameter 235 sample types defined 197 Sample Units parameter 237 Save As Compound Datastore command 33 Save changes parameter 24 Save Compound Datastore command 33 Save Compound Datastore dialog box 34 Select a custom template parameter 60 Select a report parameter 235 Select batch location parameter 51 Select Compound Datastore dialog box 38 Select Compounds from CDS parameter 68 Select Compounds to Add dialog box 68 Sensitivity parameter Genesis 99 ICIS 103 sensitivity parameter 145 Separate ion overlay display parameter 157 Set Chromatogram Reference Sample parameter 76 Set chromatogram reference sample parameter 78 Set Reference sample parameter 78 Set this mass as a new quan peak command 111 Set th
38. 51 00 EP 20 40 60 B 100 120 140 160 m z Qual Data 153 04 x per m nr Actual spectra for selected peak Relative Intensity bE c oco 3 37 151 03 ho 156 07 207 01 280 99 327 07 407 16 445 10 i 400 200 300 400 m z Peak AT min RSI MP mn entry sm fm m m em se Tan EM Isa 2Oycbheien one 355tinetyl k 23 00 dr gu Acenaphthene n im umar mos 92 9 59 Fonte 228 ToxLab Forms 3 1 User Guide Thermo Scientific Ranking Pane 5 Using the Production Mo de Working in Data Review This pane displays the three best library matches for the selected peak Use this pane to select a different library entry for the peak To change the library entry for a selected peak 1 In the Ranking pane select the check box for the library entry you want to use to identify the selected peak n the Spectra pane the reference spectra changes to show the spectra for the selected library entry In the Peaks pane the SI RSI MP and Library Entry values update to reflect the selected library entry Hank 5l ASI 1 337 337 2 obo aba Ll 3 gab gab Table 56 Ranking pane parameters Command lt Check box column gt Rank SI RSI MP Library entry Thermo Scientific MP Library entry Bl Acenaphthene 11 Eiphenyl B Naphthalene Z ethenyl Description Lets you choose a library entry for the selected peak Indicates the order of best matches betwee
39. 60 S 800c ZV v Nd 61 60 S 800c Z V v Id S 80 S 800c Z V v Nd Sc 80 S 800c Z V v Nd Sv 0L S 8002 24 7 Nd Z1 01 9 8002 24 7 Nd ZS 10 S 8002 24 7 Nd S0 20 S 8002 24 7 Nd LE 20 9 8002 24 7 Nd 6 90 9 800c Z V v Nd 1 90 9 8002 24 7 Nd Zv S0 S 800c Z V v Wd L S0 S 8002 2 V v euin eyjeq v Bnuq seuuduinu enuels3liwv jueuungjsu SIJlJU I9S oway 10 8eJOqe 7 JOyusi4 oWISU L y ueuuneds ueuumeds Z ueuimeds usw oads JUSNJOS GZL ob Ov ob oAneDou sis oJp u eo g leo e5 poejoeJixeun Sweugll uojeg esf jueuinujsu euieu qe 25 ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports Batch Summary Report Batch Name Method Cali File Operator Instrument ID Batch Summary Report Drug A ISTD Test001 Drug A ISTD Test001 Drug A IMPORTED ISTD Drug A IMPORTED ISTD Drug A ISTD Test001 calx b ThermoFisher Instrument Report Generated 6 17 2010 8 41 37AM Reviewed By Date Certified By Date Calibration Results Calibration Date Ratio Calculation Calibrate By Units Calibrator Compound Theoretical Amount Calc Value IR Window Type Curve Type Origin Type Quality Control Results Control Compound Theoretical Amount Actual Amount Permitted Range level 40 Int Std 0 000 N A 0 000 0 000 level 40 Int Std 0 000 N A 0 000 0 000 Hydrolysis Summary Sample ID Compound Mode Threshold Range Calc Amt Flags hydrolysi
40. 96 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 19 Signal parameters Sheet 2 of 2 Parameter Description Ranges A range of ions for detection and integration Entering a single value in the Start m z cell defines a range of one amu centered on that value To specify a range that is narrower or wider than this range specify both a start and end value Multiple ions are summed by adding rows to the Ranges grid m z The initial mass to charge ratio Thermo Scientific ToxLab Forms 3 1 User Guide 97 4 Using the Method Development Mode Working with Master Methods Detect Use the Detect page to define the peak detection algorithm and its options and to determine the area under a curve There are two different modes Standard Genesis and High ICIS On this page you can specify how you want each mode to run Figure 17 Detect page for Standard Genesis Quan peak 485 30 419 76 Relative Intensity Lh te gt no amp tm Popo oO oe ooo GD RT min Detect syste Standard Genesis dj BIC Wr earest AT Times Signal Smoothing 1 E S N threshold I Enable valley detection Expected width sec l Conztrain peak width Peak height gt T ailing factor Min peak height 5 M 200 0 Peak S N cutoff Valley rise gt J Valley S N background scans F 3l Report nog ze az ARS 98 ToxLab F
41. Batch Report and custom reports that are specified as batch level reports See Custom Reports on page 46 230 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific S 5 Using the Production Mode Working in Report View To print a report 1 Select the report you want to print from the Select a Report list 2 Do one of the following Choose File Print Batch from the main menu The ToxLab Forms application immediately sends all reports for the batch to your default printer There is no dialog box or confirmation message _Or a Click the Print Report icon C The Print dialog box for your default printer opens b Follow the typical procedure to print from your printer Landscape reports are automatically rotated to fit the paper To export a report Select the report you want to print from the Select a Report list Click the Export Report icon mm The Export Report dialog box opens Locate the folder where you want to write the report file and click Save The ToxLab Forms application writes the Crystal Reports rpt or custom reports file to the specified folder To search for text in a report Select a report from the Select a Report list Click the Find Text icon ifi The Find Text dialog box opens Enter your text and click Find Next When the ToxLab Forms application locates the text it encloses the text in a red box sample ID APHOO1 APHOO2
42. C Carryover Linearity limit D Detection limit Q Quan limit POS Cutoff nz Negative b Solvent blank H Hydrolysis Thermo Scientific ToxLab Forms 3 1 User Guide 275 A Reports sample Standard Reports High Density Internal Standard Report Long High Density Internal Standard Report Long Lab name Instrument User Batch Relative Intensity Drug_A Thermo Fisher Laboratory Thermo Scientific Instrument AMER jamie humphries Drug_A Quan m z 371 20 Total Area 227568 Peak Area 227568 RT 1 95min 1 95 Amount 5 581 ng mL TAmount 6 000 ng mL ive Intensity Relay Qual m z 473 20 I Area 62641 Ratio 27 53 Range 22 33 33 49 Method Drug_A_Drug_A Drug_A Cali File Drug_A calx Relative Intensity Qual m z 488 20 Area 32066 Ratio 14 09 96 Range 11 43 96 17 14 96 Page 1 of 1 Relative Intensity Int Std Quan m z 380 20 Total Area 678044 Peak Area 678044 RT 1 93min 1 94 Amount 15 000 ng mL Flag legend LOD lt J lt LOQ I lon ratio failure C Carryover Linearity limit D Detection limit Q Quan limit POS Cutoff nz Negative b Solvent blank H Hydrolysis 216 ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports High Density Sample Report 1 High Density Sample Report 1 Lab name Thermo Fisher Laboratory Page 1 of 1 Instrument Thermo Scientific Instrument Method X Drug A Drug A User AMER jamie humphries Dru
43. DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS NAPHTHALENE D8 IS Thermo Scientific Method name Master method name Current calibration file Assay type Inj vol Instrument method Tune Breakdown method Compound calibration Compound N Nitrosodimethylamine Pyridine_RCRA 2 Picoline N Nitrosomethylethylamine_APP9 Methyl methanesulfonate 2 fluorophenol sur N Nitrosodiethylamine APP9 Ethyl methanesulfonate phenol d5 sur Phenol CCC Aniline Bis 2 chloroethyl ether Pentachloroethane 2 chlorophenol 1 3 Dichlorobenzene 1 4 Dichlorobenzene CCC Benzyl_alcohol 1 2 Dichlorobenzene 2 methylphenol Bis 2 chloroisopropyl ether N Nitrosopyrrolidine APP9 3 Methylphenol amp 4 methylphenol Acetophenone N Nitroso di N propylamine SPCC o toluidine APP9 Hexachloroethane nitrobenzene d5 sur Nitrobenzene N Nitrosopiperidine Isophorone 2 Nitrophenol CCC 2 4 Dimethylphenol Bis 2 chloroethoxy methane 2 4 Dichlorophenol CCC 1 2 4 Trichlorobenzene Naphthalene p Chloroaniline 2 6 Dichlorophenol Hexachloropropene_APP9 Hexachlorobutadiene CCC N Nitroso di N butylamine 4 Ch
44. Export SRM data Recent Files The Create Master Method dialog box opens Create Master Method Method Forge Use Method Forge Performs peak detection against a raw data file i Performs library lookup if requested Import Xcalibur Processing Method Import Xcalibur Processing Method Imports a previously created processing method finding configured compounds and reference spectra Associate Haw Data File Creates a blank master method and associates a Associate a raw data file raw data file allowing manual peak selection Select Compounds from a compound datastore Creates a blank master method and displays the configured compound datastore allowing compound selection oe Select compounds from CDS 2 Select Select Compounds from CDS The Select Compounds to Add dialog box opens listing all the compounds defined in the compound datastore specified for the gas chromatography technology 68 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods select compounds to add ETIN 3 Select the check box for each compound you want to add to the method and click Apply The ToxLab Forms application adds the selected compounds to the Master Method View 4 From the Instrument Method list on the General page select an instrument method 5 To save the new method choose File Save from the main menu
45. Flag values below LOQ Flag values above LOR Flag values above ULOL Flag values above Carryover Flag values between LOD and LOQ Description Reports the concentration at all times or only when the quantified value exceeds either the limit of detection LOD the limit of quantitation LOC or the limit of reporting LOR Report concentration Always gt LOD gt LOQ or LOR Number of decimal places to be included in the report Maximum value is 6 Displays a chromatogram TIC trace of the sample on the quantitation report Prints only the positive compounds in a sample If a compound is valid within a sample and is above the specified Quan Flag Options limits the ToxLab Forms application reports the compound Shades a compound row on any of the reports if a value fails one of the criteria used for evaluation Separates the ion overlay pane from the confirming ion plots in data review Uses an alternate format for the Calibration Report that is designed to print more concisely this report is limited to a maximum of 7 calibration standards Displays manual flags confirming manual flags quan flags and a legend on high density reports Values that are above or below limits defined on the Limits page These flags appear on a variety of reports Flags values below the limit of detection LOD Flags values below the limit of quantitation LOQ Flags values above the limit of reporting LOR Flags v
46. Guide 241 5 Using the Production Mode Working in Report View Table 61 Calibration Curve Report Active View values Column RSD Level Description Relative standard deviation Applies only to internal standards and targets calibrated with an average RF curve The column specifies the level name the field value specifies the data point used in calibration This field can be Response Factor for external calibration Response Ratio for internal linear or quadratic or Relative Response factor for Internal Average RE There will be one column for each level in the curve If the batch uses an extended calibration there might be more columns than calibration standards in the current batch Table 62 Calibration Report Active View values Column Curve Type Average RF Average Response AO Al R 2 RSD Level 242 ToxLab Forms 3 1 User Guide Description The type of curve used when calibrating the compound linear quadratic or average response factor The average response factor Applicable if curve type is Average RE The average response for the internal standard across all calibration points Applies only to Internal Standard sample types The value with no X Applies only to linear and quadratic curves The X value Applies only to linear and quadratic curves The X 2 value Applies only to quadratic curves The minimum correlation coefficient r for an acceptable calibration when i
47. Guide Thermo Scientific 2 Getting Started Choosing a Mode To choose a mode 1 From the dashboard click the mode in which you want to work Your dashboard shows only the modes that you have permission to use See loxLab Forms Dashboard on page 14 2 To change modes from within any of the ToxLab Forms application modes click a mode button in the lower left corner of the window To watch the real time display from the dashboard Click Real Time Status Real Time Status The real time status is displayed at the bottom of the dashboard X C er Sample 13 M mE Instrument Devices Queues E Batch Queue 1 batch Ready E in BAtch 3B 3 samples Active Acquisitian D un H steroidsU2 INJOUT Complete ao H steroids02_INJO03 Complete on D steroids012_INJO02 Complete d H steroidsQ3 IMJOUT Complete E ee I steroids 13 030805135212 Acquiring m B steroids14 Pending S B steroids15 Pending t H stercids16 Pending 20 H steroids17 Pending 10 Processing Queue Empty Ready Reporting Queue Empty Ready es 1 0 s 2 0 RT mini For descriptions of all the features of the real time display see Real time Display on page 185 Thermo Scientific ToxLab Forms 3 1 User Guide 13 2 Getting Started Choosing a Mode ToxLab Forms Dashboard A dashboard for a Manager who has permission for all modes looks like this
48. ME 15 16 17 RT 12 52 Rank SI RSI MP AH 12143711878 aj ase js j BE Dg jme em s POs ja 79 e e Relative Intensity un o 240 13 120 02 251 97 355503 429 14 100 200 300 RT min m z ToxLab Forms 3 1 User Guide 199 5 Using the Production Mode Working in Data Review Samples List The Samples list is the same in both Quan Mode and Qual Mode and displays all the quantitative data for the samples of a batch In Quan Mode the Samples list works with the Compounds pane to select a unique sample and compound combination which then has its textual and graphical values displayed in the Quan Mode pane The list of compounds that are available for a specific method is displayed in the Compounds pane From the Samples list you can make a compound active or inactive Switching a compound to inactive status does not remove its data and calculated values from the result set Instead the ToxLab Forms application masks off the appearance of that compound for that particular sample and grays the compounds in the Compounds list For a calibration standard the application no longer uses the data files calibration point for the calibration and removes it from the graphical view of the calibration curve displayed in the Qualification pane It is no longer part of the result set n Qual Mode the Samples list works with the Peaks pane to select a unique sample and peak combination which then has its textual a
49. P Table 46 Finish parameters Sheet 1 of 2 Parameter Description Modify Calibrations or Enables the Next button that lets you access the Calibration and Active Compounds by Compound Selection page Group If you have already used the Calibration and Compound Selection page this option is not available Batch name Name of the current batch in the form MasterMethodName_MMDDYYYY_ ToxLab Forms 3 1 User Guide 193 5 Using the Production Mode Working in Batch View Table 46 Finish parameters Sheet 2 of 2 Parameter Description Back Returns you to the Batch Specification page where you can enter a sample ID sample name or comment You can also add or remove samples from the sample list or edit the column values for the samples See Specifying a Batch on page 187 Finish Saves the batch and displays it in Batch View From Batch View you can submit the batch for acquisition processing or report generation See Submitting a Batch on page 174 Next Opens the Calibration and Compound Selection page where you can edit the calibration file or edit the list of compounds you want to identify Available only when Modify Calibrations or Active Compounds by Group is checked Cancel Immediately exits the Batch Wizard and does not save the batch There is no confirming message Selecting Calibration Files and Compounds From the Calibration and Compound Selection page you can edit the calibration file or edit the
50. Production Mode Working in Report View Table 71 QC Report Active View values Sheet 2 of 2 Column Max RF Diff 96 QC Amount Calculated Amount Amount 96 Difference Max Amount Difference Description Maximum QC response factor as found on the QC Check page in the method The amount defined by the level for the compound Reportable amount of concentration Percentage difference between the calculated amount and the QC amount Use the injected concentration to calculate this value Maximum allowed percentage difference between the calculated amount and the QC amount Table 72 Quantitation Report Active View values Column RT Qlon Response Injected Concentration DE2999 Injected units Sample Conc Sample units 246 ToxLab Forms 3 1 User Guide Description Retention time for the peak The time after injection at which the compound elutes The total time that the compound is retained on the GC column Mass range for the quan peak Sum of all quan peak response values for the compound Calculated amount as the sample was injected with no conversion applied Note As each additional sample is processed calibration data changes therefore except for the final sample in a batch a report in active view or report view will show different values from a physical PDE XML or printed report created at the end of processing To avoid this discrepancy do one of the following For the s
51. Reference Guide JoxLab Forms Data Review Quick Reference Guide Thermo Scientific ToxLab Forms 3 1 User Guide V Preface To open ToxLab Forms Help From the ToxLab Forms window choose Help ToxLab Forms Help To find a particular topic use the Help Contents Index or Search panes For more information including upcoming application notes visit www thermo com Special Notices This guide includes the following types of special notices IMPORTANT Highlights information necessary to prevent damage to software loss of data or invalid test results or might contain information that is critical for optimal performance of the system Note Highlights information of general interest Tip Highlights helpful information that can make a task easier vi ToxLab Forms 3 1 User Guide Thermo Scientific System Requirements Your system must meet these minimum requirements Contacting Us Thermo Scientific System PC Instruments supported or required Software Preface Requirements 2 33 GHz processor dual core with 2 GB RAM CD R ROM drive Video card and monitor capable of 1280 x 1024 resolution XGA e 75 GB available on the C drive NTFS format Autosamplers Triplus e AS3000 GC Devices Focus GC Trace GC Ultra GC MS mass spectrometers Microsoft Windows XP Professional SP3 Microsoft Office 2007 SP2 or Excel 2007 SP2 Microsoft NET
52. Reports Level level 1 level 2 level 3 Calibrant Amt 6 000 15 000 176 000 Calc Amt 5 581 15 441 175 976 Date Printed 3 31 2010 7 01 30AM Thermo Scientific Drug A Y 5 471e 2X 3 024e 2 R 2 1 0000 Origin Ignore W Equal Area Area Ratio Page 1 of 1 ToxLab Forms 3 1 User Guide 261 A Reports sample Standard Reports Calibration Report Lab name Thermo Fisher Laboratory Instrument Thermo Scientific Instrument User AMER jamie humphries Batch Drug_A 262 Calibration summary Manually Compound integrated Int_Std Drug_A Calibration Report Method Cali File AO y Intercept Curve type Mean RF 655596 L 3 024e 2 Drug_A_Drug_A Drug_A Drug_A calx A1 A2 Slope 5 471e 2 Average RSD Page 1 of 3 R 2 R 2 RSD Flag 7 51 1 0000 3 15 Curve Type A Average RF L Linear Q Quadratic lzInternal standard Note Amounts displayed for internal standards represent the ISTD Response Calibration flags D RSD F Response factor RZR 2 A Amount X Excluded X ISNF Excluded because ISTD wasn t found Manually integrated ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports Calibration Report Lab name Thermo Fisher Laboratory Page 2 of 3 Instrument Thermo Scientific Instrument Method Drug_A_Drug_A User AMER jamie humphries Drug_A Batch Drug_A Cali File Drug_A calx Calibration data points Curve Com
53. Reports tab The Standard Reports page displays the Report Name Report Title and the options to create a hardcopy a PDF file or an XML file See Standard Reports page on page 132 2 To edit the Report Title double click the name and type your new name The ToxLab Forms application uses this name for all reports that use this master method You cannot edit the Report Title from other report views 3 To specify the type of report output to create for each report type select the check box in the appropriate column 4 To duplicate the output type for all reports click the cell to select it then right click and choose Copy Down from the shortcut menu Print Create POF Create XML O0 Oo All check boxes in the column below the selected cell duplicate the selected or cleared state of the selected cell 130 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods By default all report types are cleared To specify custom report types and output formats Click the Custom Reports tab The Custom Reports page lists all the reports that are saved in the following folder NThermoNToxLab Forms Templates Reports The Custom Reports page displays the Report Name and the options to create a hardcopy printout or XLS file See Custom Reports page on page 133 m eports Custom F Prit o Create XLS oO
54. TU 100 cei 02 L6 ewzuequou eXeH 9 eeerer C S 070 Ryu 96 9 O00 98 euezweqooupmed 4i DU 0700 iu ZOOL ZG O0ZOl amp 2 eeuseuudev u Z Si ere 070 Tiyu O 696 OZ GZ WueudqoonHZ p ne En euepewedopfooojpexeH EL MEM SS S SS SS SS LL LLLI 070 Tiyu OO SPZ OZ 869 zZ Ze DU 0700 Tiyu gO 1092 OZ 99 euepemqoojpexeH Lb EE S S S S 6Q Q 1l lll l l l ll 070 Wu grok Oo o O9 euedoidoojpexeH OL EE S S S S 6Q PE E ls s sapa io Tu 696 fco OUO 1d68 ewezwqoouupvzi 9 EE S S S S 6Q P PS S EE lo Tu grok I O8 a 9 GPeuzueqN A EE S S S S 6Q A SS ssp ioo Tu ero 4808 O0LZ 909 ewpeooueXeH 9 JU 070 fu z66 pO OUO S eewemeqoouQZi S ree TE sicco QUO es uazusgouolcC p Iun 070 Tiyu 400 ZO OUO 8 v uazusgoroqusiC 2 BN 070 Thu ho zeiod 00 9 6 eueobped L sBe J unu eq sun SuoO esuodsey uolo n eweN Punodwoy spunoduio jefe L LS 000 mu oor sS0ovlt iTS apoio Z MM UO u OOO Go OUO CC gt ZUS Z OO c css 0700 Wu O
55. Time 3 Edit the values on the instrument page 4 From the main menu on the Thermo Xcalibur Instrument Setup dialog box choose File Save and then choose File Exit Thermo Scientific ToxLab Forms 3 1 User Guide 13 4 Using the Method Development Mode Working with Master Methods The ToxLab Forms application returns you to the General page 5 To update any changes that were made to the instrument method after you created this master method click Update next to the appropriate box The Update Instrument Method dialog box opens Update Instrument Method Please choose how to update the File instrument math LU J Send ko xcalibur Method set From Xcalibur Method 6 Choose one of the following e Send to Xcalibur Method to overwrite the Xcalibur method with the current instrument method e Get From Xcalibur Method to overwrite the current instrument method with the Xcalibur method Cancel to make no changes to the instrument method in the current master method To set automated background subtraction options 1 Click Background subtraction range option and select how you want the subtraction range determined e Before Peak Averages and subtracts a specified number of scans before the apex of the peak After Peak Subtracts a specified number of scans following the apex of the peak Both Sides of Peak Subtracts a specified number of scans from each side of the apex of the peak 2
56. an empty Compound list and displays the chromatographic data for the compounds in the raw file mim c Full ms 35 00 500 00 Absolute Intensi 2 4 6 8 10 12 14 16 18 RT min RT 5 047 5459775 0 CiyxcaliburidataYLabFarms Raw Filesievell raw 2 Select a filter from the Filter list 3 Click the peak in the chromatogram that represents the compound you want to add to the method 4 Right click and choose Add this Peak as New Compound from the shortcut menu 58 D 5T Add this peak as new quan peak Add this peak as new compound Reset scaling Show graphics side by side 0 5 1 0 1 5 2 0 2 5 3 0 The ToxLab Forms application adds the new compound and displays the quantitation peak information for the compound 5 Repeat these steps for each compound you want to add to the method For a detailed description of all parameters on the Detection page see Editing the Compounds Page on page 79 For a detailed description of how to modify a master method see Editing a Master Method on page 70 Thermo Scientific ToxLab Forms 3 1 User Guide 67 4 Using the Method Development Mode Working with Master Methods Selecting Compounds from the Compound Datastore You can select compounds from the compound datastore to create a new master method To select compounds from the datastore 1 From the Method View task pane click Create Method Method View L Create method BE Open method amp
57. button and locate a raw data file to associate with the method 4 To update the target ion ratio values when you associate this raw data file click Yes 5 To set a reference spectrum do one of the following Click Yes Or Click Yes with Background Subtraction This feature is available only when you have set background subtraction values on the General page of the Master Method View See Editing the General Page on page 72 6 Click OK All compounds found in the raw data file are added to your method The ToxLab Forms application displays the General page of the Master Method View 7 From the Instrument Method list on the General page select an instrument method 8 To save the new method choose File Save from the main menu If the compounds in the associated raw data file are not found in the Compound Datastore the ToxLab Forms application will not let you save the method Follow the instructions To add compounds to the method on page 67 For a detailed description of how to modify a master method see Editing a Master Method on page 70 66 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 4 To add compounds to the method 1 Click the Compounds tab The Detection page is selected by default General Compounds N i i Reports Identification Detection L alibratian Calibration levels Compu U O The Detection page shows
58. compound from method Blank page 124 Calibration page 121 Hydrolysis page 127 ISTD page 125 Limits page 120 QC Check page 122 Solvent Blank page 126 Display retention time column Blank page 124 Calibration page 121 Hydrolysis page 127 ISTD page 125 Limits page 120 QC Check page 122 Solvent Blank page 126 Enable User Security 38 Exit ToxLab Forms 9 Fill down 309 Help dashboard 14 Import Compounds 31 Load Compound Datastore 31 Log Off 14 Methods 15 New Compound Datastore 51 Production 14 Real Time Status 14 Reset scaling 111 Save As Compound Datastore 33 Save Compound Datastore 33 Set this mass as a new quan peak 111 Set this mass as quan mass 110 Update confirming ion ratios with this spectrum 110 Compound Datastore administration 30 color coding 36 Compound Datastore selection parameter 41 Compound Datastore view 30 compound flags 206 Compound Name parameter Acquisition List 81 316 ToxLab Forms 3 1 User Guide Compound datastore 35 Compound parameter Calibration 113 Calibration levels 115 Calibration page 121 Hydrolysis page 127 Identification 83 ISTD page 124 Limits page 119 Matrix Blank page 123 QC Check page 122 QC levels 118 Solvent Blank page 126 Compound type parameter Calibration 113 Identification 84 compound types internal standards 83 quan 83 target 85 Compounds page Master Method View 79 Compounds parameter Save Compound Datastore dialog box 34 Compounds That are Missing Quans di
59. create a single report for the entire batch Batch level reports are prepended with a B to differentiate them 4 Do one of the following To return the report selections to their original state click Undo Changes Or To apply the current selections do the following a Click Apply A message reminds you that you must restart the ToxLab Forms application before your report selections are reflected in the reports available for the Method Development and Production modes b To restart the ToxLab Forms application now click Yes or to remain on the Reports page click No To import new custom report types 1 Click Import 2 In the browser locate a Custom Reports xltm file and open the file The application writes the imported report to the following folder Thermo ToxLab Forms VTemplatesWReports The Installed Reports pane adds the new report to the list 46 ToxLab Forms 3 1 User Guide Thermo Scientific 3 Using the Configuration Mode Application Configuration Figure 8 Custom Reports page Custom Reports Standard Reports Installed reports Displayed reports HighDensitys ampleHeport4 Report name FEES HighDensityS ampleR epart3L ong HighDensityS ampleR eport2Lang Alt alibrationFieport HighDensityS ampleH eportl Long HighDensityS ampleRepartb Patchhieport BlankHeport CalibrationD enit A epart CalibrationAepart Check StandardReport Compound lalibrationA eport ContirmatianA eport LContirmationRe
60. detection settings Opens the Peak Detection Settings dialog box for the selected compound See Peak Detection Settings on page 213 lon Overlay The Ion Overlay page represents an overlay of the entire ion set quantification and qualifying confirming for the selected sample and compound Use this page to graphically review the peak apex alignment and co eluting peak profiles RT 1 38 steroidat4 E m c m E m 3 d t 1 5 RT min 4 To zoom in on a peak 1 Drag the cursor to delineate a rectangle around the peak The delineated area expands to fill the view 2 To restore the method default view right click the chromatogram plot and choose Reset Scaling from the shortcut menu ToxLab Forms 3 1 User Guide 219 5 Using the Production Mode Working in Data Review Qual Mode The Qual Mode displays detected peaks for the selected sample and lets you manually add peaks samples list Peaks pane Method lib cal test Instrument ThermaFisher Instrument E Status Flags Filename Sample ID ie a uus em Te mesoa u Quan Filter c Full ms 35 00 500 00 Mode Qual Slee c Full ms 35 00 500 DU Sample type Sample level Peak RT min Sl RSI MP deem e s n a 100 i Hode E 5 36 t BD g 5 00 13 63 E sn 11 18 2 M Bug 9 42 955 ET E 40 es 5 20 12 63 1437 15 12 204 1 76 235 292 353 n T 140 SM hl ee Y n LU ML su ul f
61. for Method Development or Production modes For detailed information about configuring reports in the Configuration mode see Specifying the Reports Configuration on page 42 For detailed information about specifying reports when you create a method in the Method Development mode see Editing the Reports Page on page 130 For detailed information about viewing batch reports in the Production mode see Working in Report View on page 230 Thermo Scientific ToxLab Forms 3 1 User Guide 251 A Reports Specifying Reports Standard Reports 252 ToxLab Forms 3 1 User Guide For each standard report you generate you can create a hardcopy print a PDF pdf or an XML xml output format In addition to the report type you can specify a report title for each of your reports The default report title is the report name The ToxLab Forms application can generate the following types of standard reports Batch Report Batch Summary Report Calibration Curve Report Calibration Report Chromatogram Report Compound Calibration Report Compound Calibration Report Alternate Confirmation Report Confirmation Report 2 High Density Calibration Report High Density Internal Standard Report High Density Internal Standard Report Long High Density Sample Report 1 High Density Sample Report 1 Long High Density Sample Report 2 High Density Sample Report 2 Long High Density Sample Report 3 High Density Sample Report 3 Long Internal St
62. format for the Calibration Report designed to print more concisely and limit the report to a maximum of 7 calibration standards select the Use Alternate Calibration Report Format check box 4 To display flags and a legend on high density reports select the Display Quan Flags and Legend check box To specify quantitation flag options Huan Flag Options q values below LOD g values below LOG alues above LOR alues above ULOL alues above Carpower ag values between LOD and LOG Select the values you want to display in the report Values are above or below the limits defined on the Quan page These flags appear on a variety of reports and are defined in the Report options parameters table Thermo Scientific ToxLab Forms 3 1 User Guide 135 4 Using the Method Development Mode Working with Master Methods To correct surrogates Surrogate Correchon Option Correct surrogates Select the Correct Surrogates check box The ToxLab Forms application applies the conversion factor specified in the sample row in the batch to the sample s calculated concentrations for surrogates as the conversion factor is applied to target compounds To track the use of the tune file Tune Time Tracking Options Enable tune time tracking Tune file lifetime Hrs 1 Select the Enable Tune Time Tracking check box This option tracks the number of hours between the last instrument tune and each sample acquisition
63. from the list of subprojects Thermo Scientific 5 Using the Production Mode Working in Batch View C Select a batch from the list of batches d Click Open Open Batch Select a project subpraject and batch ta open E EM Project BH Subproject IM s _lib Sg Project Open TLF 3 0 Batches 5 To open a TLF 2 5 batch do the following a Select a batch from the list of batches b Click Open Open Batch Open TLF 25 Batches vM Open Jd Cancel c Editthe batch as you would any other batch You cannot submit the batch for processing until you save it d To save the batch choose File Save Batch or click the Save icon A text message informs you that the master method and instrument method for the batch will also be imported e Click OK to dismiss the text message and continue saving the batch or click Cancel to terminate the Save process The Batch Save dialog box opens Thermo Scientific ToxLab Forms 3 1 User Guide 169 5 Using the Production Mode Working in Batch View Batch 5ave Select a project and subpraject to save the batch rd a sa Mm Batch lib Project ve to filename B atch2 5 Cues f Select a project and subproject where you will save the batch g Type a name for the batch h Doone of the following Type a new name for the batch and click OK _Or Select a batch name to overwrite and click Overwrite To open a batch from the Recent Files
64. gt 15 00 Level Level High Limit 80 00 2 00 2 00 80 00 2 00 100 00 9 00 60 00 24 00 100 00 24 00 Page number Page number Relative To Base peak 69 69 Base peak 198 Base peak 198 Base peak 198 442 Base peak 442 Page 35 of 36 Page 36 of 36 Thermo Scientific A Reports sample Standard Reports Negative Report J perite Aenuen oAneDeN u YONI SOd Aum UENH H pwj uo 59 J q G Pu Jiup ur 198A0OAUEI I anje olje uo 2 DOI1 gt LT gt QO7T pueB8e bei O q Ssed 00591 qu bu 99p0 sDe J SuoO XEN SUN Suoo p nojeO sBe j JO eBeg qu Bu 000 SL sum Suoo pejejnoje2 Tqu Bu 99t 0 spun Suoo p 5 ul qu Bu 000 SL spun Suoo pejoefu Nd S0 10 S 800c Z V v Juswwoy Sea alld 7000 Je u asuodsay ed n 34 eBeJoAy 0000 dy eBeJeAy osuodsoy d enn 3 4 B5ei AV Swen dues xjes y Bniq elm Je v Bnig v Bug v Bniq poyjow ywodey oAnebDoN ter esuodsey LOSSLS esuodsey Oz 14 uo o 0208 uo O L6 L v Bnua lu spunodwoy joDue CO L PIS ul lu spJepuejs euJ9 u oAneDou oAneDou S SWeUD I4 di eidures SOd EIA v Bnuq uojeg seuuduinu siwel yawy esf jueuinujsu DNUBIOS oway jueuunujsu jojeJoqe Jeusij oway eujeu qe 301 ToxLab Forms 3 1 User Guide Thermo Scientific Quantitation Report sample Standard Reports A Reports pse ayu Aenuen SIS IOIP
65. highest calibrator amount Carryover limit The highest amount of a substance that does not leave a residual amount in the instrument If a substance has a carryover limit of 5 amounts higher than 5 usually dirty the instrument and leave residue behind tainting the following sample A carryover limit of less than 5 does not leave any residual amounts of the substance Shortcut menu Copy down Copies the selected column value to all rows in that column For detailed instructions about using the Copy Down command see Appendix B Using Copy Down and Fill Down Display retention time Displays or hides the RT column in the compound list column Delete compound from Removes the selected compound from the current master method method 120 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Calibration Use the Calibration page to define acceptable criteria for initial calibration The ToxLab Forms application makes the evaluation by comparing the initial calibration results for each compound found in the sample to the values defined on this page On the Calibration report the application flags the calculated values for internal standard compounds that exceed these limits Figure 25 Calibration page Group Reports General Dampounds QC Check Negative Limits HT Compound R 2 threshol
66. humphries Drug_A Batch Drug_A Cali File Drug A calx 100 8 ag 70 amp 4 30 20 Relative Intensity 1 56 1 67 1 95 1 00 1 59 1 88 133 20 201 202 203 203 2 04 1 86 1 88 1 30 1 92 1 84 1 86 1 88 2 00 2 02 2 04 RTimin Thermo Scientific ToxLab Forms 3 1 User Guide 265 A Reports sample Standard Reports Compound Calibration Report z JO eBeg qu 8u qu 8u qu 8u spun v 6niq v Bniq poul NW junowy V posenbs H H 10 08 esuodses d ASM A sbey uoneiqileo peje46eju Aj enue v 916971 6596 GLL66S 000 SL 8998lS 000 97L 949 Lvv SL 98 8 0 089689 000 SL cS 09 000 SL I A9 k8S S 9 0 Vvv0849 000 SL 899122 0009 1949 jwe 989 oneJesuodsoM Pauly S junowy SI ealy PIS junowvy pis 19497 ssed Jeour gt w A Bay Ienb3 AA esou y ui65uO 0000 1 ZvY Z 8pZ0 XZ 8 tS A v 6ng v Bnug euieN punodwoy xies y Bniq 9J yep v Bnuq v Dnuq seuuduinu eiuelvd3lNVv jueuungjsu ILMUSIOS owy AloyeJoge7 1 usid oway uode uoneJqije punoduioo yoyeg Jos jueuunujsu euieu qe 267 ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports Z JO Z abe junowy v peuenbg y Y 10 26J asuodsay 4 ASM d sBejj uoneiqileo _ E poje16eju Allenueyy Wd 6 90 S 800 L r Wd 1 90 9 8002 ZL 7 Wd Zv S0 8 8002 ZL 7 sed Sid swen ojdweg xies y Dniq eiue v Bnuq v Bniq v Bniq P
67. limit Q Quan limit POS Cutoff n2 Negative b Solvent blank H Hydrolysis 282 ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports Internal Standard Summary Report Internal Standard Summary Report Lab name Thermo Fisher Laboratory Page 1 of 1 Instrument Thermo Scientific Instrument Method Drug_A_Drug_A User AMER jamie humphries Drug_A Batch Drug_A Cali File Drug_A calx Compound Std Response Min Max Sample Response Int_Std 655596 327798 50 00 983394 150 00 678044 Std RT Min Max Sample RT Int_Std 1 93 1 68 0 25 2 18 0 25 1 93 Thermo Scientific ToxLab Forms 3 1 User Guide 283 A Reports sample Standard Reports lon Ratio Failure Report vV2Vevii vel ev ecc COOL JO eDeg uey one LOVSTVC 0c 88v Vv6 097 r Oc LLE GY969 r OC ELV V6ECOOLYV 0 LLE osuodsay eno uo eno esuodsey uendY uo ueno JuswWWoy Nd 19 80 59 800 L r eg l d Swen S dues xev Bniq li EI v Brug v niq v Bniq poul NW uode sunjie4 one uol eBoy eoJy v Bnuq esuodsey punodwoy z ueuumeds c usw oads 6 SWEUD 4 adi eidues SOd EIA v Brug yoyeg seuuduunu siwel yawy esf jueuingjsu ounuergs ouueu X jJu unmnsu jojeJoqe7 Jeusi4 oway eueu qe Thermo Scientific ToxLab Forms 3 1 User Guide 284 Manual Integration Report Manual Integration Report A Reports sample Standard Reports Page 1 of 1 EC25B 8level 322010 a EPAMethod8270B 8le
68. list 1 Click Production from the dashboard or the navigation pane Production The Production navigation pane opens When you save a batch it is added to the Recent Files list The Recent Files list displays a list of your most recently saved batches Batch Yiew L New batch E Open batch Recent Files Batch_calz Batch_call 2 Click the batch name in the Recent Files list Do not double click The selected batch opens in the Batch View To edit column values 1 Type a file name in the Filename column for each sample or right click and choose Browse in Raw File from the shortcut menu 170 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 5 Using the Production Mode Working in Batch View You can also browse in multiple raw data files to create multiple samples Select a sample type from the Sample Type list box for each sample Available TLF sample types Negative Solvent QC Specimen Qual Calibrator Hydrolysis Specimen Unextracted For a detailed description of sample types see Specifying Sample Types on page 197 For each Calibrator or QC sample select a level from the Sample Level list The sample levels are defined in the master method If there are no levels to select from the Sample Level list ask a user with Supervisor or Manager permissions to edit the method and specify the levels For detailed instructions about defining sample levels see Chapter 4 Using the
69. lon Ratio Failure Report Active View values Column Quan Ion Qual Ion Quan Ion Response Qual Ion Response Ratio Range Description The ion for quan peak The ion for the confirming peak Response of the quan ion Response of the qual ion The ratio of the confirming ion response to the quan ion response The acceptable range Table 68 Manual Integration Report Active View values Column m z Method RT Method Peak Height Method Peak Area Manual RT Manual Peak Height Manual Peak Area Description Mass to charge ratio for the quan peak Apex retention time for the method integrated peak Height for the method integrated peak Area for the method integrated peak Apex retention time for the manually integrated peak Height of the manually integrated peak Area of the manually integrated peak Table 71 QC Report Active View values Sheet 1 of 2 Column Curve Type Daily RF Mean RF Min RF RF D Description L Linear A Average RF Q Quadratic The response factor value for Average RF curve types For all other curve types this column is blank The average response factor as found in the calibration file Displayed for Average RF curve types For all other curve types this column is blank Minimum QC response factor as found on the QC Check page in the method Percent difference between daily and average response factor ToxLab Forms 3 1 User Guide 245 5 Using the
70. method to open Method 756 Methadzl42 Method2llB Open TLF 3 0 Methods pen TLF 2 5 Methods Select either Open TLF 3 0 Methods or Open TLF 2 5 Methods The ToxLab Forms application displays all available methods for the specified version of the application The list of ToxLab Forms 2 5 methods can include any method created with ToxLab Forms 2 5 or greater Select a master method and click Open The selected master method opens in the Master Method View When you open a LabForms 2 5 method the ToxLab Forms application copies all components of the selected method including its associated instrument method e Ifthe LabForms 2 5 master method does not have an associated instrument method the Master Method View for the imported method indicates that you need to select an instrument method Ifyou open a LabForms 2 5 master method that uses an instrument method name already used in your Xcalibur methods folder you are prompted to overwrite the instrument method or use the method with the same name already in your methods folder To open a saved master method from the Recent Files list Click Method Development from the dashboard or the navigation pane Method Development The Method Development navigation pane opens When you save a method it is added to the Recent Files list The Recent Files list displays a list of your most recently saved master method files ToxLab Forms 3 1 User Guide 71 4 Using th
71. not found Table 49 Samples List parameters Sheet 1 of 3 Parameter Description Status Orange for samples that are currently acquiring Blue for samples that have not been acquired Yellow for samples that have been acquired and not processed Green for samples that have been acquired and processed Flags Displayed only when a compound within the sample has an error Sample flags are always red Filename Name of the raw data file that contains the sample data 202 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific Parameter Sample type Sample level Sample ID Sample name Comment Vial Position Injection volume Integration mode Height Area Actual RT Expected RT Calc Amt Theo Amt 5 Using the Production Mode Working in Data Review Table 49 Samples List parameters Sheet 2 of 3 Description Defines how the ToxLab Forms application processes the sample data Each sample is classified as one of the following sample types Negative Calibrator QC Specimen Specimen Qual Solvent Hydrolysis Unextracted The level defined for a calibration sample or quality control sample A user defined alphanumeric string that identifies a sample A user defined name that identifies a sample A user defined comment for the sample The tray vial number used for the autosampler acquisition The injection volume in microliters of sample to be injected Minimum value 0 05 When you are
72. not open the Thermo Foundation Instrument Configuration tool while the ToxLab Forms application is running Follow these procedures To open the Instrument View e To create a new instrument method To open an instrument method To open the Instrument View 1 Click Method Development from the dashboard or the navigation pane The Method Development navigation pane opens 2 Click the Instrument View task pane New instrument method BE Open instrument method Thermo Scientific ToxLab Forms 3 1 User Guide 149 4 Using the Method Development Mode Working with Instrument Methods To create a new instrument method 1 Click New Instrument Method in the Instrument View task pane The Thermo Xcalibur Instrument Setup opens This example instrument setup shows multiple configured instruments FA untitled Thermo Xcalibur Instrument Setup File TRACE Help Bag S x So 25 000 0 20 040 0 60 0850 1 00 1 20 1 40 160 1850 200 220 230 260 250 300 Oven Enable Cryo Max Temp C 350 Past Hun Conditions Temperature C 9 Time min 9 Pressure Left psi 05 Pressure Right psi 05 Acquisition Time mir Oyen Runtime 300 1505 Hamps Hate Temp Hold Time Ce mri PC minutes Initial 40 1 00 Hamp 1 10 0 AL 1 00 Preo Aun Timeout min 10 00 E quilibratian Time min 0 50 TRACE GC Ultra C Specific Ti
73. o oc o o Relative Intensity tas E i o o co Relative Intensity ca Ln OQ o co 3 80 3 91 c 4 0 4 2 l 4 2 l F 4 2 RTimin RT min RT min Times Signal Detect Signal Detect Ratios Signal Detect Ratios Window sec 23 00 1 Filter Filter en Trace Mass range Trace Mass ranae Viens width min For a detailed description of all peak detection settings see Detection on page 84 Qualification Pane The Qualification pane displays the compound selected in the Quantification data pane and Compounds pane The Qualification pane consists of five pages Calibration Curve Spectra Confirming Ions on Overlay Thermo Scientific ToxLab Forms 3 1 User Guide 213 5 Using the Production Mode Working in Data Review Calibration Curve The Calibration curve page displays a graphical view of the calibration curve for the selected compound and key statistical values for evaluating the quality of the calibration Fropazine D 14 Average Area 1025895 RSD 94 07 To manually exclude a calibration point From the Samples list select the Excluded check box for the sample Tozoom in on an area 1 In the Calibration curve plot drag the cursor to delineate a rectangle around an area The delineated area expands to fill the view 2 To restore the method default view right click the calibration curve plot and choose Reset Scaling from the shortcut menu Changes to the cali
74. pane works with the Samples list to display textual and graphical values for a unique file and compound combination Thermo Scientific ToxLab Forms 3 1 User Guide 205 5 Using the Production Mode Working in Data Review Use the Compounds pane to select a particular compound within that sample s result set When you select a file and compound the values displayed in the data grid reflect the quantification data for that unique combination From the Samples list you can make a compound active or inactive Switching a compound to inactive status does not remove its data and calculated values from the result set instead the ToxLab Forms application masks off the appearance of that compound for that particular sample and grays the compounds in the Compounds list For a calibration standard the application no longer uses the data file s calibration point for the calibration and removes it from the graphical view of the calibration curve displayed in the Qualification pane It is no longer part of the result set Method lib cal test Instrument ThermoFisher Instrument Compounds mE Status Flags Filename ne uorabipheny 1 A a5 or 5 oalsd 5ng f Mi Acensphihenesil Sample type S ample level Sample ID EI std 100 cal std 100 ng B Chiysene d12 ae Specimen evel d 50 na uL 88 Hesachlorobenzene Tur ida Uli Hexachlorobutadiene JEN NH level 2 10ng uL ma Hexachloracyclopentadi
75. parameter values If you are editing your own user name the Enabled check box is unavailable because you cannot make your own account unavailable 4 Do one of the following When all the user information is correct click the Save Changes icon cy The ToxLab Forms application adds the new parameter values to the User Listing and the parameters in the User area are unavailable s e To discard all changes and not save the edits click the Cancel Changes icon m All changes are discarded and the parameters in the User area are unavailable To remove a user 1 In the User Listing table select a user Note Clicking anywhere in the row selects the user The user information populates the parameter fields in the User area 2 Click the Remove User icon ca If you select your current user name the Remove User icon is unavailable You cannot remove yourself 3 When prompted confirm that you want to remove this user If the user is currently logged on to the ToxLab Forms application the user s current session is not affected 4 Click OK Note Rather than completely removing the user you can disable a user logon without removing all the user information from the system Follow the instructions To edit user information on page 21 22 ToxLab Forms 3 1 User Guide Thermo Scientific 3 Using the Configuration Mode User Administration Figure 3 User Administration view User Administrati
76. select the acceptable ion ratio range In the Ion Coelution box select the maximum difference in retention time between a confirming ion peak and the quantification ion peak In the following example Signal Detect Aglio m Enable The target ratio is expected to be 61 0296 and the window is Absolute 2096 so the acceptable window for this confirming ion is 41 02 to 81 02 If instead the window type was Relative the plus or minus value would be 20 of 61 02 or 12 20 so the acceptable window for this confirming ion would be 48 8296 to 73 2290 ToxLab Forms 3 1 User Guide 111 4 Using the Method Development Mode Working with Master Methods Figure 20 Ratios page Confirming peak 1 mizz657 10 en ree ee Relative Intensity tn e j n u gt o Oo o o cgo Lo 20 0 4 0 6 0 8 1 0 RT min Signal Detect Ratios Enable Table 23 Ratios parameters Parameter Description Target ratio The theoretical ratio of the confirming ions response to the quantification ion s response Window type The absolute or relative calculation approach for determining the acceptable ion ratio range Window The acceptable ion ratio range Ion coelution min The maximum difference in retention time between a confirming ion peak and the quantification ion peak 112 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods C
77. selected sample ToxLab Forms 3 1 User Guide 183 5 Using the Production Mode Working in Batch View Creating a Batch Using the Batch Wizard Using the Batch Wizard you can define a sequence composed of various sample types to be assembled into a batch of samples The batch wizard requires a batch template and a master method to compile a standardized sample batch Before you can create a batch with the Batch Wizard you must have a master method and a batch template See Creating a New Master Method on page 53 and Using a Batch Template on page 178 Use the following procedures in the Batch Wizard to create and submit a batch Selecting a Batch Template Specifying a Batch Submitting the Batch Optional Selecting Calibration Files and Compounds The Batch Wizard includes the following pages Batch Template Selection Batch Specification Finish Calibration and Compound Selection 4 To open the Batch Wizard Choose File New Batch Using Wizard from the main menu The Batch Template Selection page of the Batch Wizard opens See Batch Template Selection page on page 186 184 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Batch View Selecting a Batch Template From the Batch Template Selection page you can create a list of samples to acquire or process To create a sample list 1 From the Project list select a project 2 From the Subproject list selec
78. selected samples in the batch When you submit a batch you can choose to acquire process or create reports for the submitted samples l 174 ToxLab Forms 3 1 User Guide To submit all samples in the batch Do one of the following Right click and choose Submit Batch from the shortcut menu Or Click the Submit Batch icon EB From the Submit Options dialog box select if you want to process data and create reports in addition to acquiring the samples You can choose to process samples that have already been acquired You can choose to acquire and process unacquired samples including re injections You can choose to create reports for all submitted samples Click OK To submit selected samples Select the samples you want to submit Do one of the following Right click and choose Submit Selected Samples from the shortcut menu E Click the Submit Selected Samples icon ER From the Submit Options dialog box select if you want to process data and create reports in addition to acquiring the samples You can choose to process samples that have already been acquired You can choose to acquire and process unacquired samples including re injections You can choose to create reports for all submitted samples Click OK Thermo Scientific 5 Using the Production Mode Working in Batch View Observing the Real time Display Thermo Scientific You can access the real tim
79. the Test The Test is the acceptable difference as a percentage between the known amount and the calculated measured amount of each QC level 116 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 4 Continue adding QC levels and values for percentage test When you finish adding QC levels you can specify the concentrations for each level for each compound 5 To enter the concentration values to the table do the following a Select the first QC level table cell b Click the cell again to make it editable c Typea concentration value 6 Repeat Step 5 for all ed levels associated with the first compound Acquisition List Identification Detect Calibration Calibration levels QC levels alinae HC QC2 Ble Be 7 bz 1 Maethuldadeculamine 7 To specify the same concentration values for all compounds select the value you want to copy right click and choose Copy Down from the shortcut menu Acquisition List Identification Detection Calibration Calibration levels QC levels angel HET Hr OCS 2 752 1Metyldodoodenine 10 000 15 000 25 000 3 415 53 5 53 Allidachlor 10 000 15 000 25 000 4 373535 Acephate 10 000 15 000 25 000 Thermo Scientific ToxLab Forms 3 1 User Guide 117 4 Using the Method Development Mode Working with Master Methods Figure 23 OC Levels page General Compounds JA LC L
80. the selected compound from the current master method method 126 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Hydrolysis Use the Hydrolysis page to specify the hydrolysis checks for compounds Figure 30 Hydrolysis page Reports Compounds General Upper limit Br check ISTD Besar Blank m HT Compound Method o name en QA Table 34 Hydrolysis parameters Hegatiwe Threshnold Lower limit Thermo Scientific Parameter RT Compound Method Threshold Lower Limit Upper Limit Shortcut menu Copy down Display retention time column Delete compound from method Description Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column The compound name The evaluation process to use specified as either a lower threshold or a range To deactivate the hydrolysis test for a specific compound select None For compounds using the Threshold method this specifies the threshold value for the hydrolysis test Values below this threshold are flagged in the Hydrolysis report For compounds using the Range method this specifies the lower limit of the range For compounds using the Range method this parameter specifies the upper limit of the range Copies the selected column value to all rows in that column For detailed instructions ab
81. to add to the Installed Reports list Undo changes Returns the report selections to their original state when you first opened this view Apply Applies the current selections and reminds you that you must restart the application before the report selections are available 48 ToxLab Forms 3 1 User Guide Thermo Scientific EN NH Using the Method Development Mode This chapter includes method development tasks assigned to the Supervisor or Manager roles Contents Working with Master Methods Working with Instrument Methods Working with Development Batches From the Method Development mode you can create a master method or an instrument method and you can create a development batch to test your instrument method with a sample batch To access the Method Development mode Click Method Development from the dashboard or the navigation pane The Method Development navigation pane opens Thermo Scientific ToxLab Forms 3 1 User Guide 49 4 Using the Method Development Mode Figure 9 Method Development navigation pane i Method Development Method View L Create method BE Open method amp Export SRM data Recent Files Instrument View New instrument method ES Open instrument method Development Batch ES Select batch location n Mew sample lisk Open Qual Browser Production Method Development Configuration Table 12 Method Development navigation pane functions Sheet 1 of 2
82. to make it easier to identify the peak you want to add to the results set 2 93 2 90 3 05 2 8 3 0 ToxLab Forms 3 1 User Guide 223 5 Using the Production Mode Working in Data Review 2 Right click the chromatogram navigation pane and choose Add Peak from the shortcut menu 3 Click to indicate the left and right base points for the peak The ToxLab Forms application marks the peak in the chromatogram navigation pane 2 9 3 0 The ToxLab Forms application places the peak delimiter tags at the base point locations and automatically updates the peak values in the Peaks pane and Qual Peak pane RT 2 93 MA 53515847 Be MH 288043603 78 SH INF 100 Eg c g 60 m 40 20 Manually added 2 5 7 4 3 0 b UM RT min ase poin Feak HT min Sl RSI MF Library entry 930 1333 34 Phenol 2 fluoro a45 Ethanamine M ethyl M nitroso sm C E u Te 224 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Data Review Figure 50 Navigation Chromatogram pane Filter c Full ms 35 00 500 00 00 5 an z 60 Z m 40 t 2011 76 2 35 292 353 L ML d 2 3 4 12 52 7 85 3 60 L 5 O6 5 00 oe 13 63 11 18 4 45 aos 999 qu 2 42 9 59 ae IL 3 17 L pev 1437 15 12 14 90 k YW WI JI E LM n i l F IE ln il N r 5 6 7 40 11 12 13 14 15 RT min Table 54 Navigation Chromatogram shortcut menu Qual Peak Pane Command Ad
83. to notify user of a randomly generated password Allows or disallows access for this user When this user is currently logged on disallowing takes effect after the user logs off Enables the fields in the User area where you can enter information for a new user Deletes all information for the selected user Enables the User area where you can edit any of the parameters for the selected user Adds the new parameter values to the User Listing table and disables the parameters in the User area Discards all new or edited information Thermo Scientific User Roles User Permissions Manager IT Administrator Thermo Scientific 3 Using the Configuration Mode User Administration This section describes the responsibilities for five different types of users Manager IT Administrator Supervisor Technician and QAQC A Manager or an IT Administrator assigns you to a role that gives you permission to access specific modes of the ToxLab Forms application When you log on the dashboard displays links to only the modes that you can access Table 6 User roles and permissions User role neun Production Configuration Development Manager x x x IT Administrator x Supervisor x x Technician x QAQC x As a user in the role of Manager you review graphically applicable data and manipulate data batches methods and instruments A manager is responsible for these tasks Creating or editing methods for new l
84. view of the Configuration mode and create a new subproject See Project Administration on page 28 3 To change the current method click Select Method and select a new method zs Project k SIE uiae 5ubprojecti k Method Select Method Assay Type Assay name Toadda sample to the list 9 Thermo Scientific Right click the sample list pane and choose Add Sample from the shortcut menu or click the Add Sample icon In The ToxLab Forms application adds a new Specimen sample to the end of the Samples list To insert a sample into the list Select the sample above which you want to insert a new Specimen sample Right click the Samples list pane and choose Insert Sample from the shortcut menu The new Specimen sample is inserted above the selected sample Repeat Sample Sample Sample type S ample level ID a Comment a Inserted sample i w Bg To copy a sample Select the sample you want to copy Right click and choose Insert Copy Sample from the shortcut menu The ToxLab Forms application inserts the copy above the selected sample ToxLab Forms 3 1 User Guide 179 5 Using the Production Mode Working in Batch View 180 ToxLab Forms 3 1 User Guide S l To remove samples from the list Select the sample you want to remove Use the Shift or Ctrl keys to select multiple samples Right click and choose Remove Selected Samples fro
85. x PHOOS ToxLab Forms 3 1 User Guide 231 5 Using the Production Mode Working in Report View To enlarge the report text 1 Select a report from the Select a Report list i 2 Click the Zoom icon Ki and select a zoom scale Page Width Whole Page 400 30s es 150 100 Fos aU eoo Customize 232 ToxLab Forms 3 1 User Guide Thermo Scientific Report View cm Batch Report Figure 51 Report View page 5 Using the Production Mode Working in Report View Lah name Thermo Fisher Laboratory Instrument Thermo Scientific Instrument User Batch Filename Filel File File3 File4 Thermo Scientific AMER dana power Patch20427 Daie time sample ID Sample name HIA samplel NIA sample2 HIA sample3 NIA sample4 Baich Report Page 1 of 1 Method Batch2042C Method20e2 Wethod2042 Cali Fik Batch20420 calx Level Sample type Pos Inj vol Conv Factor Comment Nia Matrix Blank 1 gt 0 000 1 0 NIA Unknown 2 50 000 1 0 Nia Unknown 3 gt 0 000 1 0 Nik Unknown 4 50 000 1 0 Table 57 Report View parameters Select a report Export Report a Print Report 5 Find Text Zoom hi Description Displays the report types created for the current batch Writes the Crystal Reports rpt or custom reports file to a specified folder Sends all reports for the batch to your default printer There is no dialog box or confirmation message Locates the specified text and enclo
86. 0 0 00 nitrobenzene d5 sur 0 000 0 00 0 00 0 00 Nitrobenzene 0 000 0 00 0 00 0 00 N Nitrosopiperidine 0 000 0 00 0 00 0 00 Isophorone 0 000 0 00 0 00 0 00 2 Nitrophenol CCC 0 000 0 00 0 00 0 00 2 4 Dimethylphenol 0 000 0 00 0 00 0 00 Bis 2 chloroethoxy methane 0 000 0 00 0 00 0 00 2 4 Dichlorophenol CCC 0 000 0 00 0 00 0 00 1 2 4 Trichlorobenzene 0 000 0 00 0 00 0 00 Naphthalene 0 000 0 00 0 00 0 00 p Chloroaniline 0 000 0 00 0 00 0 00 2 6 Dichlorophenol 0 000 0 00 0 00 0 00 Hexachloropropene APP9 0 000 0 00 0 00 0 00 Hexachlorobutadiene CCC 0 000 0 00 0 00 0 00 N Nitroso di N butylamine 0 000 0 00 0 00 0 00 4 Chloro 3 methylphenol CCC 0 000 0 00 0 00 0 00 Safrole APP9 0 000 0 00 0 00 0 00 2 Methylnaphthalene 0 000 0 00 0 00 0 00 Hexachlorocyclopentadiene SPCC 0 000 0 00 0 00 0 00 1 2 4 5 Tetrachlorobenzene 0 000 0 00 0 00 0 00 2 4 5 Trichlorophenol 0 000 0 00 0 00 0 00 2 4 6 Trichlorophenol CCC 0 000 0 00 0 00 0 00 2 fluorobiphenyl sur 0 000 0 00 0 00 0 00 Isosafrole APP9 0 000 0 00 0 00 0 00 2 Chloronaphthalene 0 000 0 00 0 00 0 00 2 Nitroaniline 0 000 0 00 0 00 0 00 1 4 Naphthoquinone APP9 0 000 0 00 0 00 0 00 Dimethyl phthalate 0 000 0 00 0 00 0 00 1 3 Dinitrobenzene app9 0 000 0 00 0 00 0 00 2 6 Dinitrotoluene 0 000 0 00 0 00 0 00 Thermo Scientific ToxLab Forms 3 1 User Guide 297 A Reports sample Standard Reports Method name Master method name Current calibration file Assay type Inj vol Instrument method Tu
87. 0 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 ToxLab Forms 3 1 User Guide 299 A Reports sample Standard Reports 300 Method name Master method name Current calibration file Assay type Inj vol Instrument method Tune Breakdown method Breakdown Groups GroupName DDT Breakdown Members 4 4 DDE 4 4 DDD p p DDTs Method name Master method name Current calibration file Assay type Inj vol Instrument method Tune Breakdown method QAQC Tune Tune compound Tune method Use selected method only EC25B 8level 322010 a EPAMethod8270B 8level EPAMethod8270B 8level EC25B 8level 322010 a calx Robustness 1 000 TargetsSplit DFTPPSplit EC25B 8level 322010 a EPAMethod8270B 8level lon range calc method EPAMethod8270B 8level EC25B 8level 322010 a calx Robustness 1 000 TargetsSplit DFTPPSplit Require background subtraction Step off Eval mass 51 68 70 197 197 198 199 275 365 441 442 443 Base peak True True ToxLab Forms 3 1 User Guide Method Report Max 96 breakdown 20 00 Method Report lon range calc method DFTPP 8270D True True 20 Low Op Low Limit 96 gt 10 00 gt 10 00 gt 50 00 gt 5 00 gt 10 00 gt 1 00 gt 0 00 gt 50 00
88. 00 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 Page number ULOL 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 160 000 Carryover 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 Page 7 of 36 Thermo Scientific Method name Master method name Current calibration file Assay type Inj vol Instrument method Tune Breakdown method Groups DDT Breakdown 4 4 DDE 4 4 DDD p p DDTs Thermo Scientific EC25B 8level 322010 a EPAMethod8270B 8level EPAMethod8270B 8level EC25B 8level 322010 a calx Robustness lon range calc method 1 000 TargetsSplit DFTPPSplit Met
89. 000 5 581 ng mL A Reports Sample Standard Reports Tune report not found 4 17 2008 5 05 47 PM Tune Report Date Acquisition Date Cali File Date 3 11 2010 9 01 23 AM Operator ID AMER jamie humphries Instrument ID Thermo Scientific Instrument Vial Number 2 1 98 1 99 2 00 2 01 2 02 2 03 2 03 2 04 1 98 2 00 2 02 2 04 Composite RT 1 83 cal 1 100 30 a0 gt 70 9 50 40 E a 20 10 0 1 50 1 85 2 00 R Tiimin Target Range Ratio 100 00 15 69 23 54 19 91 Composite RT 1 85 cal 1 19 Pen a0 a0 gt 70 60 50 40 m 20 158 zm 2D 10 n 1 85 2 00 1 0 1 95 2 00 RTimm ATimin Target Range Ratio 4 800 7 200 100 00 22 33 33 49 27 53 11 43 17 14 14 09 Page 1 of 1 ToxLab Forms 3 1 User Guide 307 A Reports sample Standard Reports Solvent Blank Report Solvent Blank Report Lab name Thermo Fisher Laboratory Instrument Thermo Scientific Instrument User AMER jamie humphries Batch Drug_A Page 1 of 1 Method Drug_A_Drug_A Drug_A Cali File Drug_A calx Internal Standards RT Qlon Int_Std 1 92 380 20 Target Compounds RT Qlon Drug_A 1 93 371 20 308 ToxLab Forms 3 1 User Guide Response Method Upper Limit 746596 None Response Method Upper Limit 1071 Quan lon RT 0 Fail Manually integrated Thermo Scientific UR Using Copy Down and Fill Down This appendix describes the Copy Down and Fill Down commands that you can use to make entering column values easier
90. 2 Click the Tune File Lifetime spin box and set the number of hours you want to allow between the last instrument tune and a sample acquisition Any sample acquired outside this maximum allowable time is flagged on the Batch report Figure 34 Report Options Quan Limits Flags Quan Flag Options Surrogate Correction Option Report concentration Always ag values below LOD Correct surrogates Decimal pl to be reported ag values below LOQ Show chromatogram on Quantitation Report Dove LOR Tune Time Tracking Options Display valid compounds only Enable tune time tracking ez above ULOL User Interface Options Tune file lifetime hrs Shade row when sample is outside of evaluation criteria m gt s above Carryover ag values between LO ari d LU Use alternate calibration report format d Display Quan flags and legend d 136 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 38 Report options parameters Sheet 1 of 2 Parameter Quan Limits Flags Report concentration Decimal places to be reported Show chromatogram on Quantitation Report Display valid compounds only User Interface Options Shade row when sample is outside of evaluation criteria Separate ion overlay display Use alternate calibration report format Display Quan flags and legend Quan Flag Options Flag values below LOD
91. 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 Min RF 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 050 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 000 0 050 0 000 0 000 0 000 0 000 0 000 0 000 Page number Max amt diff 96 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 20 000 Page 15 of 36 Thermo Scientific A Reports sample Standard Reports Method Report Method name EC25B 8level 322010 a EPAMethod8270B 8level Page number Page 18 of 36 Master method name EPAMethod8270B 8level Current calibration file EC25B 8level 322010 a calx Assay type Robustness lon range calc method Level 4 Inj vol 1 000 Instrument method TargetsSplit Tune Breakdown method DFTPPSpli
92. 8 30 00 6 98 30 00 7 05 30 00 7 08 30 00 7 13 30 00 7 14 30 00 7 19 30 00 7 23 30 00 7 51 30 00 7 51 30 00 7 54 30 00 7 68 30 00 7 76 30 00 View Width 1 00 1 00 0 75 1 00 0 75 0 75 0 75 0 75 0 75 0 75 0 30 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 30 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 0 75 Page number Use as reference No No No No No No No No No No No No No No No Yes No No No No No No No No No No No No No No No No No No No No No No Yes No No No No No No No No No No Page 1 of 36 Reference compound 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE D4 IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4 DICHLOROBENZENE DA IS 1 4
93. 9 e o omm Pec Kisakikalasa d8 Compound flags Compound Flags Compounds Ta 2 Fluorobiphernyl ia Acenaphthene d1 0 E Chrysene d12 H Hexachlorobenzene When are flags displayed The ToxLab Forms application displays compound flags for any of the following conditions When a compound has violated or is activated by any of the values set in the method See Editing the QAQC Page on page 119 For compounds that are not found in Calibrator QC and Surrogate sample types For compounds that are outside the specified ion ratio range For compounds that are not found These criteria do not apply to Negative sample types when the compound is an internal standard 206 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Data Review What do the flag colors mean The ToxLab Forms application defines the colors of the compound flags as follows Red flags for compounds that have ion ratio failures method validation failures or have values above the ULOL or carryover limits Orange flags for compounds that are below the LOQ below the LOD or between the LOD and LOQ values specified in the method Green flags for compounds that are over the LOR amount specified in the method Yellow flags for compounds that are not found in Unknown sample types No flag for compounds that have no errors or where there were no report options selected Follow these pro
94. A Reports sample Standard Reports Confirmation Report Lab name Thermo Fisher Laboratory Instrument Thermo Scientific Instrument User AMER jamie humphries Batch Drug_A Injected Conc 5 581 ng mL Retention time 1 95 Area 227568 Height 226730 Calibration curve Drm 6 w 5 47 dmn 3 024e 2 RWS 1 0000 Origin ia 8 a NH amp mm Oc 4 amp MS Data cal 1 Drug A 1 95 31140 Relative Intensity MS METHOD 31140 Relative Intensity Confirmation Report Drug A Drug A Page 1 of 1 Relative Intercity 1 85 RTimin Qual lon 1 473 20 Ratio 27 53 Range 22 33 33 49 194 18 15 19 201 2m 1 80 1 85 2 00 RTimin Qual lon 2 488 20 Ratio 14 09 Range 11 43 17 14 g m E a a E m T IE Relative Intensity 1 85 RTimin RT 1 85 cal 1 Relates Intensity 1 60 1 65 2 0 RTimin Flag legend LOD lt J lt LOQ I lon ratio failure C Carryover Linearity limit D Detection limit Q Quan limit POS Cutoff n Negative b Solvent blank H Hydrolysis 272 ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports Confirmation Report 2 Confirmation Report 2 Page 1 of 1 Lab name Thermo Fisher Laboratory Instrument Thermo Scientific Instrument User AMER jamie humphries Batch Drug_A Method X Drug A Drug A Drug A Cali file Drug A calx Compound Name Druq A Iniected Conc 5 581 na
95. Active check box for each compound that you want to identify in the samples When you are finished with the Calibration and Compound Selection page click Next The Finish page opens See Submitting the Batch on page 192 Figure 47 Calibration and Compound Selection Page Batch Wizard BE uM Method2D0b 12212003 b r Com pau nd Grow p al Juan Group Thermo Scientific Create New Extend Calibrations r Included Compounds ax 588 im Compound Achye Peaktad 90 c SAM ms Pest sheeSA mz E taeraren T me Do s 0 BE ToxLab Forms 3 1 User Guide 195 5 Using the Production Mode Working in Batch View Table 47 Calibration and Compound Selection parameters Parameter Description Calibration File Name of the current batch in the form MasterMethod Name MMDDYYYY _ Create New Saves calibration data from all calibration files to the current calibration file Available only after you use Extend Calibrations to append calibration data from another calibration file Extend Calibrations Adds calibration data from the current batch to the selected calibration file Compound Groups Displays all available groups defined in the Groups page of the Master Method View See Editing the Groups Page on page 128 Included Compounds Displays all available compounds that you can identify in the samples Compounds marked as Active are identified in the batch samples Back Returns you to the Batc
96. C Check Standard Compound N Nitrosodimethylamine Pyridine RCRA 2 Picoline N Nitrosomethylethylamine APP9 Methyl methanesulfonate 2 fluorophenol sur N Nitrosodiethylamine APP9 Ethyl methanesulfonate phenol d5 sur Phenol CCC Aniline Bis 2 chloroethyl ether Pentachloroethane 2 chlorophenol 1 3 Dichlorobenzene 1 4 Dichlorobenzene CCC Benzyl_alcohol 1 2 Dichlorobenzene 2 methylphenol Bis 2 chloroisopropyl ether N Nitrosopyrrolidine APP9 3 Methylphenol amp 4 methylphenol Acetophenone N Nitroso di N propylamine SPCC o toluidine APP9 Hexachloroethane nitrobenzene d5 sur Nitrobenzene N Nitrosopiperidine Isophorone 2 Nitrophenol CCC 2 4 Dimethylphenol Bis 2 chloroethoxy methane 2 4 Dichlorophenol CCC 1 2 4 Trichlorobenzene Naphthalene p Chloroaniline 2 6 Dichlorophenol Hexachloropropene APP9 Hexachlorobutadiene CCC N Nitroso di N butylamine 4 Chloro 3 methylphenol CCC Safrole APP9 2 Methylnaphthalene Hexachlorocyclopentadiene SPCC 1 2 4 5 Tetrachlorobenzene 2 4 5 Trichlorophenol 2 4 6 Trichlorophenol CCC 2 fluorobiphenyl sur Isosafrole APP9 2 Chloronaphthalene EC25B 8level 322010 a EPAMethod8270B 8level EPAMethod8270B 8level EC25B 8level 322010 a calx Robustness 1 000 TargetsSplit DFTPPSplit 292 ToxLab Forms 3 1 User Guide lon range calc method Method Report Level Max RF diff 96 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00
97. Calibration for this compound was below the specified minimum correlation coefficient r Back calculation of the calibration points for this compound exceeded the specified maximum percent difference Max 96D Calibration point for this compound was excluded from the overall calibration by manual selection X ISNF Calibration point for this compound was excluded from the overall calibration because its associated internal standard was not found A QAQC failure is identified by an asterisk a shaded row or the word Fail 254 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific A Reports Report Flags Values on a report that are the result of a manual integration will use an uppercase M to signify a manually integrated quantification ion and a lowercase m to signify a manually integrated qualifying confirming ion On alternative reports manual integration are signified by a black box around the value ToxLab Forms 3 1 User Guide 255 A Reports Sample Standard Reports Sample Standard Reports This section shows samples of the following standard report types Batch Report Batch Summary Report Calibration Curve Report Calibration Report Chromatogram Report Compound Calibration Report Compound Calibration Report Alternate Confirmation Report Confirmation Report 2 High Density Calibration Report High Density Internal Standard Report High Density Internal Standard Repor
98. Click Number of Scans to Subtract and use the spin box to select a number or type a number in the box After averaging this is the number of scans that the ToxLab Forms application subtracts from the background If you specified to subtract scans from both sides of the peak the application subtracts this number of scans from EACH side of the peak 3 Click Stepoff Value and use the spin box to select a number or type a number in the box This offset value lets the ToxLab Forms application average and subtract scans that are not adjacent to the apex of the peak For example 74 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Background subtraction range option Delor peak Humber of scans to subtract Stepoff value If you have specified to subtract 3 scans before the peak and the Stepoff value is 5 the ToxLab Forms application ignores the first 5 scans to the left of the peak and applies the averaging and subtraction to the 6th 7th and 8th scans to the left of the peak ToxLab Forms 3 1 User Guide 15 4 Using the Method Development Mode Working with Master Methods To specify a chromatogram reference sample 1 Click Set Chromatogram Reference Sample and select External from the list 2 Click Select File The Open Chromatograph Reference Sample dialog box opens Open Chromatograph Reference Sample E BN Project cal std 5 l Subpr
99. Concentration 0 500 p Chloroaniline Concentration 0 500 2 6 Dichlorophenol Concentration 0 500 Hexachloropropene APP9 Concentration 0 500 Hexachlorobutadiene CCC Concentration 0 500 N Nitroso di N butylamine Concentration 0 500 4 Chloro 3 methylphenol CCC Concentration 0 500 Safrole APP9 Concentration 0 500 2 Methylnaphthalene Concentration 0 500 Hexachlorocyclopentadiene SPCC Concentration 0 500 1 2 4 5 Tetrachlorobenzene Concentration 0 500 2 4 5 Trichlorophenol Concentration 0 500 2 4 6 Trichlorophenol CCC Concentration 0 500 2 fluorobiphenyl sur Concentration 60 000 Isosafrole APP9 Concentration 0 500 2 Chloronaphthalene Concentration 0 500 2 Nitroaniline Concentration 0 500 1 4 Naphthoquinone APP9 Concentration 0 500 Dimethyl phthalate Concentration 0 500 1 3 Dinitrobenzene app9 Concentration 0 500 Thermo Scientific ToxLab Forms 3 1 User Guide 293 A Reports sample Standard Reports 294 Method name Master method name Current calibration file Assay type Inj vol Instrument method Tune Breakdown method QAQC ISTD Compound 1 4 DICHLOROBENZENE DA IS NAPHTHALENE D8 IS ACENAPHTHENE D10 IS PHENANTHRENE D10 CHRYSENE D412 IS PERYLENE D42 IS Method Report EC25B 8level 322010 a EPAMethod8270B 8level EPAMethod8270B 8level EC25B 8level 322010 a calx Robustness lon range calc method 1 000 TargetsSplit DFTPPSplit Min recovery 96 50 00 50 00 50 00 50 00 50 00 50 00 ToxLab For
100. Create method 50 Create PDF Batch Template Editor 183 standard reports 133 Create XLS 133 Create XML 183 Batch Template Editor 183 standard reports 133 Curve type Calibration 113 Method Template Editor 145 CV Test 125 dashboard 14 Decimal places to be reported 137 Delete condition 314 Detection method Genesis 99 ICIS 103 Detector Detection 96 Display Mass Precision 41 Display Quan flags and legend 137 Display valid compounds only 137 Displayed Reports custom 47 Displayed Reports standard 44 Edit user 24 Email Address 23 Enable peak threshold 145 Enable tune time tracking 138 Enable valley detection 99 Enabled 23 Energy Ramp Acquisition List 82 Compound datastore 36 Example 132 Exclude matching quan peaks 147 Expected RT Detection 95 Expected width 99 Export SRM data 51 Extend Calibrations 196 Filter Detection 96 320 ToxLab Forms 3 1 User Guide Flag values above Carryover 137 Flag values above LOR 137 Flag values above ULOL 137 Flag values below LOD 137 Flag values below LOQ 137 Flag values between LOD and LOQ 137 Full name 23 Import custom 48 Import standard 45 Import Xcalibur Processing Method 62 Include compound peak spectrum as reference spectrum 145 Include confirming ions 145 Injection amount 60 Injection concentration 237 Injection Units 237 Injection volume 78 Installed Reports custom 47 Installed Reports standard 44 Instrument method General page 78 Method Forge 60 Instrument Name 41
101. Development Batch task pane By default the ToxLab Forms application writes the temporary files raw data files and sld method file to the following folder Thermo ToxLab Forms Temp 2 In the browser do one of the following e Locate the folder you want to use for the development batch files and click OK Or Do the following a Locate and select the folder where you want to create a new folder for the batch files b Click Make New Folder The ToxLab Forms application creates a new folder in the selected folder c Right click the New Folder filename and choose Rename from the shortcut menu d Type the name for the folder e Click OK The ToxLab Forms application creates all development batch files in the specified folder To add samples to the development batch Do one of the following Right click and choose Add Sample from the shortcut menu QOQr Use the spin box to select the number of rows and click the Add Sample icon to add multiple sample rows New empty samples appear at the end of the sample list 154 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Development Batches To insert samples into the development batch 1 Select the sample above which you want to insert empty samples 2 Do one of the following Right click and choose Insert Sample from the shortcut menu _Or Use the spin box to select the number of rows and click t
102. Eo Xx xnJq 9 NED xDBnup xBnip x xniq pouje N xBnup x6nip eureN punoduioo ojeuJeyv yod y uonesqeg Punodwoyg 00007 80 xBnup 00007 40 xBnup 00001 90 xDnup 0009 co xDnup 0057 yo xDnup 00 0L co xDnup 00 OL zo xBnup 00 0L LO xBnup junouy pis OWEN l d4 x xniq eiuer jueuunJjsu Jeusi ouuJeu AloyeJoge7 Jousi JouuJ9U pejeJ469ju Ajenueyy 9 e2 G eo r eo e g eo jeo 1ed Jeo Jo 9 eV les onespen yoyeg Jes JUNI SU OWEN qe 269 ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports V N V N V N seld ASH Jo z eDeq 00 0021 00 096 000227 o buey XxeyN 00 008 00 079 00087 abuey ui juu 6d ju 6d ju 6d spun junowy y pasenbs Y Y 10 28J suodS 4 GSY A s8e J uoneiqileo 99 816 v9c 0c L6EFrEOL 00 001 08019602 8 188 l L CS8626 00 00L LECOGELL t 06S GV Cl 689786 00 001 98915021 wy 9 eO oneJesuodsoM E IV SI junowy SI Peay pis e N ogey een vt w Bey ZyX b M 910u5 uiBuQO 09460 p 9v09 4 XC 9 80 Z cyX8 9648 8 A x nup xDBnup X Eo X xni 9 i4 NED xDBnup xBnuip x xniq POY N ojeuJejv uode uoneuqi je punoduioo uteN punoduioo 000001 LL7x6nup 00 008 O01 xBnup 00 009 60 xBnup junowy p S OWEN l x xq s wer jueuungjsu Jeusi JouJJ9u Asoyesoqge 7 J8usi JouuJ9U peje469ju Aj enue N
103. Figure 18 Detect page for High ICIS Quan peak Confirming peak 1 465 30 gt 419 76 a 485 30 420 38 093 D 23 ao w 80 0 54 70 60 3 50 40 30 20 10 0 2 0 4 0 6 0 2 0 4 0 6 RT min J RTimin Times Signal Detect j Signal Detect Ratios Sensitivity un Iris F Sees High ICIS Detection method Detection method Smoothing Relative Intensity b m to Relative Intensity Ra m Smoothing Area noise factor Area noise Factor Peak noise factor L L es S ae wn A r ae wr sha P eg E na ze ta chor rear hare ae Baseline window Baseline window I DES I ao Constrain peak width E Constrain peak width Peak height z 5 0 SE Peak height 3 S T ailing Factor 2 DU S Talling Factor 2 00 Min peak height 5 M 3 0 Min peak height 5 M 3 0 f Note method Inicas Noise method Incos Min peak width 3 Min peak width Multiplet resolution 10 E Multiplet resolution Area tail extension 5B Area tail extension Area scan window WORMS RMS Area scan window 102 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 21 Detect parameters for High ICIS Sheet 1 of 3 Parameter Sensitivity Detection method Smoothing Area noise factor Peak noise factor Baseline window Constrain peak width Thermo Scientific Descr
104. Framework 3 5 SP 1 Thermo Foundation 1 0 1 available on the Xcalibur 2 1 0 CD Xcalibur 2 1 and Xcalibur 2 1 QF There are several ways to contact Thermo Fisher Scientific for the information you need To contact Technical Support Phone Fax E mail 800 532 4752 561 688 8736 us techsupport analyze thermofisher com Knowledge base www thermokb com Find software updates and utilities to download at mssupport thermo com To contact Customer Service for ordering information Phone Fax E mail Web site 800 532 4752 561 688 8731 us customer support analyze thermofisher com www thermo com ms ToxLab Forms 3 1 User Guide vii Preface To copy manuals from the Internet Go to mssupport thermo com and click Customer Manuals in the left margin of the window To suggest changes to documentation or to Help Fill out a reader survey online at http www surveymonkey com s aspx sm R7gKOvhLXn3NTkpK2BefHQ 3d 3d e Send an e mail message to the Technical Publications Editor at techpubs lcms thermofisher com Vill ToxLab Forms 3 1 User Guide Thermo Scientific MEN E Introduction This chapter describes the general features of ToxLab Forms 3 1 quantitative software Contents About the ToxLab Forms Application ToxLab Forms Feature Summary Reporting Features Ahout the ToxLab Forms Application The ToxLab Forms application is next in the series of Thermo Scientific GC MS analytical
105. Groups i Reports Acquisition List Identification Detection Calibration Calibration levels QC levels F RT Compound grim Oe OCS 6 05 0800 s ope 3 4259859 975375373 www Table 26 QC levels parameters Parameter Description RT Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Compound The compound name QCI QCz User defined quality control levels for the compound QC levels Level User defined quality control level names Test A value for the acceptable difference as a percentage between the known amount and calculated measured amount of each QC level Shortcut menu Copy down Copies the selected column value to all rows in that column For detailed instructions about using the Copy Down command see Appendix B Using Copy Down and Fill Down Display retention time Displays or hides the RT column in the compound list column Delete compound from Removes the selected compound from the current master method method 118 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Editing the QAQC Page General Thermo Scientific Use the QAQC page to set limits and ranges so the ToxLab Forms application can review the data and results as an aid to final approval From the QAQC page of the Master Method View you can access these additional pag
106. H Report Name Print To specify the type of report output to create for each report type select the check box in the appropriate column To duplicate the output type for all reports right click the cell and choose Copy Down from the shortcut menu All check boxes in the column below the selected cell duplicate the selected or cleared state in the selected cell ToxLab Forms 3 1 User Guide 131 4 Using the Method Development Mode Working with Master Methods Figure 32 Standard Reports page Print Create Create mn PDF SML EE m L cu mq Report Title 1 Bannen thet D D Do o Hu B 4 Calibration Repot Calibration Report 7 Comma Tcorimainnemm GB CortmaionRepen 2 conten Rept 12 Hin Dersi Sane evot HehDeniSamdeRpot iiie High Density Sample Report 2 15 High Density Sample Report 2 Long 16 High Density Sample Report 3 dee High Density 5 ample Report 3 Long UL Internal Standard Summary Report RE lan Ratio Failure Report 20 Manual Integration Report BS Jualitative Peak Report 24 UJualtatyve Summary Report 25 Quality Control Report BB Quantitation Report 27 Quantitation Report 2 30 Solvent Blank Report Table 36 Standard Reports parameters Sheet 1 of 2 Parameter Description Example Displays a sample of the report type Report Name The name of a report 132 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo
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108. I MF Library entry 222 ToxLab Forms 3 1 User Guide Thermo Scientific Table 53 Peaks pane parameters Command Filter Peak RT min SI RSI MP Library entry Remove selected peak Chromatogram Navigation Pane Thermo Scientific 5 Using the Production Mode Working in Data Review Description Filter used to identify the peaks Specified in the raw data file or the master method Peak retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Search index method used to search the NIST library Reverse search index method used to search the NIST library Match probability Library compound that matches the identified peak Shortcut menu command that removes the selected peak from the peaks list The chromatogram navigation pane displays all peaks in the selected sample The peak selected in the Peaks pane is indicated with a red marker Follow these procedures To zoom in on a peak To manually add a peak 4 To zoom in on a peak 1 In the chromatogram navigation pane drag the cursor to delineate a rectangle around the peak The delineated area expands to fill the view to help you examine the peak limits for enhanced review and confirmation 2 To restore the default view right click the chromatogram navigation pane and choose Reset Scaling from the shortcut menu To manually add a peak 1 Zoom in
109. IeWo ebene 163 Creatine a New Dates ite gene ER EX ra Pd ee fakes es 4 163 Patine a Batch unse Eie sete Ee a ees ead mar Ode d ed 168 bobo DA deren des Arnis ant uie a ae rS Dalee t edite 174 Observing the Real time Display 175 Usine a batch Templie ac ohn a ma uqa hu passt r tops 178 Creating a Batch Using the Batch Wizard 184 Specityine Sample Types rs eec idet a3 tes d iub atten dolet und is 197 Working qn Data Reviews quce eee xot ERE Qd EE x 198 Data Review lines wer ite tuer sat Rice 198 Oan Mode nee ae SUMMERS Bee Area pe demerit 205 ual NO ss dio utbs ea malen apu dade du 220 Wothke In ReDOBE Views Em d neben PR Uter pe bes 230 Displaying the Report View Page 230 Displaying the Active View Page uu Senatus era loda tox ate 234 Working in the Local Method View 248 RGDONS ai nee 251 Speeilyins Reporisru unse Pad E teed as heat he teed bageee cant 251 Standard REPO oan i i et br EI petendo giao a Snap abdo Wee axe 252 Custom Reports ars ts audita Ute ce m Cox ut Ex aio m ace Gesa 253 Report ags voe oran e ene pam uya uy QO iy dur cs 254 Sample Standard REPOS i t yaa u a Ret pce iH p Uc a 256 Barh leDOLbssu soe sioe ood Ld peter dr SAM UE 257 Batch Summary Reports ee Hide 258 Calibration Cure Report ner nee acte Spa ber Sau Db EEUU 261 Calibrqton ReDOPL qd ea lt u Karren Oe eu eost d 262 Chromatogram Repor
110. Index N background scans 101 Test 118 Account Number 23 Acquire a new raw data file 60 Active Identification 84 Add a condition 314 Add user 24 Amount 113 And conditions 314 Area noise factor 103 Area scan window 105 Area tail extension 105 Assay type Batch Wizard 186 General page 77 Associate a Raw Data File 65 Automatically create the master method 60 Available Methods 186 Available Templates 186 Background subtraction range option 78 Baseline window 103 Batch Level Report 46 Best match method 145 call caln 115 Calibration method 145 Cancel changes 24 Carryover limit 120 CAS No 84 Category Acquisition List 81 Compound datastore 35 Chemical Formula Acquisition List 81 Compound datastore 35 Chromatogram Intensity Scale 41 Collision Energy precursor Acquisition List 82 Compound datastore 36 Compound Calibration 113 Calibration levels 115 Calibration page 121 Hydrolysis page 127 Identification 83 ISTD page 124 Limits page 119 Matrix Blank page 123 QC Check page 122 QC levels 118 Solvent Blank page 126 Compound Datastore selection 41 Compound Name Acquisition List 81 ToxLab Forms 3 1 User Guide 319 Index P Compound datastore 35 Compound type Calibration 113 Identification 84 Confirming n Ion Ratio 237 Confirming n Ion Ratio Flag 237 Confirming n Manual Flag 237 Confirming n Mass 237 Confirming n Range 237 Confirming n Response 237 Constrain peak width Genesis 99 ICIS 103 Correct surrogates 138
111. Int Std Quanm z 380 202 Drug A Qual m z 473 20 Ar Ra Rar 62641 194 27 53 96 e 22 33 96 te ive Rela w o Qual m z 488 20 Relative Intensity Relative Intensity 1 90 1 95 2 00 RTimin 1 95 cal_1 100 80 70 60 50 40 30 20 10 1 90 1 85 2 00 RTimin Flag legend LOD lt J lt LOQ I lon ratio failure C Carryover Linearity limit D Detection limit Q Quan limit POS Cutoff n Negative b Solvent blank H Hydrolysis Thermo Scientific ToxLab Forms 3 1 User Guide 281 A Reports Sample Standard Reports High Density Sample Report 3 Long High Density Sample Report 3 Long Page 1 of 1 Lab name Thermo Fisher Laboratory Instrument Thermo Scientific Instrument User AMER jamie humphries Batch Drug_A Method Drug_A_Drug_A Drug_A Cali File Drug_A calx Relative intensity Relative intensity Int_Std Qual m z 479 20 Quan m z 380 20 Area 134976 Total Area 678044 Ratio 19 91 Peak Area 678044 Range 15 69 23 54 RT 1 93min 1 94 Amount 15 000 ng mL RTimin Drug_A Qual m z 473 20 Qual m z 488 20 Quan m z 371 20 Area 62641 Area 32066 Total Area 227568 Ratio 27 53 96 Ratio 14 09 96 Peak Area 227568 Range 22 33 96 33 49 96 Range 11 43 96 17 14 96 RT 1 95min 1 95 Amount 5 581 ng mL TAmount 6 000 ng mL Flag legend LOD lt J lt LOQ l lon ratio failure C Carryover Linearity limit D Detection
112. Lab Forms 3 1 User Guide 311 _ Bj Using Filter Criteria The filter criteria tool is available from the compound datastore in the Configuration mode and the acquisition list in the Method Development mode To filter the compound list 1 To display only a filtered list of compounds click the funnel icon NO in the column header For each column a list of filterable criteria is displayed On all columns your filter choice are All Blanks and NonBlanks Other filter criteria is specific to the individual columns 2 To create a custom filter based on compound values in a specific column choose Custom from the column list box The Enter Filter Criteria dialog box opens See Enter Filter Criteria on page 314 3 From the Operator list box select an operator 4 From the Operand list box select an operand 5 When all conditions are defined click OK The complete filter string is displayed at the bottom of the dialog box For example chemical formula Blanks Thermo Scientific ToxLab Forms 3 1 User Guide 313 C Using Filter Criteria Enter Filter Criteria Enter Filter Criteria The Enter Filter Criteria dialog box is specifically named for the column on which you are filtering In this example the selected column is the Compound Name column Figure 54 Enter Filter Criteria dialog box Enter filter criteria for Compound Name Operator Cancel Table 77 Enter Filter Criteria parameters Paramete
113. Lu ah t ll n AL u SER um 2 4 5 6 7 10 11 12 13 14 15 16 17 ES RT 12 52 228 00 Age 270400783 15 gt AH 121437116 78 114 00 m SN 34113 IH ps A SEDE cee g 100 100 150 200 E r an 240 13 1055 25187 35503 429 14 12 4 12 6 100 200 300 a RT min m z m M Chromatogram Qual peak pane opectra pane Ranking pane navigation pane Tip To resize the panes drag the separators that divide the panes In addition to the Samples List the Qual Mode view displays data in the following panes e Peaks Pane Chromatogram Navigation Pane Qual Peak Pane Spectra Pane reference and selected Ranking Pane 220 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Data Review Peaks Pane The Peaks pane works with the Samples list to display graphical values for a unique sample and peak combination To display peaks for a specific compound 1 From the Samples list select a sample Note When you choose a calibration sample the ToxLab Forms application returns you to Quan Mode The Peaks pane is not displayed in Quan Mode The Peaks pane lists the retention time for peaks identified in the selected sample the values for the best match methods for each peak and the compound match The number of peaks that are listed is specified in the method You can change the number of identified peaks in the Method Template Editor See Identify the peaks
114. Method Development Mode Type a vial position in the Vial Position column for the new sample Type a volume in the Injection Volume column for the new sample The minimum injection volume value allowed is 0 05 uL To re inject a sample from a previously acquired batch From the Samples list select the sample you want to re inject Right click and choose Reinject this Sample from the shortcut menu The ToxLab Forms application creates a copy of the selected sample and appends INJ001 to the file name Additional re injections of the same sample are numbered INJ002 INJ003 and so forth The ToxLab Forms application copies all parameter values from the original sample Previously acquired samples are indicated with a green status indicator acquired and processed and are grayed out Samples created for re injection are indicated with a blue status indicator not acquired Q ca sd 50 INJDOI Cal Std 10 Q ca sd 50 INJDO2 Cal Std 10 Cal Std 10 To save this batch with the new samples for re injection choose File gt Save gt Batch from the main menu ToxLab Forms 3 1 User Guide 171 5 Using the Production Mode Working in Batch View Lo urnam Methadzl4z v SENE Filename sample type sample Figure 38 Batch View page eines Thermo Scientific Instrument Sample Vial Injection name position volume i Dilution ail Comment level Sample ID Table 41 Batch View parame
115. ON uode uoneJqije punoduioo A9 Z e e 1949 9197 je9 w Bu 97 29 Z leo Tuu Bu s z Je e2 quu Bu 9 Jeo Ssweugllg di eidures SOd EIA v Bnuq yoyeg seuuduinu aiwel yanv 1osN jueuunugjsu OYNUSIOS oway 3ueuinujsu Asoyesoqge7 JOysi4 ouu u weu qe Thermo Scientific ToxLab Forms 3 1 User Guide 268 A Reports sample Standard Reports Compound Calibration Report Alternate V N V N V N V N V N V 09 98 V 09 98 V 09 98 sejd ASH Jo oDeg 00087 00 0vc 00021 00 09 00 0 00 L 00 L 00 L obuey xe 00 0c 00 091 00 08 00 0r 00 02 00 8 00 8 00 8 oBue ui juu Bd Iuu Bd Juu Bd Juu Bd Juu Bd Juu Bd juu Bd juu Bd spun junowy V pasenbs y H Joe asuodsay 4 GSY A sBe 4 uoneiqileo L8 88e L9 S6L L0 26 es IG LLOC tO L J N OL L Quy JIED 0 8 00 t 9r6 L 666 0 89v 0 9610 J N Z640 01 e1 osuodsay L6S9E0L 9V0E001 CCVCS6 c80Lv6 68Sr6 9878 6 200096 LVEC86 ealy SI 00 001 00 001 00 001 00 001 00 001 00 001 00001 00001 JUNOWY S GL11ZE8 21205107 8v0 S8l 98 076 96 cVvv 8L7 8l J N 8v 6l E9JV PIS ce ex gt 2 9 A 2 k w amp amp iV ZyX L M 81ouB UGUO 0S16 0 ZvM Z 8r09 4 XZ 9 80Z ZvX8 96 8 S A X
116. OO Go 0098 0960 gp tient OL EE S S S S 6Q s S sss ss 070 Wu OOP vesielie OO 8621 OQOpPeuequdeuov gh MEME S S S S S S S LL uL l LLL vlvlTVjOTTT 070 qiu ogor Cic OO 968 peugeot 6 nca 070 Wu OO z8ecfOS O09 Sr vpevezeqoopikL sBe J uiu eg I spun 2U09 esuodsey uo o 18 ewen Punodwog N SPIBPUR S Ieuu ul I xsrz e e eJequiodes q uo9 egvs uo1egunej qulnej cvs o8 oidvisuuiojJ qe xo OWISU I VO 4 SYNSOY JuenO xjes uodey uojeg e esuodsey 0001 Jidninw jueuinujsu OYNUSIOS ouu u sul E c EIN jeusi4ouueu L aSAY LOA ogesedo ec U9WWOI Joenus poujey boy eyeq lduies Wd LO SS Z 0L0Z 2 2 eyepdp jse 1 WY 9 2 6 800Z ZZ Z uO boy weu Aessy enr 1 zieng Ol ejyeq soy je uodey uojeg poul N ueno aw L JuenO soy Jeo sureJeg Beyu SW a 303 ToxLab Forms 3 1 User Guide ientific Thermo Sc sample Standard Reports A Reports SISAJOIP H H 4 peje4Be1jui Ajjenueyy yuelq JUsAjOS q eAneBeN u HOINI SOd Aui UENH H luu uo 599 q d Pwu AueeurTz eA0 Je2 2 nje oles uo DOT 001 pueB8e Be J se eo Nd81 99 72 OLOC Z Z ZL JO z obed Limaj em of um ABURU TEES OLS ga BC DD oe Cho Bit LE 0007 000 00 80L Ss 00 001 00 9 L J ddn JOMO one uoj ag Sed iod Zea Ue low Cx S OSEL zum ELIE
117. Peak Labels Choose to display labels for the peak retention time peak height peak area or signal to noise The label types in the list are selected for displayed labels and cleared for labels that are not displayed To remove a label select the label type again and clear it Label settings are globally applied to quan peaks confirming peaks and internal standard peaks Note The labels do not always update on all peak displays To update all labels select a different compound and then reselect the compound whose labels you changed To modify the peak detection settings Right click the chromatogram view and choose Peak Detection Settings from the shortcut menu The Peak Detection Setting dialog box opens This dialog box contains the detection settings defined in the method Thermo Scientific Thermo Scientific 5 Using the Production Mode Working in Data Review Peak detection settings progesterone E QuanPeakl Quan peak 315 30 gt 109 00 279 10 297 0 Em m E 7 E m ir 3 0 RT min Times Signal Expected AT min EET Wir d ON I 30 LIC 31 View width min 1 00 4 Appl toALL J Cancel 2 Edit any of the detection settings For a detailed description of all detection settings see Detection on page 84 3 To save your changes to this compound in all samples in this batch click Apply to All Table 50 Quantification Peak shortcut me
118. SUMENTATION SURVEY 2010 Thermo Fisher Scientific Inc All rights reserved LCquan and TSQ Vantage are trademarks and Xcalibur and TSQ Quantum are registered trademarks of Thermo Fisher Scientific Inc in the United States Windows Excel and Windows Vista are registered trademarks of Microsoft Corporation in the United States and other countries Acrobat Flash and Acrobat Reader are registered trademarks of Adobe Systems Inc in the United States and other countries All other trademarks are the property of Thermo Fisher Scientific Inc and its subsidiaries Thermo Fisher Scientific Inc provides this document to its customers with a product purchase to use in the product operation This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited except with the written authorization of Thermo Fisher Scientific Inc The contents of this document are subject to change without notice All technical information in this document is for reference purposes only System configurations and specifications in this document supersede all previous information received by the purchaser Thermo Fisher Scientific Inc makes no representations that this document is complete accurate or error free and assumes no responsibility and will not be liable for any errors omissions damage or loss that might result from any use of this document even if the information in the document is follow
119. Sample File cal_1 cal_2 cal_3 negative hydrolysis qc 40 specimen 1 specimen 2 specimen 3 specimen 4 qc 125 Calibration Flags Quan Flags ToxLab Forms 3 1 User Guide Batch Name Method Cali File Operator Instrument ID 6 17 2010 8 41 37AM Instrument Tune Report not available not available not available not available not available not available not available not available not available not available not available A Amount C Carry Over Linearity Limit D Detection Limit Q Quan Limit H Hydrolysis A IS Area Range R IS RT Range lon Ratio Failure n Negative b Solvent M Quan ion manually integrated m Qualifier ion manually Batch Summary Report Drug_A_ISTD_Test001 Drug_A_ISTD_Test001_Drug_A_IMPORTED_ISTD Drug_A_IMPORTED_ISTD Drug_A_ISTD_Test001 calx b ThermoFisher Instrument Instrument Tune Date time Legends of Abbreviations Page 3 of 3 Thermo Scientific Calibration Curve Report Calibration flags D RSD F Response factor RZR 2 A Amount X Excluded X ISNF Excluded because ISTD wasn t found Batch Name Method Cali File Cali File Date Operator Instrument ID Calibration Curve Report Drug A Drug A Drug A Drug A Drug A calx 3 11 2010 8 58 27 AM AMER jamie humphries Thermo Scientific Instrument Calibration passed Compound Drug_A Cal Lev el File Name level 1 cal_1 level 2 cal_2 level 3 cal_3 A Reports sample Standard
120. Scientific 4 Using the Method Development Mode Working with Master Methods Table 36 Standard Reports parameters Sheet 2 of 2 Parameter Description Report Title The user defined title to be used on a report Print Reports to be sent to the printer Create PDF Reports to be saved as PDF files Create XML Reports to be exported in XML format Figure 33 Custom Reports page Report Mame Altlalbratonheport BatchReport BlankAeport CalibrationD ensityA eport CalibrationA epart Check StandandA eport Compound CalibrationA eport Confirmation eport ContirmationA epar OCCReport HighDensity 5 ampleR epartl Long HighDensityS ampleFiepartzLong Hight ensityS ampleH eport3Long HighD ensityS ampleFi epart4 Hight ensityS ampleH eportb LuantitationA eport Table 37 Custom Reports parameters Parameter Description Report Name The name of a report Print Reports to be sent to the printer Create XLS Reports to be exported in Excel spreadsheet xlsm format ToxLab Forms 3 1 User Guide 133 4 Using the Method Development Mode Working with Master Methods Specifying Report Flag Options Use the report options to choose parameters for flagging values and displaying information in standard report types Follow these procedures To specify quantitation limits To specify user interface options To specify quantitation flag options To correct surrogates To track the use of the tune file To speci
121. Table 21 Detect parameters for High ICIS Sheet 2 of 3 Parameter Peak height 96 Tailing factor Min peak height S N Noise method Min peak width Multiplet resolution ToxLab Forms 3 1 User Guide Description A signal must be above the baseline percentage of the total peak height 10096 before integration is turned on or off This text box is active only when the Constrain Peak Width check box is selected Range 0 0 to 100 096 A factor that controls how the ToxLab Forms application integrates the tail of a peak This factor is the maximum ratio of the trailing edge to the leading side of a constrained peak This text box is active only when the Constrain the Peak Width check box is selected Range 0 5 through 9 0 For the valley detection approximation method to use the Nearest RT Peak Identification criteria this peak signal to noise value must be equaled or exceeded For component identification purposes the ToxLab Forms application ignores all chromatogram peaks that have signal to noise values that are less than the S N Threshold value Range 0 0 all peaks through 999 0 The options are INCOS or Repetitive INCOS uses a single pass algorithm to determine the noise level The ICIS peak detection algorithm uses this value Repetitive uses a multiple pass algorithm to determine the noise level The ICIS peak detection algorithm uses this value In general this algorithm is more accurate in analyzi
122. Thermo ToxLab Forms Kek Real Time Status Help Log Off po Production To begin 2 Method Development Select a work area Configuration SCIENTIFIC Table 3 ToxLab Forms dashboard parameters Sheet 1 of 2 Parameter Description Real Time Status Opens the real time display for the current acquisition The acquisition progress is displayed within the current mode window Help Opens the ToxLab Forms Help Log Off Logs off the current user and displays the logon screen This function is available only when user security is enabled See Specifying the General Configuration on page 37 Production Opens the Production mode where you can create and review batches batch data reports and local methods See Using the Production Mode on page 161 14 ToxLab Forms 3 1 User Guide Thermo Scientific 2 Getting Started Choosing a Mode Table 3 ToxLab Forms dashboard parameters Sheet 2 of 2 Parameter Description Method Development Opens the Method Development mode where you can create a master method an instrument method or a development batch See Using the Method Development Mode on page 49 Configuration Opens the Configuration mode where you can set permissions assign users to roles configure available reports and import new reports and maintain the various databases including the Compound Datastore See Using the Configuration Mode on page 17 Thermo Scientific ToxLab Forms 3
123. To acquire the batch Right click and choose Submit Batch from the shortcut menu or click the Submit Batch icon ER The ToxLab Forms application creates a raw data file for each sample in the batch and an sld method file The ToxLab Forms application writes the raw data files the sld method file and all temporary working files to the specified folder When the acquisition is complete the application deletes all the temporary working files Only the raw files and a MethodDevelopment sld file remain in the folder If a sample is acquired more than once the subsequent raw data files are time stamped with the acquisition time Thermo Scientific 4 Using the Method Development Mode Working with Development Batches To open the Qual Browser In the Development Batch task pane click Open Qual Browser The Thermo Xcalibur Qual Browser opens BLE File wiew Tools Help gt B Allil CAT hermo TraceFinder M ethadD evelopment sld 3 Hle raw flez raw 3 files raw For detailed instructions about using the Qual Browser refer to the Qual Browser Help Thermo Scientific ToxLab Forms 3 1 User Guide 159 ee I Using the Production Mode This chapter includes instructions for using the features of the Production mode Contents Working in Batch View Working in Data Review Working in Report View Working in the Local Method View From the Production mode you can create and review batches revi
124. When the ToxLab Forms application automatically creates a master method for you it PP y y performs the following functions Reviews your raw data file and identifies compounds that are present in your sample Uses your mass spectral reference libraries to assign compound names and CAS numbers Uses mass spectral information to select potential quantification and confirming ions and a reference mass spectrum for the compound A master method contains a list of compounds and an initial set of information for detecting processing and reporting those compounds Follow these procedures To automatically select compounds to create a new method To manually select compounds to create a method 4 To automatically select compounds to create a new method 1 From the Method View task pane click Create Method Create method amp Open method Export SRM data Recent Files Thermo Scientific ToxLab Forms 3 1 User Guide 53 4 Using the Method Development Mode Working with Master Methods The Create Master Method dialog box opens Create Master Method Method Forge Use Method Forge Performs peak detection against a raw data file i Performs library lookup if requested Import Xcalibur Pracessing Method Import Xcalibur Pr Imports a previously created processing method finding configured compounds and reference spectra Associate Raw Data File Creates a blank master method and associates a Associate a raw dat
125. ZESS dsoy 00 91 uo 164 NV 9 7 6 8007 2217 boy ZI A 9 4 qe S 00 0 LM eyed mx ose UBIS 96 S IM m lt i 000 USIU0I gp euejeujudeN oor Oe tr L 6 Zee yea om oe COS L uec Limi F ar ir eue D m Ausg euge i F EL Mes Bas 00 09 000 98 2 00 84 0092 0051 vl OV 00 SLL 00001 00251 OOL J ddn J AO7 oney uo Le SFL zer Weg MUL St rlees Suec Z98 v0Sl dsesj 00 Z8l uo 361 WY 9 4 6 8002 2212 boy ZI A 9 4 qe 000 LY eye egg UBDS Sv IM cm 00 0t u92u02 pp euezueqoauo u9IQ r EE l YS Huu St rlees c Z pod y uoneyueno Thermo Scientific ToxLab Forms 3 1 User Guide 304 A Reports sample Standard Reports Quality Control Report Quality Control Report Lab name Thermo Fisher Laboratory Page 1 of 1 Instrument Thermo Scientific Instrument Method Drug_A_Drug_A User AMER jamie humphries Drug_A Batch Drug_A Cali File Drug_A calx Compound Curve Type Daily RF Mean RF Min RF RF D MaxRF D QCamt Calc amt Amt D Max Amt 96D Flag Drug A L 0 000 6 000 5 603 6 62 20 00 Pass Internal standard summary Compound Std Response Min Max Sample Response Int Std 655596 327798 50 00 983394 150 00 639922 Std RT Min Max Sample RT Int_Std 1 93 1 68 0 25 2 18 0 25 1 93 Manually integrated Fail Curve Type A Average RF L Linear Q Quadratic R Recovery limits exceeded Thermo Scientific ToxLab Forms 3 1 Us
126. a file raw data file allowing manual peak selection Select Compounds from a compound datastore Creates a blank master method and displays the configured compound datastore allowing compound selection MES ZZ Select compounds from CDS 2 Select Use Method Forge 3 Click OK The Method Forge dialog box opens See Method Forge on page 59 Use the Method Forge to create a master method from an existing raw data file or to create a new raw data file to use for the master method 4 n the Method Forge dialog box do one of the following Select the Use the Default Template option Or Select the Select a Custom Template option and highlight your custom template in the Method template table For detailed instructions on creating a custom method template see Creating a Method Template on page 139 5 Select the Name the Master Method check box and type a name for your master method You can enter an existing method name and overwrite it when you create the method If you do not specify a name the method is named for the raw file used to create the method 6 Select the Automatically Create the Master Method check box 54 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 7 Do one of the following a In the Raw File Selection area choose Use an Existing Raw Data File b Click the browse button and locate a raw data file to use for the me
127. a peak The red box indicates the selected peak Right click and choose Add This Mass as New Quan Peak from the shortcut menu A new quan peak is added to the compound c WuaPeM2 O Quan peak miz176 02 Relative Intensity You can use the shortcut menu on the spectrum pane for this new quan peak to perform any of the tasks you could perform on the original quan peak ToxLab Forms 3 1 User Guide 89 4 Using the Method Development Mode Working with Master Methods 90 To add amass as a new compound 1 In the raw file spectrum pane pause the cursor over a peak 3 ToxLab Forms 3 1 User Guide The red box indicates the selected peak Right click and choose Add This Mass as New Compound from the shortcut menu The ToxLab Forms application performs a library search for the selected compound The application uses the first match it finds as the compound name the base peak of the mass spectrum as the quan peak and the second and third largest ions as the confirming ions If the name of the first match is already in the library the Add New Compound dialog box opens with the matching compound selected Add new compound Mame of new compound Methylene Chloride Methylene Chloride HL 95508 BP 48 89 Relative Intensity amo o ooo ha m 7207 73 00 Library results Methylene Chloride MAIMLIB HL 993 BP 49 00 Relative Intensity 14 00 24 00 31 00 79 00 Pwrazine 1 4 dio
128. a remote location or computer 4 Click Browse and locate your QED library in the C Thermo folder 5 Click OK The Xcalibur application reports that it has added the library to the NIST software 6 Click Dismiss to close the message box The application adds the QED library to the NIST Libraries list in the Library Manager dialog box Thermo Scientific ToxLab Forms 3 1 User Guide 11 2 Getting Started Choosing a Mode Thermo Library Manager Manage libraries Convert Libraries MIST libraries NIST Add GEO NIST Library 7 Click Exit in the Thermo Library Manager dialog box 8 Start the ToxLab Forms application 9 Go to the Method Development mode 10 Click Method View in the navigation pane 11 Choose File gt New gt Method template from the main menu The QED NIST Library is listed in the Use These Libraries list on the Method Template Editor dentity the peaks Use these libraries NIST QED NIST Library Choosing a Mode When user security is enabled the dashboard provides the current user with options applicable to the role assigned to that user The following table shows the available modes for each user role Table 2 User roles and permissions Method User role Development Production Configuration Manager x x x IT Administrator x Supervisor x x Technician x QAQC x Note When user security is not enabled all modes are available to all users 12 ToxLab Forms 3 1 User
129. ab Forms application uses it only for graphical display ToxLab Forms 3 1 User Guide 95 4 Using the Method Development Mode Working with Master Methods Signal Use the Signal page to define the detector and its parameters as you display each chromatogram trace Figure 16 Signal page Quan peak Confirming peak 1 465 30 gt 419 76 465 30 gt 420 39 nr m cn m cn m Relative Intenaity e Relative Intensity u e WM D GQ c oup D Bi te D Q D RT min RT min Times Detector Detector i UEP c SRM ms2 465 30 eidz3 00 s LER c SRM ms2465 30 amp cid23 00 x w mz 413 76 d mz 420 39 Table 19 Signal parameters Sheet 1 of 2 Parameter Description Detector MS Mass spectrometers Analog Supplemental detectors for example FID ECD AD card If you have a detector not under data system control you can capture the analog signal and convert it to digital using an interface box for example SS420X for storage in the raw file Filter Represents a particular data acquisition channel For example the filter option c Full ms 35 00 500 00 represents a positive ion centroid signal acquired in single stage full scan mode from m z 35 to 500 Trace Represents a specific range of the data In conjunction with the filter the ToxLab Forms application uses the trace to identify the characteristic ions for a compound The options are Mass Range TIC or Base Peak
130. alibration Use the Calibration page to set or edit the mathematical model used for preparing the initial calibration evaluation for one or more calibration standards Each target compound can have its own initial calibration settings independent of the other compounds You can modify the calibration approach on this page or in Production mode when you view the results of an actual calibration batch Figure 21 Calibration page General i Compounds HAB Groups Reports Acquisition List Identification Detection Calibration Calibration levels QC levels DER RT Compound Compound type ome dud m Origin Weighting Units ISTE Amount Table 24 Calibration parameters Parameter Description RT Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Compound The compound name Compound type Displays the compound type as an internal standard an external standard or a target compound Standard type Specifies Internal or External standards Response via The use of area or height Curve type Specifies Linear Quadratic or AverageRF curve types Origin Theorigin treatment as Ignore Include or Force The Origin and Weighting columns are active only when you are using Linear or Quadratic curve types Weighting Specifies the weighting as Equal 1 X 1 X 2 1 Y or 1 Y 2 Units The units to be displayed wit
131. alibration curve for each compound Quality check Contains a known amount of one or more specific target compounds The ToxLab Forms application places check standard samples in the sequence so that it can test quantitative analysis results for quality assurance purposes After the application analyzes the check standard sample it compares the measured quantity with the expected value and an acceptability range The quantitative analysis of a check standard sample is classified as passed if the difference between the observed and expected quantities is within the user defined tolerance A check standard sample is classified as failed if the difference between the observed and expected quantities is outside the user defined tolerance Checks the degradation of compounds dissolved in water Similar to a Negative sample but contains target compounds By analyzing a sample you can confirm that there are no residual compounds in the solvent system that can cause erroneous results Contains only solvent Used for quantitative analysis of samples Used for quantitative and qualitative analysis of samples ToxLab Forms 3 1 User Guide 197 5 Using the Production Mode Working in Data Review Working in Data Review From the Data Review view you can view the data generated by the master method Use the Data Review view to verify the data for a sample specific compound before you generate reports You can use the functions in the Data Revie
132. alog box 33 Configuration command 15 Configuration navigation pane 18 Confirming Ions page Peak detection settings 216 Confirming n Ion Ratio Flag parameter 237 Confirming n Ion Ratio parameter 237 Confirming n Manual Flag parameter 237 Confirming n Mass parameter 237 Confirming n Range parameter 237 Confirming n Response parameter 237 Constrain peak width parameter Genesis 99 ICIS 103 Continue to Method command 64 Copy down command 309 Correct surrogates parameter 138 Create Master Method dialog box 54 Create method parameter 50 Create PDF parameter Batch Template Editor 183 standard reports 133 Create XLS parameter 133 Create XML parameter 183 Batch Template Editor 183 standard reports 133 Curve type parameter Calibration 113 Method Template Editor 145 custom reports list of 5 Thermo Scientific CV Test parameter 125 D dashboard parameters 14 Data Review view 198 Decimal places to be reported parameter 137 Default parameter 34 Delete compound from method command Blank page 124 Calibration page 121 Hydrolysis page 127 ISTD page 125 Limits page 120 QC Check page 122 Solvent Blank page 126 Delete condition parameter 314 Detection method parameter Genesis 99 ICIS 103 Detection page Master Method View 84 Detector parameter Detection 96 Development Batch view 153 dialog boxes Add Library 11 Associate a Raw Data File 65 Compounds That are Missing Quans 33 Create Master Method 54 Edit Compound Dependen
133. alues above the upper limit of linearity ULOL Flags values above the carryover limit Flags values between the limit of detection and the limit of quantitation known as the J flag ToxLab Forms 3 1 User Guide 137 4 Using the Method Development Mode Working with Master Methods Table 38 Report options parameters Sheet 2 of 2 Parameter Description Surrogate Correction Option Correct surrogates Applies the conversion factor specified in the sample row in the batch to the samples calculated concentrations for surrogates as the conversion factor is applied to target compounds For example if you added surrogates to the sample as part of sample preparation and you require a dilution for analysis the ToxLab Forms application dilutes the surrogates and target compounds and applies a dilution correction to correct for this dilution However if you added surrogates after a dilution has occurred then you can leave the option cleared so that while the target compounds are corrected for the dilution the surrogates are reported as is Tune Time Tracking Options Enable tune time Tracks the number of hours between the last instrument tune and tracking each sample acquisition Tune file lifetime Specifies the maximum number of hours between the last instrument tune and a sample acquisition Any sample acquired outside this maximum allowable time is flagged on the Batch report 138 ToxLab Forms 3 1 User Guide Thermo Sci
134. ample or the data file Performs a manual acquisition Performs an autosampled acquisition The tray vial number used for the autosampler acquisition The volume in milliliters injected by the autosampler acquisition Overwrites the specified master method name This function is enabled only when the specified master method name already exists Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 13 Method Forge parameters Sheet 2 of 2 Parameter Description OK Creates a master method using the data and parameters you specified Cancel Closes the Method Forge and does not create a master method Thermo Scientific ToxLab Forms 3 1 User Guide 61 4 Using the Method Development Mode Working with Master Methods Importing an Xcalibur Method You can create a new master method from an existing Xcalibur processing method To import an Xcalibur method 1 From the Method View task pane click Create Method L Create method BE Open method amp Export SRM data Recent Files The Create Master Method dialog box opens Create Master Method Method Forge Use Method Forge Performs peak detection against a raw data file Performs library lookup if requested Import Xcalibur Pracessing Method Import scalibur Proces Imports a previously created processing method finding confiqured compounds and reference spectra Associate Haw Data File I Creates a blank master me
135. ample type Sample level Sample ID Compounds Vll 1 2 4 5 Tetrachlorobenzene gt 3 Q9 Tem UspecmenQua asua gg store dis adici is Vli 1 4 Dichlorobenzene j S Hexachlorobutadiene Hevarhloraeurlonentardiene LS Quan Peak 1 QED Spectra Confirming lons lonoverla 1 3 Dichlorobenzene RT 4 38 I RT 4 38 leveld RT 4 38 leveld RT 4 38 RT 4 38 RT 4 38 AR 29239420 11 AA 18174603 22 AA 8953539 78 AH 21283268 25 AH 13295232 39 AH 6493744 30 ri SN 25476 20 nme H SN 9316 951u SN 4633 Any 100 i 2 go ie ja 40 40 20 20 0 0 45 45 45 RT min RT min RT min m z 146 00 m z 148 00 m z 111 00 35 00 95 00 10 00 70 00 Apex RT 4 38 Apex RT 4 38 Apex RT 4 38 Use the Qual Mode and the associated Peaks pane to view qualitative information that complements the textual information for the selected Specimen Qual sample See Qual Mode on page 220 Data Review lik Method lib cal test Instrument ThermoFisher Instrument Status Flags Filename Sample type Sample level Sample ID PEHR c Full ms 35 00 500 00 v calstd5 Calibrator c5 cal std 5 ng uL ME Peak AT min sl RSI MP caso Calbrator 100 calstd 100ng 2 1252 498 330 13 18 Filter c Full ms 35 00 500 00 z100 80 yw 60 i an 11 39 9 40 za i a 12 63 14 27 15 12 20 1480 15 72 16 35 0 A
136. and NIST Libraries Choosing a Mode ToxLab Forms Workflow The ToxLab Forms application is structured with a typical laboratory workflow in mind the user creates a batch and the system injects samples into the instrument runs the samples analyzes the data and generates a report You can set up a master method for specific compound groups or assays you expect to run in your lab When you are ready to run a particular type of sample select the appropriate method and you are ready to start When using the ToxLab Forms application follow these basic steps 1 Create and save a master method in the Method Development mode A master method combines the instrument method and processing method that define how the raw data is acquired and processed how the QAQC information evaluates the results and how the results appear in reports 2 Create and submit a batch in the Production mode A batch lists samples for processing and reporting using a specified method Each row of a batch represents a unique sample 3 Monitor the status of the batch in the Real Time Status view The real time display is visible from the dashboard and all the ToxLab Forms modes You can begin another batch while you watch the real time display of the currently acquiring batch Thermo Scientific ToxLab Forms 3 1 User Guide 1 2 Getting Started Installing the ToxLab Forms Application 4 Evaluate the data in the Production mode The Production mode include
137. andard Summary Report Ion Ratio Failure Report Manual Integration Report Method Report Method Validation Report Negative Report Qualitative Peak Report Qualitative Summary Report Quantitation Report Quantitation Report 2 Quality Control Report Sample Report Sample Report Long Solvent Blank Report To view an example of each type of standard report see Sample Standard Reports on page 256 Example PDFs of standard report formats are also located in the following folder C Thermo Shared ExampleReports Thermo Scientific Custom Reports Thermo Scientific A Reports Specifying Reports For each custom report you generate you can create a hardcopy printout or an XLS xlsm output file The default report title is the report name A user in the role of IT Administrator or Manager can configure custom reports to generate a single report for an entire batch or to create separate reports for each sample Rather than creating separate reports for each sample this method uses data from only the last sample to create a single report for the entire batch The ToxLab Forms application includes the following custom reports AltCalibrationReport BatchReport BlankReport CalibrationDensityReport CalibrationReport CheckStandardReport e CompoundCalibrationReport ConfirmationReport ConfirmationReport2 HighDensitySampleReportl Long HighDensitySampleReport2Long HighDensitySampleRepo
138. antification workflows supporting capabilities present in the LCquan and LabForms 2 5 applications Customized report formats Features of the common workflow core include the following Acquisition and processing Peak detection Quantification to include calibration QAQC analysis and flag setting Reporting Data persistence Raw data file handling ToxLab Forms 3 1 User Guide 3 1 Introduction Reporting Features Reporting Features The report engine can generate several different types of reports designed to meet the needs of the laboratory the laboratory s customers and key regulatory agencies that might review the results The ToxLab Forms application can produce both standard reports and custom reports The following types of reports meet the requirements of various methods and worldwide regulatory agencies and are designed to help track the performance of the GC system and method The reports are divided into two groups Standard and Custom Standard Report Types Batch Report Batch Summary Report Calibration Curve Report Calibration Report Chromatogram Report Compound Calibration Report Compound Calibration Report Alternate Confirmation Report Confirmation Report 2 High Density Calibration Report High Density Internal Standard Report High Density Internal Standard Report Long High Density Sample Report 1 High Density Sample Report 1 Long High Density Sample Report 2
139. application You cannot configure an instrument while the ToxLab Forms application is running Opens a browser where you can choose an instrument method to open See Working with Development Batches on page 153 Specifies a location to store temporary development batch raw data files Removes acquired samples from your development batch so you can begin a new sample list Opens the Qual Browser where you can monitor the acquisition of your samples ToxLab Forms 3 1 User Guide 51 4 Using the Method Development Mode Working with Master Methods Working with Master Methods The ToxLab Forms application uses a master method to specify the nature and types of acquisition processing and reporting that occur with a batch of samples When you are testing for compounds in an assay you can create a method designed specifically for that type of application When you create a master method the ToxLab Forms application uses the method to determine how the software works with a set of samples to provide a set of meaningful results The application uses an instrument method to define how raw data is acquired The rest of the master method defines how the raw data is processed how the flags information evaluates the results and how the reporting functionality defines the way your data and results are output into reports The ToxLab Forms application applies your master method to a batch which is a list of one or more samples to be proc
140. arameter 121 Max Conc parameter 124 Max recovery parameter ISTD page 125 Max RF Diff parameter 122 Max RSD parameter Calibration page 121 Max RT min parameter ISTD page 125 Method parameter Matrix Blank page 124 Solvent Blank page 126 Method Template Editor 144 Method view 53 Thermo Scientific methods importing Xcalibur 62 instrument 149 local 248 master 52 Method Template Editor 144 Methods command 15 Min peak height S N parameter Genesis 100 ICIS 104 Min peak width parameter 104 Min recovery parameter ISTD page 125 Min RT min parameter 125 modes choosing 13 defined 14 Modify Calibrations or Active Compounds by Group parameter 193 Multiplet resolution parameter 104 Name the master method parameter 60 Negative sample type defined 197 New Compound Datastore command 31 New instrument method parameter 51 New sample list parameter 51 NIST library installing 10 Noise method parameter 104 Number of Scans to Subtract parameter 74 Number of scans to subtract parameter 78 0 Only select top peaks parameter 145 Open Chromatograph Reference Sample dialog box 76 Open Compound Datastore dialog box 31 Open instrument method parameter 51 Open method parameter 50 Open Qual Browser parameter 51 Operand parameter 314 Operator parameter 314 Or conditions parameter 314 Origin parameter Calibration 113 Method Template Editor 146 Overwrite parameter 60 P parameters Thermo Scientific
141. ard Reports Method Report Method name EC25B 8level 322010 a EPAMethod8270B 8level Page number Page 12 of 36 Master method name EPAMethod8270B 8level Current calibration file EC25B 8level 322010 a calx Assay type Robustness lon range calc method Level 4 Inj vol 1 000 Instrument method TargetsSplit Tune Breakdown method DFTPPSplit QAQC Calibration Compound Max RSD 96 Min RF R 2 threshold Max amt diff 96 N Nitrosodimethylamine 20 00 0 00 0 990 20 000 Pyridine RCRA 20 00 0 00 0 990 20 000 2 Picoline 20 00 0 00 0 990 20 000 N Nitrosomethylethylamine APP9 20 00 0 00 0 990 20 000 Methyl methanesulfonate 20 00 0 00 0 990 20 000 2 fluorophenol sur 20 00 0 00 0 990 20 000 N Nitrosodiethylamine APP9 20 00 0 00 0 990 20 000 Ethyl methanesulfonate 20 00 0 00 0 990 20 000 phenol d5 sur 20 00 0 00 0 990 20 000 Phenol CCC 20 00 0 80 0 990 20 000 Aniline 20 00 0 00 0 990 20 000 Bis 2 chloroethyl ether 20 00 0 70 0 990 20 000 Pentachloroethane 20 00 0 00 0 990 20 000 2 chlorophenol 20 00 0 80 0 990 20 000 1 3 Dichlorobenzene 20 00 0 00 0 990 20 000 1 4 Dichlorobenzene CCC 20 00 0 00 0 990 20 000 Benzyl alcohol 20 00 0 00 0 990 20 000 1 2 Dichlorobenzene 20 00 0 00 0 990 20 000 2 methylphenol 20 00 0 70 0 990 20 000 Bis 2 chloroisopropyl ether 20 00 0 00 0 990 20 000 N Nitrosopyrrolidine APP9 20 00 0 00 0 990 20 000 3 Methylphenol amp 4 methylphenol 20 00 0 60 0 990 20 000 Acetophenone 20 00 0 01 0 990 20 000 N Nitroso di N propyla
142. astore 36 Print Batch Template Editor 183 custom reports 133 standard reports 133 Product Mass Acquisition List 82 Compound datastore 36 QAQC Flags 236 QC1 QCn 118 Thermo Scientific Index P Qlon 237 Qualitative peak processing template 78 Quan Flags 236 Quan mass 237 Quan peak m z 236 Quan peak response 236 Quan peak RT 237 Quick mode 186 R 2 threshold 121 Ranges Detection 97 Raw filename 60 Recent Files master methods 51 Reference compound 84 Remove user 24 Report concentration 137 Report Name Batch Template Editor 183 custom reports 133 standard reports 132 Report noise as 101 Report Title standard reports 133 Response 237 Response via Calibration 113 Method Template Editor 146 Retention Time 237 RMS 105 Role 23 RT Acquisition List 82 Calibration 113 Calibration levels 115 Calibration page 121 Compound datastore 36 Hydrolysis page 127 Identification 83 ISTD page 124 Limits page 119 Matrix Blank page 123 QC Check page 122 QC levels page 118 Solvent Blank page 126 S N threshold 99 Sample comment 60 Sample Concentration 237 Sample file 235 Sample Units 237 Save changes 24 Select a custom template 60 Select a report 235 Select batch location 51 Select Compounds from CDS 68 ToxLab Forms 3 1 User Guide 321 Index Sensitivity Genesis 99 ICIS 103 sensitivity 145 Separate ion overlay display 137 Set Chromatogram Reference Sample 76 Set chromatogram reference sample 78 Set Reference sample 78
143. atch Template Editor File Edit Help E E I Template method information Subprojec Method select Method Method DET au rare Assay Type Sample level Sample ID Sample type Specimen Automated Batch Heports Standard I Custom Batch Level Bui Report Name Print Create POF Create ML Batch Report P F F Bach sumay Root D m oO Cabe nCuveRept O m O CaibratonRepot 1 MW FL Lhramatagram Report nm 2B Fl Compound Calibration Repot O O O Compound Calibration Repot At O O O I E Sample name es KK U U 3 TUT Comment Repeat sample count Compound Active Status awpa name Active Pam im e a Table 43 Batch Template Editor parameters Sheet 1 of 2 Parameter Description Template Method Information Project The top level project for the batch Subproject The lower level project for the batch Method The master method to use for the batch The Select Method button opens the Open Method dialog box where you can select a master method for the batch template Assay Type The name for the analysis type to be targeted by the method The assay type associates the method with the analysis of a compound or specific class of compounds for example an assay type of PAH might be used for the analysis of Polynuclear Aromatic Hydrocarbons The ToxLab Forms application uses this assay type in the batch template Y
144. ated You can also edit the list of characteristic ions for a specific compound Refining these parameters in the master method for each compound and its ions can reduce the degree of manual integration that would otherwise be required You can change the parameters used to identify a quantification peak mass range or confirming ion The ToxLab Forms application automatically assumes the first match it finds is the compound name the base peak of the mass spectrum is the quan peak and the second and third largest ions are the confirming ions Follow these procedures To filter the displayed compounds To add compounds to the method To change the compound reference spectrum To replace a quan mass To add a mass to the existing quan mass ranges To add a quan peak ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To add a mass as a new compound To replace a confirming ion To add a mass as a new confirming ion e To save the new method To filter the displayed compounds From the Show list box select the type of compounds you want to display in the compounds list Show Juan compounds Juan compounds Target compounds Internal Standards Compound Type Description Quan compounds Displays only quan compounds such as target compounds and internal standards Target compounds Displays only target compounds Internal Standards Dis
145. ated by a comma Extensible Markup Language xml A generic framework for storing any amount of text or any data whose structure can be represented as a tree The only indispensable syntactical requirement is that the document has exactly one root element also called the document element This means that the text must be enclosed between a root start tag and a corresponding end tag Instrument method meth A proprietary file format for the Xcalibur software suite that contains specific instructions that let connected scientific instruments perform data acquisition Processing method pmd A proprietary file format for the Xcalibur software suite with specific instructions about how to process data that was acquired through the instruments attached to the system Raw data raw A file type used for acquired samples on the system ToxLab Forms Directory Structure The ToxLab Forms application creates folders for projects subprojects batches and templates in the Thermo ToxLab Forms directory Within each batch folder the application creates folders for data methods and reports IMPORTANT You cannot rename or move the folders created by the ToxLab Forms application ToxLab Forms 3 1 User Guide Thermo Scientific 1 Introduction ToxLab Forms Feature Summary ToxLab Forms Feature Summary Thermo Scientific The ToxLab Forms system provides a workflow oriented approach to high throughput quantitation The sy
146. ation Report Confirmation Report Confirmation Report 2 High Density Calibration Report Internal Standard Summary Report lon Ratio Failure Report Manual Integration Report Method Report Negative Report Qualitative Peak Report Qualitative Summary Report Quality Control Report Quantitation Report Quantitation Report 2 Solvent Blank Report _Undo changes _ Table 10 Standard Reports parameters Sheet 1 of 2 Parameter Description Standard Reports Displays all available standard reports Custom Reports Displays all available custom reports Installed reports All reports listed in the Installed Reports pane are potentially available for this application but are not selected for the Method Development or Production modes Displayed reports All reports listed in the Displayed Reports pane are selected for the Method Development and Production modes By default the application displays all reports gt gt Moves all reports from the Installed Reports list to the Displayed Reports list gt Moves the selected reports from the Installed Reports list to the Displayed Reports list 44 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 3 Using the Configuration Mode Application Configuration Table 10 Standard Reports parameters Sheet 2 of 2 Parameter lt lt lt Import Undo changes Apply Description Moves the selected reports from the Displayed Reports list to the Installed Reports
147. ave not been acquired a message confirms that you want to clear them and start a new list 3 To create a new empty list click Yes Note You cannot save a development batch when you create a new one you can only create acquire and discard each batch after you use it The ToxLab Forms application saves only the generated raw files in the specified batch location Thermo Scientific ToxLab Forms 3 1 User Guide 157 4 Using the Method Development Mode Working with Development Batches Acquiring Samples in a Development Batch In a development batch you can submit the entire batch for acquisition or submit only selected samples Follow these procedures To acquire selected samples 158 ToxLab Forms 3 1 User Guide To acquire the batch To open the Qual Browser To acquire selected samples Select the samples you want to acquire Right click and choose Submit Selected Samples from the shortcut menu or click the Submit Selected Samples icon EH The ToxLab Forms application creates a raw data file for each selected sample It writes the raw files and all temporary working files to the following folder Thermo ToxLab Forms Temp When the acquisition is complete the application deletes all the temporary working files Only the raw files and a MethodDevelopment sld file remain in the folder If a sample is acquired more than once the subsequent raw data files are time stamped with the acquisition time
148. ay and qual ion display High Density reports m z values on Ratio Failure Report quan ion and qual ion Manual Integration Report m z value Qualitative Peak Report all m z values and spectra displays Qualitative Summary Report all m z values Quantitation Report Olon All peaks on the Detection pages in the Method Development mode The spectrum display in the Data Review view in the Production mode The spectrum display in the Method Forge dialog box 4 n the Application Configuration view click Apply Thermo Scientific ToxLab Forms 3 1 User Guide 39 3 Using the Configuration Mode Application Configuration To specify a default chromatogram intensity display In the Defaults area select Relative or Absolute from the Chromatogram Intensity Scale list This sets the default display type for both quan and qual chromatograms displayed in data review and reports Figure 6 General page User Security Enable user security Technology selection ae Ts un geleitete Cas Chromatography GC w Compound Datastore selection E Enable compound datastore Thermo sEnviraL ab Forms sD atabases sG SD efaull sD eFault srl Defaults Lab name Thermofisher Laboratory Instrument name ThermoFisher Instrument Display mass precision L hramatagram Intensity Scale Table 9 General configuration parameters Sheet 1 of 2 Parameter Description User Security Enables applicati
149. bration settings are immediately applied to the entire results set but they are saved only when you save the batch Table 51 Calibration Curve shortcut menu Sheet 1 of 2 Command Description Standard type Sets the standard type to External or Internal Calibration curve type Sets the calibration curve type to Linear Quadratic or Average RE Linear Allows all settings with this exception When Origin is set to Include all Weighting values are grayed out and Weighting is set to Equal Quadratic Allows all settings with this exception When Origin is set to Include all Weighting values are grayed out and Weighting is set to Equal Average RF Allows no Weighting or Origin selections All Weighting and Origin values are grayed out Weighting is set to Equal and Origin is set to Ignore 214 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 5 Using the Production Mode Working in Data Review Table 51 Calibration Curve shortcut menu Sheet 2 of 2 Command Description Response via Sets the response via to Area or Height Weighting Sets the weighting to equal 1 X 1 X 2 1 Y or 1 Y 2 Origin Sets the origin to Ignore Force or Include Units Sets the units Done with settings Closes the shortcut menu Reset scaling Resets the original scale in the calibration curve pane Spectra The Spectra page displays a comparison of the spectra found in the data and the method reference 133 04 100
150. cans to subtract Stepoff value Set chromatogram reference sample Set Reference sample gt Thermo Scientific To create a method template Click Production from the dashboard or the navigation pane The Production navigation pane opens From the Production navigation pane click Local Method The Local Method View for the currently selected batch opens Local methods are named BatchName_MasterMethodName From the main menu choose File gt New gt Method Template The Method Template Editor opens Beginning with Step 3 follow the instructions To create a method template on nave 139 T 2 oe lt r et lt e ToxLab Forms 3 1 User Guide 249 MEN NH Reports This appendix contains information about standard and custom reports Contents Specifying Reports Report Flags Sample Standard Reports The report engine can generate several different types of reports designed to meet the needs of the laboratory the laboratory s customers and key regulatory agencies that might review the results The following types of reports meet the requirements of various methods and worldwide regulatory agencies and are designed to help track the performance of the system and method The ToxLab Forms application can produce both standard reports and custom reports Specifying Reports As an IT Administrator or Manager you can configure a list of reports that are available
151. cation adds the specified samples to the Samples list Thermo Scientific ToxLab Forms 3 1 User Guide 165 5 Using the Production Mode Working in Batch View 4 To copy a sample 1 Select the sample you want to copy 2 Right click and choose Insert Copy Sample from the shortcut menu The ToxLab Forms application inserts the copy above the selected sample 4 Tore inject a sample 1 From the Samples list select the sample you want to re inject 2 Right click and choose Reinject this Sample from the shortcut menu The ToxLab Forms application creates a copy of the selected sample and appends INJ001 to the file name Additional re injections of the same sample are numbered INJ002 INJ003 and so forth The ToxLab Forms application copies all parameter values from the original sample To edit column values 1 For each sample double click the Filename column or right click and choose Browse in Raw File from the shortcut menu and locate the raw data file to use for the sample You can also browse in multiple raw data files to create multiple samples 2 For each added sample click the Sample Type column and select a sample type from the list Available TLF sample types Negative Solvent QC Specimen Qual Calibrator Hydrolysis Specimen Unextracted 3 For each Calibrator or QC sample click in the Sample Level cell and select a level from the list The sample levels were defined in the master method If there is nothing to s
152. cedures To display peaks for a specific compound To change the sort order To display the compound nonconformance To make a compound active or inactive To exclude a calibration point To display peaks for a specific compound 1 From the Samples list select the sample The Compounds pane lists all compounds specified in the method 2 From the Compounds pane select the compound in the sample The Quan peak pane displays the peaks for the selected compound and its internal standard To change the sort order Right click the Compounds pane and choose one of the following from the shortcut menu Sort by Flag and Alphabetical the default Sort by Flag and Retention Time Sort by Alphabetical Sort by Retention Time To display the compound nonconformance Pause the cursor over the compound or compound flag The ToxLab Forms application displays the error condition RSD 25 496 is greater than Calibration Max RSD 20 H U Anir EOT TODEN ZEE d Thermo Scientific ToxLab Forms 3 1 User Guide 207 5 Using the Production Mode Working in Data Review To make a compound active or inactive 1 Select the sample from the Samples list All compounds in that sample are displayed in the Compounds pane The status of a compound in a sample is determined by the Component Active Status pane in the Batch View for the batch Inactive compounds are grayed out 2 From the Compounds pane select the compo
153. ch user role and the permissions and responsibilities for each role see User Roles on page 25 Follow these procedures To open the User Administration view To add a user To edit user information To remove a user 4 To open the User Administration view 1 Click Configuration from the dashboard or the navigation pane 7 Configuration The Configuration navigation pane opens Note The User Administration view is available only when you enable user security Follow the instructions Io enable user security on page 38 2 Click the User Administration task pane User Administration Pr The User Administration view opens See User Administration view on page 23 To adda user 1 Click the Add User icon The parameters in the User area at the bottom of the view are enabled co ME e IT Administrator Phone number Dr FF Full name Enabled 2 Enter a unique name in the Username field 20 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 3 Using the Configuration Mode User Administration 3 Select a role from the Role list All users must be assigned to one of these defined roles For detailed information about the permissions allowed for each role see User Roles on page 25 4 Enter the user s password There is no confirmation for the encrypted password you enter so carefully type it and make sure to communicate it to the user
154. d Max ASD X Min RF Max Amt Diff 4 1 1 51 Methylene Chloride 0 9900 20 00 0 000 20 00 2 1444 pem E 0 3900 20 00 0 000 20 00 Table 28 Calibration parameters Parameter Description RT Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Compound The compound name R 2 threshold The minimum correlation coefficient r for an acceptable calibration when in linear or quadratic mode Max RSD 96 The maximum relative standard deviation RSD for an acceptable calibration when in average RF mode Min RF The minimum average response factor RF for an acceptable calibration when in average RF mode Max Amt Diff The maximum deviation between the calculated and theoretical concentrations of the calibration curve data points when in linear or quadratic mode Shortcut menu Copy down Copies the selected column value to all rows in that column For detailed instructions about using the Copy Down command see Appendix B Using Copy Down and Fill Down Display retention time Displays or hides the RT column in the compound list column Delete compound from Removes the selected compound from the current master method method ToxLab Forms 3 1 User Guide 121 4 Using the Method Development Mode Working with Master Methods QC Check Use the QC Check page to review the calibration on an ongoing basis The ToxLab Forms application ma
155. d libraries set a value in the Limit Library Hits box 3 To specify how to sort the library searches choose a value from the Best Match Method list box 4 To specify confirming ions Handle confirming ions Include confirming ons Number af confirming iong Specify default ian ratio ranges lon coelutior mini 1 025 E Window Lupe Absolute Window X 20 00 d Include compound peak spectrum as reference spectrum 1 To set the number of confirming ions select the Include Confirming Ions check box and set a value in the Number of Confirming Ions box This value is the number of other ions in the spectrum whose ratio is compared to the quantitation ion Using this ratio you can then determine if it is the target compound or something else This value defaults to 2 because you typically perform a 3 ion experiment with one quan mass and two confirming ions The system selects the most intense ion to use as the quantitation mass and uses this mass for the mathematical operations Thermo Scientific ToxLab Forms 3 1 User Guide 141 4 Using the Method Development Mode Working with Master Methods 2 To define the criteria for evaluating confirming or qualifying ions select the Specify Default Ion Ratio Ranges check box and set the following values a To specify the maximum difference in retention time between a confirming ion peak and the quantification ion peak set a value in the Ion Coelution min box b To
156. d peak Reset scaling Description Lets you manually add a peak Resets the original scaling after a zoom operation The Qual Peak pane displays the selected peak Follow these procedures Thermo Scientific 9 9 To zoom in on a peak To manually add a peak To remove a peak To switch between method and manual integration modes To change the displayed information for detected peaks To zoom in on a peak In the chromatogram plot drag the cursor to delineate a rectangle around the peak The delineated area expands to fill the view to help you examine the peak limits for enhanced review and confirmation To restore the default view right click the chromatogram plot and choose Reset Scaling from the shortcut menu To manually add a peak Right click anywhere in the Qual Peak pane and choose Add Peak from the shortcut menu If a peak is already detected the Add Peak command is not enabled Click to indicate the left and right base points for the peak ToxLab Forms 3 1 User Guide 225 5 Using the Production Mode Working in Data Review The ToxLab Forms application places the peak delimiter tags at these locations and automatically updates the peak values area height and so forth in the result set progesterone RT 3 19 ste RT 3 20 la 711697 52 MH 69491 11 SH IHF Relative Intensity Manually added 3 base points RT min m z 103 00 273 10 237 30 4 T
157. displayed information for detected peaks To modify the peak detection settings 208 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Data Review 4 Tozoom in on a peak 1 In the chromatogram plot drag the cursor to delineate a rectangle around the peak The delineated area expands to fill the view to help you examine the peak limits for enhanced review and confirmation 2 To restore the default view right click the chromatogram plot and choose Reset Scaling from the shortcut menu To manually integrate a quantification or qualification ion 1 Place the cursor over one of the two peak delimiter tags in the Quantification Peak pane When the tag can be selected the cursor changes to a crosshair style cursor You can zoom in on the baseline to make it easier to select the tag 2 Drag the tag to another location and release the cursor to place the peak delimiter tag at its new location and automatically update the peak values area height and so forth into the result set Both the Quantification Peak pane and the Integration Mode column in the Quantification data pane reflect the change between method and manual modes The generated reports for these data identify the manual modifications To manually add a peak 1 Right click anywhere in the Quantification Peak pane and choose Add Peak from the shortcut menu 2 Click to indicate the left and right base points for the peak Th
158. e Mass precision decimal places P oc e If the compounds in the imported Xcalibur method file are not in the Compound Datastore the ToxLab Forms application displays the compounds in the Edit Compound Dependent Parameters dialog box Continue to Method Addtocds 10 Optional Select the compounds you want to add to the Compound Datastore and click Add to CDS Thermo Scientific ToxLab Forms 3 1 User Guide 63 4 Using the Method Development Mode Working with Master Methods The selected compounds are added to the current compound datastore Note To add these compounds to the datastore you must use the Add to CDS command before you continue to the method 11 To add these compounds to your method and close the dialog box click Continue to Method All compounds found in the imported Xcalibur method are added to your method The ToxLab Forms application displays the General page of the Master Method View 12 From the Instrument Method list on the General page select an instrument method 13 To save the new method choose File gt Save from the main menu For a detailed description of how to modify a master method see Editing a Master Method on page 70 64 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Associating a Raw Data File You can use the compounds in a previously acquired raw data file to create a n
159. e 20 1 2 4 5 Tetrachlarab 10 496 5 04 516 535 551 Hexachlorocyclopen 5 2 RTimin 4 8 5 0 5 2 5 4 z Fluarabiphenul RT min 2L hlerenaphthalene IF Times ii Signal Jetect s on Signal Detect Ratios Acenaphthene d1 0 spected AT min 14a Detector Hydrogen bromide I HT min gt Hexachlarobenzene Filter Fhenanthrene d1 0 p T erphenul d14 L hrisene d17 windo SEC i E Trace Mass range w Whew width min nes we cum cum cum EM c SAM ms2 330 1 3c9cid 20 00 70 151 32 07 NL 10441216 BP 14 149 92 100 Relative Intensity E ch er c ha m 154 86 281 02 419 23 m 4 0 4 5 5 0 200 400 RT min m z RT 4 435 32791478 0 Cy XcaliburidatayLabFarrr Thermo Scientific ToxLab Forms 3 1 User Guide 93 4 Using the Method Development Mode Working with Master Methods Parameter Compound list Quan peak Filter Reference chromatogram and spectra Additional pages Times Signal Detect Spectrum Ratios 94 ToxLab Forms 3 1 User Guide Table 17 Detection page parameters Description Lists all compounds in the master method Displays a chromatogram for the quan peak and its confirming ions The quan peak and confirming ion panes include additional pages for retention time signal detection spectrum and ratio parameters Displays the filter used for the raw data file Displays a reference chromatogram and spectra f
160. e Method Development Mode Working with Master Methods L Create method amp Open method al Export SRM data Recent Files cal test_1 cal best 2 Click the method name in the Recent Files list Do not double click The General page for the selected method opens in the Method View See General page on page 77 Editing the General Page The General page defines basic information about the master method Follow these procedures To specify general information for a master method To edit the instrument method parameters To set automated background subtraction options To specify a chromatogram reference sample To specify general information for a master method 1 In the Lab Name box type the name to be displayed on the top of each printed saved or exported report The default name is ThermoFisher Laboratory 2 In the Assay Type box type the assay type to be targeted by the method 3 From the Injection Volume box select the injection volume in uL to be used for sample injection Use either the up down arrows to change the volume in increments decrements of 1 uL or the keyboard to enter non integer injection volumes IMPORTANT The ToxLab Forms application uses the injection volume you specify here in the master method not the injection volume from the instrument method 4 From the Ion Range Calc Method box select a method for calculating the ion ratio range windows 12 ToxLab Forms 3 1 Us
161. e ToxLab Forms application places the peak delimiter tags at these locations and automatically updates the peak values area height and so forth in the result set progesterone RT 3 19 ste RT 3 20 hd 711697 52 E hH 69491 11 SH INF 2400 E qi Z a S t Manually added base points 3 RT min m z 103 00 273 10 237 30 To remove a manually created peak Right click the chromatogram plot and choose Remove Peak from the shortcut menu The ToxLab Forms application removes the manually added peak Thermo Scientific ToxLab Forms 3 1 User Guide 209 5 Using the Production Mode Working in Data Review 210 S ToxLab Forms 3 1 User Guide To switch between method and manual integration modes Right click the chromatogram view and choose Method Integration Settings or Manual Integration Settings from the shortcut menu Initially the method and manual integration settings that are stored for a compound and file are identical and when you select one mode it does not affect the saved result set However when manual data are available the chromatogram plots and the result set update as you switch between method and manual modes As you switch between modes the changes are reflected in each pane The generated reports for this data identify the manual modifications To change the displayed information for detected peaks Right click the quantification chromatogram plot and pause the cursor over
162. e Vial Position column for the new sample type a vial position ON In the Injection Volume column for the new sample type a volume The minimum allowed injection volume value is 0 05 uL N Optional Type or edit the values for the remaining columns Note This function is not available when Quick Mode is selected 188 ToxLab Forms 3 1 User Guide Thermo Scientific S Thermo Scientific 5 Using the Production Mode Working in Batch View To remove samples from the batch Select the samples you want to remove Right click and choose Remove Selected Samples from the shortcut menu or click the remove samples icon The ToxLab Forms application removes the selected samples from the sample list Note This function is not available when Quick Mode is selected To insert samples into the batch Select the sample above which you want to insert a new sample Right click and choose Insert Sample from the shortcut menu The ToxLab Forms application inserts a new Specimen sample above the selected sample Note This function is not available when Quick Mode is selected To copy a sample Select the sample you want to copy Right click and choose Insert Copy Sample from the shortcut menu The ToxLab Forms application inserts the copy above the selected sample Note This function is not available when Quick Mode is selected To move a sample up or down in the sample list
163. e compound chosen by the ToxLab Forms application scroll to the spectrum for that compound and select the compound name in the header of the spectrum pane Pyrazine 1 4 dioxide MAINLIB RSi 740 SE 410 HF 1 select compound NL 899 BP 112 00 112 00 S0 00 g5 p 10 After you manually select your compound click Create to create the master method All compounds found in the raw data file are used in your method The ToxLab Forms application displays the General page of the Master Method View 11 From the Instrument Method list on the General page select an instrument method 12 To save the new method choose File gt Save from the main menu For a detailed description of how to modify a master method see Editing a Master Method on page 70 Figure 10 Method Forge Method Forge create master method from raw data file Method template selection Haw file selection Use the default template L Use an existing raw data file Select a custom template drugs LI Template Libraries Drug Method D Acquire a new raw data file Steroids Method eee aaa Pesticides and Herbicides meth Haw filename zn Calibur Sample comment Mame the master method EEE New Method Manual injection Use autosampler Automatically create the master method Thermo Scientific ToxLab Forms 3 1 User Guide 59 4 Using the Method Development Mode Working with Master Methods Table 13 Method Forge parame
164. e criteria is displayed in a list In all lists you can choose to filter by All Blanks NonBlanks or by custom filter criteria Other filter criteria are specific to the individual columns 2 To create a custom filter based on column values choose Custom from the list For detailed instructions about creating a custom filter see Appendix C Using Filter Criteria Figure 5 Compound Datastore view 20 00 0 000 Table 8 Compound Datastore parameters Sheet 1 of 2 Parameter Description Function icons Adds a compound transition to the datastore Adds a quantitation items row to the selected compound transition or adds a confirming items row to the selected quantitation item Deletes the selected compound transition Compound parameters Compound Name Alphanumeric name assigned to the compound Category Optional Alphanumeric identifier Ionization Optional Alphanumeric identifier Valid values ESI APCI EI CI APPI Chemical Formula Optional Alphanumeric chemical identifier Thermo Scientific ToxLab Forms 3 1 User Guide 35 3 Using the Configuration Mode Compound Datastore Table 8 Compound Datastore parameters Sheet 2 of 2 Parameter Precursor Mass Product Mass Collision Energy Lens Polarity RT min Window sec Energy Ramp Color coding 36 ToxLab Forms 3 1 User Guide Description The mass to charge ratio of a precursor ion The location of the center of a target pr
165. e datastore click the Add Compound icon When the application imports a compound that contains multiple quan peaks it lists all the peaks under a single compound name as in this example for Cocaine To add a single compound or right click the compounds list and choose Add Compound from the shortcut menu A new empty compound row is added to the bottom of the compounds table Cllick the first table cell and enter the required Compound Name parameter Optional Enter values for the Category Ionization or Chemical Formula columns To add a transition to the compound do the following a Select the compound b Click the Add Transition Information icon Ex Transition Information from the shortcut menu A new empty transition row is added to the compound A transition includes quantitative values for the compound Each compound requires at least one transition Thermo Scientific 3 Using the Configuration Mode Compound Datastore 5 Enter all required parameters For a list of required and optional parameters see the list of Compound Datastore parameters on page 35 Tip You cannot add another new compound or save the compound datastore until you enter all required transition parameters or remove the transition from the compound To remove a transition right click the row and choose Cancel To save the new datastore click Save Compound Datastore in the Compound Datastore task pane To
166. e display from the dashboard and from any mode in the ToxLab Forms application To access the real time display from the dashboard Click Real Time Status Real Time Status The real time status displays at the bottom of the dashboard To access the real time display from any of the modes Click Real time status ni Real time status The real time status displays at the bottom of the current view The real time status display has four additional pages of information Acquisition Page nstrument Page Devices Page Queues Page ToxLab Forms 3 1 User Guide 175 5 Using the Production Mode Working in Batch View Figure 39 Acquisition page Pete or Instrument Devices Queues 100 us m Acquisition Queue Wi BatchB gr cal std 10 Relative Intensity nm E o oo o 40 30 20 10 0 5 1 0 1 5 2 0 2 5 RT min Table 42 Acquisition Queue functions PL Function Description Start button starts an acquisition begins the next sample in the batch Pause button pauses the batch queue Use the Start button to e Stop button stops the acquisition for the current sample and restart a paused acquisition Figure 40 Instrument page Acquisition TE g Devices Queues 0 57 100 Instrument callbur Instrument an 50 Run state HieadB arcade gt 70 Batch Batch t 60 50 Sample D cal std 50 not a Sample ID cal std 50 ngul 3 40 ta m Vial 4
167. eak You can choose to update the ion ratios or not update the ion ratios using this reference spectrum Add this mass to Adds the selected mass to your existing quan mass range You can existing quan mass range choose to update the ion ratios to adjust the confirming ion comparisons to the new summed quan peak signal 110 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 22 Spectrum shortcut menu functions Sheet 2 of 2 Functions Description Set this mass as new Adds a new quan peak to an existing compound quan peak Add this mass as new Adds one or more confirming ions to an existing compound confirming ion Reset scaling Returns the chromatogram or spectrum display to its original size Ratios Use the Ratios page to define the criteria for evaluating the confirming or qualifying ions The ToxLab Forms application detects compounds that have confirming ion values outside their acceptable window and flags them in Production mode and on reports L l 2 Thermo Scientific To specify ion ratio criteria Enable or disable the use of the particular confirming ion In the Target Ratio box select the theoretical ratio of the confirming ions response to the quantification ions response In the Window Type box select Absolute or Relative as the calculation approach for determining the acceptable ion ratio range In the Window box
168. eak to the first subtracted peak Valid values None External Default None This parameter is enabled only when Set Chromatogram Reference Sample is set to External The Select button lets you choose a reference sample from the project folders Notes you add about the method Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Editing the Compounds Page Thermo Scientific Use the Compounds page to set all parameters for the identification detection and quantification for the target compound list From the Compounds page of the Master Method View you can access the following pages Acquisition List Identification Detection Calibration Calibration Levels QC Levels Acquisition List The Acquisition List page displays all compounds defined for the current method From this page you can add or delete compounds from the method See Acquisition List page on page 81 The Acquisition List page is displayed only when the Enable Compound Datastore option is checked on the General page on the Application Configuration view See Application Configuration on page 37 Follow these procedures To display a filtered list of compounds click the funnel icon To filter the compound list To delete a compound from the list To add a compound transition to the list To filter the compound list l in the column header For each column a list of filterable criteria is di
169. ected E Matris Blank cal std 1l Matrix Blank Selected samples 5 EBENE Matrix Blank gt 5 MORE AN Matris Blank Right click and choose Remove Selected Samples from the shortcut menu or click the Remove Samples icon m ToxLab Forms 3 1 User Guide 167 5 Using the Production Mode Working in Batch View Editing a Batch In Batch view you can open a saved batch and edit the list of samples You can add edit or remove samples If the batch has already been acquired you can select specific samples for re injection Follow these procedures 168 ToxLab Forms 3 1 User Guide To open a saved batch To edit column values To re inject a sample from a previously acquired batch To submit all samples in the batch To submit selected samples To open a saved batch Click Production from the dashboard or the navigation pane Production The Production navigation pane opens In the Batch View task pane click Open Batch or choose File Open Batch The Open Batch dialog box opens where you can select a saved batch Open Batch Select a project zubproject and batch ta open E EE Project Open TLF 3 0 Batches pen TLF 2 5 Batches Select either Open TLF 3 0 Batches or Open TLF 2 5 Batches To open a TLF 3 0 batch go to Step 4 To open a TLF 2 5 batch go to Step 5 To open a TLF 3 0 batch do the following a Selecta project from the list of projects b Select a subproject
170. ection contains information about the following tasks Creating a New Batch Editing a Batch Submitting a Batch Using a Batch Template Creating a Batch Using the Batch Wizard Specifying Sample Types Creating a New Batch Thermo Scientific From Batch view you can create a new batch Follow these procedures To create a batch To add samples to the list To insert samples into the list To import samples into the list To copy a sample To re inject a sample To edit column values To rearrange the columns To remove samples from the list ToxLab Forms 3 1 User Guide 163 5 Using the Production Mode Working in Batch View 9 l 164 ToxLab Forms 3 1 User Guide To create a batch Click Production from the dashboard or the navigation pane The Production navigation pane opens In the Batch View task pane choose New Batch or choose File New Batch A new unnamed batch opens with one Specimen sample You must choose a master method before you can save your new batch Choose a master method from the Method list Method1 5 Method 64 Method BB Methad22B Methadz2C Choose Eile gt Save gt Batch The Batch Save dialog box opens Batch Save e EE Project E Subproject Project Select a project and a subproject and enter a name for your new batch Tip To enable the Save button you must select a subproject and enter a unique batch name If t
171. ecursor ion peak in mass to charge ratio m z units Default 0 0 Range 10 000 to 2999 999 The mass to charge ratio of the quan ion The location of the center of a target quan ion peak in mass to charge ratio m z units Default 0 0 Range 10 000 to 2999 999 The energy used when ions collide with the collision gas Range 250 00 to 250 00 Optional Range 400 to 400 positive or negative Retention time The application uses RT and Window values to determine the start and stop time for the acquisition Range 0 00 to 999 00 Start time RT Window 2 Stop time RT Window 2 Start and stop range 0 00 to 999 00 Acquisition window The application uses RT and Window values to determine the start and stop time for the acquisition Range 0 00 to 499 50 Start time RT Window 2 Stop time RT Window 2 Start and stop range 0 00 to 999 00 Optional Range 0 00 to 200 00 Blue indicates a compound Yellow indicates a quantitative transition Green indicates a confirming transition Pink fields are editable when you import new transitions into the datastore from the method editor Thermo Scientific 3 Using the Configuration Mode Application Configuration Application Configuration This section includes instructions for the following groups of tasks Specifying the General Configuration Specifying the Reports Configuration Specifying the General Configuration Th
172. ed compound and key statistical values for evaluating the quality of the calibration Displays a comparison of the spectra found in the data and the method reference Displays a graphical view of all qualifying confirming ions for the selected sample and compound and displays calculated ion ratios and ion ratio acceptance windows Thermo Scientific 5 Using the Production Mode Working in Report View Active View Report Contents Thermo Scientific Fach standard report that uses the Active View displays values that are common to all reports Common Active View report values In addition to the common values the following reports display additional active view features Blank Report Active View values Calibration Curve Report Active View values Calibration Report Active View values High Density 1 and High Density 1 Long Report Active View values High Density 2 and High Density 2 Long Report Active View values High Density 3 and High Density 3 Long Report Active View values Internal Standard Report Active View values Ion Ratio Failure Report Active View values Manual Integration Report Active View values QC Report Active View values Quantitation Report Active View values Sample Report and Sample Report Long Active View values Solvent Blank Report Active View values ToxLab Forms 3 1 User Guide 239 5 Using the Production Mode Working in Report View Table 59 Common Active View report values Column Status C
173. ed background subtraction options 74 Automatically create the master method parameter 60 Thermo Scientific Available Methods parameter 186 Available Templates parameter 186 background subtraction options 74 Background subtraction range option parameter 78 Baseline window parameter 103 Batch Level Report parameter 46 Batch view 163 batches development batch 153 Production mode 163 Best match method parameter 145 Blank page Master Method View 123 C call caln parameter 115 Calibration Curve page Peak detection settings 214 Calibration Levels page Master Method View 114 Calibration method parameter 145 Calibration page Master Method View 113 Calibration page QAQC page Master Method View 121 Calibrator sample type definition 197 Cancel changes parameter 24 Carryover limit parameter 120 CAS No parameter 84 Category parameter Acquisition List 81 Compound datastore 35 caution flags 201 Chemical Formula parameter Acquisition List 81 Compound datastore 35 Chromatogram Intensity Scale parameter 41 Collision Energy parameter precursor Acquisition List 82 Compound datastore 36 ToxLab Forms 3 1 User Guide 315 Index C color coding Compound Datastore 36 comma separated values defined 2 commands Add a mass as new confirming ion 111 Add Compound 32 Add Group 129 Add this mass to existing quan mass ranges 110 Add to CDS 63 Add Transition Information 32 Configuration 15 Continue to Method 64 Copy down 309 Delete
174. ed in the associated instrument method For those autosamplers the value entered in this field is ignored and the instrument uses a default method injection volume Other autosamplers such as the TriPlus use the ToxLab Forms application method injection volume for sample analysis and override the instrument method For a more detailed explanation refer to the documentation for the autosampler The ToxLab Forms application uses the selected ion range calc method to calculate the ion ratio range windows Manual default Average Level or Weighted average When you select Level an additional list box is displayed where you can choose a calibration level amount To define these calibration levels on the Compounds page see Editing the Compounds Page on page 79 Instrument method used for processing samples Opens the Thermo Xcalibur Instrument Setup dialog box where you can edit the instrument method Lets you choose one of the following Send to Xcalibur Method to overwrite the Xcalibur method with the current instrument method Get From Xcalibur Method to overwrite the current instrument method with the Xcalibur method The ToxLab Forms application uses the qualitative peak processing template to perform peak detection on quantitative samples following compound analysis Valid values None Before Peak After Peak Both Sides of Peak Default None Valid values Even numbered integers Default 0 Offset from the selected p
175. ed properly This document is not part of any sales contract between Thermo Fisher Scientific Inc and a purchaser This document shall in no way govern or modify any Terms and Conditions of Sale which Terms and Conditions of Sale shall govern all conflicting information between the two documents Release history Revision A Minimum software requirements Xcalibur 2 1 0 Microsoft Windows XP Professional SP 3 For Research Use Only Not for use in diagnostic procedures O HW Contents dign d V Related Documentation V S e RA oir e CL vi CUBE MIU EP vii our AP CT asagi a maques wu EEE EEE e asa vii Chapter 1 luni memP 1 About the ToxLab Forms Application ToxLab Forms Feature Summary 3 Reportne L Gata eS oue Beeren arena Ebern ee 4 Standard Report Types core Rer eq a EC ed OR ous HE UR eite dO 4 Custom Report 1ypcs seges ersparen uses 5 Chapter2 Getting Started a 7 ToxLab Forms Workflow 7 Installing the ToxLab Forms Application 8 Installing the QED and NIST Libraries 10 Choosing a Mode Pn 12 Chapter3 Using the Configuration Mode
176. ee 0 50 100 150 200 0 50 100 150 200 0 50 100 150 200 ng uL ng uL ng uL N Nitrosomethylethylamine APPS Methyl methanesulfonate 2 fluorophenol sur Average RF 0 73259 RSD 6 9090 Average RF 0 43292 RSD 17 0844 Average RF 1 43598 RSD 5 6978 a la 0 75 0 70 u 0 65 0 60 0 55 0 50 8 8 8 0 45 8 e u u 0 40 c c amp 0 35 amp amp o o 2 a 0 30 a x 0 25 0 20 0 15 0 10 0 05 0 00 0 50 100 150 200 ng uL N Nitrosodiethylamine APPS Ethyl methanesulfonate phenol d5 sur Average RF 0 72094 RSD 10 8937 Average RF 1 09666 RSD 10 0240 Average RF 1 95705 RSD 2 9812 Response Factor Response Factor ng uL Phenol CCC Aniline Bis 2 chloroethyl ether Average RF 2 16082 RSD 7 7879 Average RF 2 74670 RSD 4 8229 Average RF 1 47904 RSD 7 9864 E a a a o o o m m m u u u 3 2 c amp amp amp 7 7 o o x x 0 50 100 150 200 ng uL 274 ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports High Density Internal Standard Report High Density Internal Standard Report Lab name Thermo Fisher Laboratory Page 1 of 1 Instrument Thermo Scientific Instrument Method Drug_A_Drug_A User AMER jamie humphries Drug_A Batch Drug_A Cali File Drug_A calx Qual m z 473 20 Qual m z 488 20 Area 62641 Area 32066 in Ratio 27 53 Ra Flag legend LOD lt J lt LOQ I lon ratio failure
177. ee ne N Kuq didi ecd 306 Sample REPO LONE Lotes eolit uska ed ere d ori apa 307 Solvent Blank Report S uoa tUe ULCUS bee ehe dw Ta St d 308 Appendix B Using Copy Down and Fill Down 309 Examples cu os era e PLENAS seid d qs 311 Example C 311 Appendix C Using Filter Criteria a 313 Enter ileer Oiid enri Dacodohd e Seed d ted eene dU Que tuba Rabat 314 lode EE 315 ToxLab Forms 3 1 User Guide iii pP Preface The ToxLab Forms 3 1 application is next in the series of Thermo Scientific GC MS analytical software Contents e Related Documentation Special Notices System Requirements Contacting Us To suggest changes to documentation or to Help Complete a brief survey about this document by clicking the link below Thank you in advance for your help SURVEY Related Documentation The ToxLab Forms documentation includes Help that you can access from the application and also includes the 7oxLab Forms User Guide and three quick reference guides as PDF files that you can access from the Start menu To view the ToxLab Forms user guide or quick reference guides Go to Start gt All Programs gt Thermo ToxLab Forms 3 1 gt Manuals and choose one of the following documents ToxLab Forms User Guide JoxLab Forms Administrator Quick Reference Guide JToxLab Forms Production Quick
178. eine Compound Compound DA DC Quan Manual Quan Total Quan peak Duan Theoretical Concentration Mame Type Flags Flags Flags peak m z response response peak HT amount WEB Fess Tacoma 0 ea NS 0 oo Ta a QED Spectra Confirming lans l lon ove 2j No Data No data Apex AT 0 00 Table 58 Active View parameters Sheet 1 of 4 Parameter Description Display selection Select a report Displays the report types created for the current batch Sample file Used when the report type includes separate reports for each sample Showing Lists the available compound types to display in Active View Quan Non quan Target Internal Standards or Surrogates Thermo Scientific ToxLab Forms 3 1 User Guide 235 5 Using the Production Mode Working in Report View Table 58 Active View parameters Sheet 2 of 4 Parameter Column headings Status Description The status of the reported compound A yellow warning flag indicates one of the following conditions The compound was manually integrated Any of the confirming peaks was manually integrated The compound has quan flags A red warning flag indicates that the QAQC checks failed A green flag indicates that none of these conditions exist When the compound is an internal standard warning flags are displayed only on the internal standard report The Status column is blank for Manual Integration reports Compound Name Compound Type Alp
179. elect in the Sample Level list do the following a Return to the Method Development mode b Open the method c Click the Compounds tab d Click the Calibration Levels tab e Add the levels f Savethe method g Return to the Production mode and begin this batch again You must close your original batch without saving and start a new batch For detailed instructions see Chapter 4 Using the Method Development Mode 4 Enter or edit the values for the remaining columns 166 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 9 5 Using the Production Mode Working in Batch View When you use the scroll bar at the bottom of the Samples list the Status and Filename columns remains fixed and only the other columns scroll right and left For instructions on automatically copying or filling values in these columns see Appendix B Using Copy Down and Fill Down To rearrange the columns Do one of the following To resize a column drag the header separator on the right side of the column To move a column drag the column header When you close the ToxLab Forms application it saves the new column order and width Note The Status and Filename columns can be swapped with each other but they cannot be moved to any other location in the table To remove samples from the list Select the samples you want to remove Ensure that the first column indicates that the samples are sel
180. en you have selected Enable User Security on the General page of the Application Configuration view See Application Configuration on page 37 Project Administration Opens the Project Administration view where you can create and manage projects and subprojects See Project Administration on page 28 18 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 3 Using the Configuration Mode Table 4 Configuration navigation pane functions Sheet 2 of 2 Function Compound Datastore Application Configuration Description Opens the Compound Datastore view where you can manage the definition of compounds in the current datastore See Compound Datastore on page 30 This task pane is available only when you have selected Enable Compound Datastore on the General page of the Application Configuration view See Application Configuration on page 37 Opens the Application Configuration view where you can specify a compound datastore to use for the gas chromatography technology and specify defaults to use for laboratory name instrument name and mass precision See Application Configuration on page 37 ToxLab Forms 3 1 User Guide 19 3 Using the Configuration Mode User Administration User Administration In the User Administration view of the Configuration mode in the role of Manager or IT Administrator you can add remove or edit user accounts and permissions For detailed descriptions of ea
181. entific 4 Using the Method Development Mode Working with Master Methods Creating a Method Template In the ToxLab Forms application you can create a processing method using a method template that contains the basic settings as defined by a user in the role of Manager or Supervisor Follow these procedures To create a method template To specify peak criteria To choose a library To specify confirming ions To calibrate the compounds To enter a note for the method To save the method template 4 To create a method template 1 Click Method Development from the dashboard or the navigation pane The Method Development navigation pane opens 2 Click Method View in the navigation pane 3 From the main menu choose File New Method Template The Method Template Editor opens See Method Template Editor on page 144 Thermo Scientific ToxLab Forms 3 1 User Guide 139 4 Using the Method Development Mode Working with Master Methods To specify peak criteria Find the peaks s Sensitivity High ICIS Limit the retention time range Min AT min Max RT min Enable peak threshold of largest peak By height L By area Only select top peaks Select the top By height By ara 1 In the Find the Peaks area choose a sensitivity level In selecting the degree of sensitivity you define how extensively the peak detector algorithm searches for low level peaks
182. enzene Naphthalene p Chloroaniline 2 6 Dichlorophenol Hexachloropropene APP9 Hexachlorobutadiene CCC N Nitroso di N butylamine 4 Chloro 3 methylphenol CCC Safrole_APP9 2 Methylnaphthalene Hexachlorocyclopentadiene SPCC 1 2 4 5 Tetrachlorobenzene 2 4 5 Trichlorophenol 2 4 6 Trichlorophenol CCC 2 fluorobiphenyl sur Isosafrole APP9 2 Chloronaphthalene EC25B 8level 322010 a EPAMethod8270B 8level EPAMethod8270B 8level EC25B 8level 322010 a calx Robustness 1 000 TargetsSplit DFTPPSplit 288 ToxLab Forms 3 1 User Guide lon range calc method LOD 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 0 500 LOQ 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 Method Report Level LOR 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 000 1 0
183. enzene d5 sur Nitrobenzene N Nitrosopiperidine Isophorone Phenol pentachloro 2 Nitrophenol CCC 2 4 Dimethylphenol Bis 2 chloroethoxy methane DFTPP 2 4 Dichlorophenol CCC 1 2 4 Trichlorobenzene NAPHTHALENE D8 IS Naphthalene p Chloroaniline 2 6 Dichlorophenol Hexachloropropene APP9 Hexachlorobutadiene CCC Benzidineperf N Nitroso di N butylamine 4 4 DDE 4 Chloro 3 methylphenol CCC Safrole APP9 EC25B 8level 322010 a EPAMethod8270B 8level EPAMethod8270B 8level EC25B 8level 322010 a calx Robustness 1 000 TargetsSplit DFTPPSplit Quan mass 74 00 79 00 93 00 88 00 80 00 112 00 102 00 79 00 99 00 94 00 93 00 93 00 167 00 128 00 146 00 152 00 146 00 108 00 146 00 107 00 45 00 100 00 107 00 105 00 70 00 106 00 117 00 82 00 77 00 114 00 82 00 265 75 139 00 122 00 93 00 197 92 162 00 180 00 136 00 128 00 127 00 162 00 213 00 225 00 184 14 84 00 246 00 107 00 162 00 286 ToxLab Forms 3 1 User Guide lon range calc method Method Report Level RT Window 2 54 30 00 2 59 30 00 3 36 30 00 3 46 30 00 3 80 30 00 4 02 30 00 4 29 30 00 4 63 30 00 5 11 30 00 5 13 30 00 5 18 30 00 5 24 30 00 5 24 30 00 5 32 30 00 5 51 30 00 5 57 30 00 5 59 30 00 5 71 30 00 5 77 30 00 5 84 30 00 5 88 30 00 5 99 30 00 6 02 30 00 6 03 30 00 6 03 30 00 6 07 30 00 6 17 30 00 6 21 30 00 6 23 30 00 6 40 30 00 6 50 30 00 6 52 30 00 6 61 30 00 6 64 30 00 6 75 30 00 6 75 30 00 6 8
184. er Guide 305 A Reports Sample Standard Reports Sample Report Data File cal_1 Method Drug_A_Drug_A Drug_A Cali File Drug_A calx Sample ID cal 1 6 ng mL Diln Factor 1 00 Comments 100 30 80 70 so so E 40 30 20 10 1 86 1 87 188 158 E 1 86 1 88 m z 380 20 100 PE 80 a0 5 70 2 ao 50 b CO E c c c 18 158 20 20 1 85 2 00 R Tiimi RT min lon Int_Std 1 93 m z 380 20 1 93 m z 479 20 m z 371 20 100 r a0 a0 m a s E an 30 20 10 1 85 R Tiimi RT min lon Drug_A 1 95 m z 371 20 1 94 m z 473 20 1 94 m z 488 20 142 1 90 1 92 m z 479 20 n Cu S amp od amp c c c cC CO C Relative Intensity d 1 2 1 85 R Tiimi Response 678044 134976 m z 473 20 100 50 m m an 5n oan 30 20 10 1 85 R Tiimi Response 227568 62641 32066 Report Generated 3 31 2010 7 02 27AM 306 ToxLab Forms 3 1 User Guide Sample Report Tune Report Date Tune report not found Acquisition Date 4 17 2008 5 05 47 PM Cali File Date 3 11 2010 9 01 23 AM Operator ID AMER jamie humphries Instrument ID Thermo Scientific Instrument Vial Number 2 1 93 1 95 1 99 2 00 2 01 2 02 2 03 2 03 2 04 1 94 1 96 98 2 00 2 02 2 04 RTimin Composite RT 1 83 eal 1 100 a0 a0 gt 70 5 an 50 S 40 a 20 10 D 2 00 1 50 1 85 2 00 RTimm Amount Target Range Ratio 15 000 ng mL
185. er Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods When you select Level the ToxLab Forms application displays an additional list box where you can choose a calibration level To define the calibration levels on the Compounds page see Editing the Compounds Page on page 79 5 From the Qualitative Peak Processing Template box select a template for performing peak detection on quantitative samples following target compound analysis 4 To edit the instrument method parameters 1 From the Instrument Method list on the General page select an instrument method 2 To edit the instrument method for this master method click Edit next to the appropriate box The Thermo Xcalibur Instrument Setup dialog box opens This example instrument setup shows multiple configured instruments FJ untitled Thermo Xcalibur Instrument Setup File TRACE Help a So 2a ya Ham m a a a KG Ha N SS aa a HH a a a a aa 000 0 20 040 060 080 1 00 120 1 40 160 Jal 200 220 230 260 250 300 Oven Enable Cryo Max Temp C 350 Past Hun Conditions Temperature C Bi Time min 9 Pressure Left psi 05 Pressure Right psi s Eust Time mir Oven Runtime 500 1505 Hamps z Hate Temp Hold Time C mri PC minutes Initial 40 Preo Aun Timeout min 10 00 E quilibratian Time min 0 50 TRACE GC Ultra C Specific
186. erent instrument methods and optimize parameters such as MS source parameters and autosampler variables to find the best conditions for a master method Development batches are not designed for high throughput in everyday analysis This section includes instructions for the following tasks Creating a Development Batch Editing Samples in a Development Batch Acquiring Samples in a Development Batch Creating a Development Batch You create a development batch to test your instrument method and use it to acquire samples only once You cannot save a development batch Follow these procedures To open the Development Batch view To specify a location for development batch data To add samples to the development batch To insert samples into the development batch To copy a sample To open the Development Batch view 1 Click Method Development from the dashboard or the navigation pane The Method Development navigation pane opens 2 In the Method Development navigation pane click Development Batch Filename Sample ID Sample name Vial position Injection volume Instrument Method Comment a 0 000 v Thermo Scientific ToxLab Forms 3 1 User Guide 153 4 Using the Method Development Mode Working with Development Batches To specify a location for development batch data 1 To specify a location for the files click Select Batch Location in the
187. ermo Scientific In the role of Manager or IT Administrator you can specify a default compound datastore and specify defaults to use for laboratory name instrument name and mass precision in the Application Configuration view of the Configuration mode Follow these procedures To open the General page of the Application Configuration view To enable user security To specify a datastore to use in method development To specify a default laboratory name instrument name and mass precision To specify a default chromatogram intensity display To open the General page of the Application Configuration view Click Configuration from the dashboard or the navigation pane The Configuration navigation pane opens Click Application Configuration The General page of the Application Configuration view opens See General page on page 40 ToxLab Forms 3 1 User Guide 37 3 Using the Configuration Mode Application Configuration To enable user security In the User Security area select the Enable User Security check box When checked all users are required to log on to the ToxLab Forms application and have access to only those modes assigned to their user role See User Roles on page 25 When cleared users are not required to log on to the ToxLab Forms application When they start the application the dashboard is the first screen the users see and all modes are available to them However the User Administratio
188. es Limits Calibration QC Check IS TD Solvent Blank Hydrolysis Limits Use the Limits page to define levels of review for quantified results Quantified results appear on printed and electronic reports You can also define when a quantified value is reported instead of reporting less than a particular limit Figure 24 imits page Negative STE Solvent Blank LOD Detection limit LOG Quantitation limit Cutoff ULOL Linearity limit Carpower limit Table 27 Limits parameters Sheet 1 of 2 Parameter Description RT Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Compound The compound name LOD Detection limit Limit of detection The lowest amount that can be detected Usually derived from a method detection limit mdl study LOQ Quantitation Limit of quantitation The lowest amount that can be confidently limit and accurately quantitated This is usually the lowest calibrator amount LOR Reporting limit Limit of reporting Also called cutoff in some industries This is the highest amount that can be reported as determined by each laboratory s standard operating practices ToxLab Forms 3 1 User Guide 119 4 Using the Method Development Mode Working with Master Methods Table 27 Limits parameters Sheet 2 of 2 Parameter Description ULOL Linearity limit Upper limit of linearity This is usually the
189. essed and reported Together the master method and batch provide a workflow oriented approach to the processing of data and the reporting of information for small and large sets of samples To speed up the creation of master methods you can create a method template Using a method template helps you to develop methods faster because all of your commonly used method settings such as number of confirming ions are saved in a template This section includes instructions for the following tasks Creating a New Master Method Editing a Master Method Creating a Method Template Exporting SRM Data 52 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Creating aNew Master Method You can use any of four different procedures to begin a master method Creating a Method with Method Forge Importing an Xcalibur Method Associating a Raw Data File Selecting Compounds from the Compound Datastore Fach procedure lets you begin the method in a specific way and then use the common features of the Master Method View to complete and save your master method Creating a Method with Method Forge With Method Forge you can create a new master method by manually selecting peaks selecting multiple compounds renaming peaks or comparing mass spectra from the library searches You can also choose to let the ToxLab Forms application automatically create a master method for you
190. etect Ratios NL 656115 BP 200 78 IPP e m m Relative Intensity ho e 209 03 213 83 i To zoom in the chromatogram or spectrum displays 1 Drag the cursor to delineate a rectangle The display zooms into the specified rectangle 2 To return to the original display right click and choose Reset Scaling from the shortcut menu Thermo Scientific ToxLab Forms 3 1 User Guide 109 4 Using the Method Development Mode Working with Master Methods Figure 19 Spectrum page luanPeak1 Quan peak 5 1 RT min Signal Detect Spectrum ML 100 BP 201 00 201 00 Applv background subtraction to peak and set as reference spectrum B gt Update confirming ion ratios with this spectrum E 117 06 en Set this mass a5 quan mass E M 166 05 Add this mass En existing quan mass range O4 05 204 98 Set this mass as new quan peak 20 214 59 Add this mass as new confirming ion n got 100 200 30 Reset scaling m z Table 22 Spectrum shortcut menu functions Sheet 1 of 2 Functions Description Apply background Applies the background subtraction values specified on the subtraction to peak and General page and uses this spectrum as the reference spectrum set as reference spectrum Update confirming ion Updates the confirming ion ratios using the selected peak ratios with this spectrum Set this mass as quan Adds the quan mass of the selected ion to the quantitation mass mass used for the quan p
191. evels of detection or adding new compounds to the existing database Reviewing data from the mass spectrometer Running samples and reviewing data collected by others Reporting the data Understanding the results and giving final approval of the released data before archiving As a user in the role of IT Administrator you set security manage users into roles and manipulate the various databases You are responsible for adding compounds into the various compound databases An IT administrator is responsible for these tasks Handling the databases Applying roles to users Understanding security users and groups Creating local users and network groups ToxLab Forms 3 1 User Guide 25 3 Using the Configuration Mode User Administration Supervisor Technician As a user in the role of Supervisor you are responsible for putting samples on the instrument and using previously built sequences and methods for processing and acquiring data You also develop and edit methods for processing and acquiring data review the data and distinguish between the need to rerun samples or pass reports up to the lab manager or QAQC technician for final review On a daily basis you establish the priority for a list of samples to run and create the sequence of events A supervisor is responsible for these tasks Submitting samples Creating and submitting batches Reporting the data to management Creating or editing methods
192. ew batch data and reports and edit local methods To access the Production mode Click Production from the dashboard or the navigation pane The Production navigation pane opens Thermo Scientific ToxLab Forms 3 1 User Guide 161 5 Using the Production Mode Figure 37 Production navigation pane Production Batch Yiew L Mew batch fr Open batch Recent files Data Review Report View Local Method Methods Eur u B Production Batch View See Working in Batch View on page 163 New batch Opens a new unnamed batch with one Specimen sample See Creating a New Batch on page 163 Openbath Opens the Open Batch dialog box where you can select a saved batch to edit Editing a Batch on page 168 Recent Files Displays recently saved batches Data Review See Working in Data Review on page 198 Report View See Working in Report View on page 230 Local Method See Working in the Local Method View on page 248 162 ToxLab Forms 3 1 User Guide Thermo Scientific Working n Batch View From the Batch view you can manually create and edit a new batch or open and edit a 5 Using the Production Mode Working in Batch View previously saved batch You can also use a batch wizard to define a sequence of various sample types to be assembled into a batch of samples When you submit a batch you can acquire process or create reports for the submitted samples This s
193. ew master method Follow these procedures To associate a raw data file with the method To add compounds to the method To associate a raw data file with the method 1 From the Method View task pane click Create Method Method Yiew L Create method BE Open method amp Export SRM data Recent Files The Create Master Method dialog box opens Create Master Method Method Forge Use Method Forge Performs peak detection against a raw data file Performs library lookup if requested Import Xcalibur Pracessing Method Import Scalibur Processing Method Imports a previously created processing method finding configured compounds and reference spectra Associate Raw Data File Creates a blank master method and associates a Associate a raw data file raw data file allowing manual peak selection Select Compounds from a compound datastore Creates a blank master method and displays the configured compound datastore allowing compound selection Select compounds from CDS 2 Select Associate a Raw Data File The Associate a Raw Data File dialog box opens Thermo Scientific ToxLab Forms 3 1 User Guide 65 4 Using the Method Development Mode Working with Master Methods Associate a Raw data file x m P a i re L vs callbursdata sL abForms Raw Files slevel raw Update target ion ratio values Mo ve Automatically set reference spectrum Mo ve 3 Click the browse
194. f all Quan Peak Response values for the compound Response of the quan peak Retention time for the quan peak Theoretical amount of the compound Reports N A when not applicable Calculated injected amount Mass of the confirming peak Response of the confirming peak Indicates a manually integrated confirming peak Indicates that the ion ratio is out of range Actual ratio of the confirming ion response to the quan ion response Acceptable range for the confirming ion Table 65 High Density 3 and High Density 3 Long Report Active View values Column m z Total Response Quan Peak Response Quan Peak RT Description Mass to charge ratio for the quan peak Sum of all Quan Peak Response values for the compound Response of the quan peak Retention time for the quan peak ToxLab Forms 3 1 User Guide 243 5 Using the Production Mode Working in Report View Table 65 High Density 3 and High Density 3 Long Report Active View values Column T Amount Conc Confirming 1 Mass Confirming 1 Response Confirming 1 Manual Flag Confirming 1 Ion Ratio Flag Confirming 1 Ion Ratio Confirming 1 Range Confirming 2 Mass Confirming 2 Response Confirming 2 Manual Flag Confirming 2 Ion Ratio Flag Confirming 2 Ion Ratio Confirming 2 Range Description Theoretical amount of the compound Reports N A when not applicable Calculated injected amount Mass of the confirming peak Response of the confirming peak
195. for new levels of detection or adding new compounds to the existing database Reviewing data from the mass spectrometer Understanding the results who ran the batch and who passed along the results before giving intermediate approval and sending the data to management Modifying new compounds or adjusting methods for specific result sets As a user in the role of Technician you are responsible for putting samples on the instrument and using previously built sequences and methods for processing and acquiring data You also edit existing methods for processing and acquiring data and are responsible for reviewing collected data and distinguishing between the need to rerun samples or pass reports up to the supervisor On a daily basis you are responsible for gathering the list of samples to run and creating the sequence of events A technician is responsible for these tasks Submitting samples Creating and submitting batches Creating data to be reviewed by management Receiving instructions for new sets of samples for the ToxLab Forms application to analyze after finishing the current analysis Reviewing data from the mass spectrometer Understanding the resulting data making integration changes and passing those changes up for further approval 26 ToxLab Forms 3 1 User Guide Thermo Scientific 3 Using the Configuration Mode User Administration QAQC As a user in the role of a QAQC technician you review graphical
196. fy quantitation limits Quan Limits Flags Report concentration Decimal places to be reported Show chromatogram on Quantitation Report Display valid compounds only 1 To report the calculated concentration at all times or only when the quantified value exceeds LOD LOQ or LOR choose the appropriate value from the Report Concentration list box These concentration limits are defined in Limits on page 119 2 To select the number of decimal places to report for calculated concentrations set the value in the Decimal Places to be Reported box 3 To include a chromatogram of the sample in the report select the Show Chromatogram on Quantitation Report check box 4 To display only valid compounds select the Display Valid Compounds Only check box 134 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To specify user interface options User Interface Options Shade row when sample is outside of evaluation criteria MI Separate ton overlay display Use alternate calibration report format d Display Quan flags and legend A 1 To shade a compound row on any of the reports if a value fails one of the criteria used for evaluation select the Shade Row when Sample is Outside of Evaluation Criteria check box 2 To separate the ion overlay pane from the confirming ion plots select the Separate Ion Overlay Display check box 3 To use an alternate
197. g the QED and NIST Libraries Installing the QED and NIST Libraries When you are using triple quad instruments follow these instructions to install the NIST and QED libraries To install the NIST library 1 Launch the XInstall executable file 2 Click the NIST button The NIST 08 MS Search and AMDIS Setup wizard opens 3 Follow the instructions in the setup wizard 4 When the wizard prompts you to select a program folder select C Thermo 4 To install the QED library 1 On your desktop double click the Xcalibur icon Em The Thermo Xcalibur Roadmap opens X Thermo Xcalibur Roadmap Sele File Actions View Tools GoTo Help j Status Acquisition Queue E Run Manager o c Waiting For Devices Sequence Sample Mame Working Un Position Raw File o Inst Method Accela AS i M Za baih als ra ii E B For Help press F1 mm 10 21 2009 3 33 PM E 10 ToxLab Forms 3 1 User Guide Thermo Scientific 2 Getting Started Installing the QED and NIST Libraries 2 Select Tools Library Manager The Thermo Library Manager dialog box opens The NIST library is displayed in the NIST Libraries list Thermo Library Manager Manage libraries Conwert Libraries MIST libraries NIST Add 3 Click Add The Add Library dialog box opens Add Library Source EAThermosQED NIST Library Acton Copy the library to the local computer Link to the library from either
198. g_A Batch Drug_A Cali File Drug_A calx Flag legend LOD lt J lt LOQ I lon ratio failure C Carryover Linearity limit D Detection limit Q Quan limit POS Cutoff n Negative b Solvent blank H Hydrolysis Thermo Scientific ToxLab Forms 3 1 User Guide 277 A Reports sample Standard Reports High Density Sample Report 1 Long High Density Sample Report 1 Long Lab name Thermo Fisher Laboratory Page 1 of 1 Instrument Thermo Scientific Instrument Method X Drug A Drug A User AMER jamie humphries Drug_A Batch Drug_A Cali File Drug_A calx Relative Intensity Relative Intensity Int_Std Drug_A Quan m z 380 20 Quan m z 371 20 Total Area 678044 Total Area 227568 Peak Area 678044 Peak Area 227568 RT 1 93min 1 94 RT 1 95min 1 95 TAmount 6 000 ng mL Amount 15 000 ng mL Amount 5 581 ng mL Flag legend LOD lt J lt LOQ I lon ratio failure C Carryover Linearity limit D Detection limit Q Quan limit POS Cutoff n Negative b Solvent blank H Hydrolysis 278 ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports High Density Sample Report 2 High Density Sample Report 2 Lab name Thermo Fisher Laboratory Page 1 of 1 Instrument Thermo Scientific Instrument Method Drug_A_Drug_A User AMER jamie humphries Drug_A Batch Drug_A Cali File Drug_A calx Int Std Quanam z 380 20 m z 473 20 62641 27 53 96 Flag legend LOD lt J lt LOQ I lon ratio fa
199. ge RF Average RF Average RF Average RF Average RF Average RF Linear Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Linear Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Level Weighting Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Equal Origin Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Ignore Page number Units ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL ng uL
200. h Specification page where you can enter a sample ID sample name or comment You can also add or remove samples from the sample list or edit the column values for the samples See Specifying a Batch on page 187 Next Opens the Finish page where you can change the name of the batch or save the batch to the Batch View See Submitting the Batch on page 192 Cancel Immediately exits the Batch Wizard and does not save the batch There is no confirming message 196 ToxLab Forms 3 1 User Guide Thermo Scientific Specifying Sample Types 5 Using the Production Mode Working in Batch View The ToxLab Forms application uses the following sample types in all sample definitions and reports To view example standard reports specific to each sample type see Appendix A Reports Table 48 Sample type definitions Sample type Negative Calibrator QC Hydrolysis Unextracted Solvent Specimen Specimen Qual Thermo Scientific Definition Contains no target compounds but might contain an ISTD when you use the internal standard quantitative analysis technique By analyzing a negative sample you can confirm that there are no residual compounds in the solvent system that can cause erroneous results Calibrator standard Contains known amounts of all target compounds The purpose of a calibrator standard is to measure the response of the instrument to the target compounds so that the processing software can generate a c
201. h rows Available Templates BatchTemplate3 BatchTemplatez BatchTemplate Template Layout Sample Assay type Thermo Assay Quick mode MEI T r Available Methods hethodzlb level Table 44 Batch Template Selection parameters Sheet 1 of 2 Parameter Starting vial number Total batch rows Assay type Quick mode Available Templates Template Layout Available Methods 186 ToxLab Forms 3 1 User Guide Description The vial position at which you want to begin acquiring samples Default 1 The number of sample rows in the batch template The assay type specified in the master method used to create the batch template Limits the columns of information in the Batch Specification page to the following Sample Type Sample ID Injection Volume Conversion Factor All batch templates saved in the Thermo ToxLab Forms Templates Batches folder Displays sample information in the selected batch template Lists all master methods created with the same assay type as the selected batch template Thermo Scientific Table 44 Batch Template Selection parameters Sheet 2 of 2 Parameter Description Next Cancel Specifying a Batch 5 Using the Production Mode Working in Batch View Returns you to the Batch Specification page where you can enter a sample ID a sample name or comment You can also add or remove samples from the sample list or edit the c
202. h the calculated values ISTD The internal standard IST D for a target compound or surrogate if the standard type is set to Internal If you set the standard type to External this field is inactive Amount The amount of the internal standard for ISTD compounds Thermo Scientific ToxLab Forms 3 1 User Guide 113 4 Using the Method Development Mode Working with Master Methods Calibration Levels On the Calibration levels page for a master method you can define the standards for calibration You can edit calibration levels and concentrations for master methods only The contents of this page are read only when you are editing a local method To specify calibration levels and concentrations 1 Select the compound whose calibration levels and concentrations you want to define Compound 6 00 Acetamiprid 2 1 Methyldodecylamine 2 In the Manage Calibration Levels area type a value for the first calibration level The ToxLab Forms application adds a new empty calibration level row beneath the edited row 3 Continue adding calibration levels Manage Calibration levels When you finish adding calibration levels you can specify the concentrations for each level for each compound 4 To enter the concentrations to the table do the following a Select the first calibration level table cell b Click the cell again to make it editable c Type a concentration value Acq
203. hanumeric name assigned to the compound Target Compound Internal Standard or Surrogate Indicates that the QAQC check for the sample failed QAQC Flags The QAQC column is not used for Manual Integration reports Quan Flags Quantification flags include imit of Detection LOD Limit of Quantitation LOQ Limit of Reporting LOR Values between the limit of detection and the limit of quantitation known as the J flag Upper Limit of Linearity ULOL Quan flags do not apply to the following sample types Calibrator QC Negative or Solvent The Quan Flag column is not used for Manual Integration reports Manual Flags Indicates manually integrated peaks M indicates a manually integrated quan peak mindicates a manually integrated confirming peak Depending on the selected report the active view page contains any or all of the following parameters Quan peak m z Mass to charge ratio for the selected quantitation peak Total response The sum of all Quan Peak Response values for the compound Quan peak response 236 ToxLab Forms 3 1 User Guide Response of the quan peak Thermo Scientific Thermo Scientific 5 Using the Production Mode Working in Report View Table 58 Active View parameters Sheet 3 of 4 Parameter Quan peak RT Theoretical amount Concentration Confirming n Mass Confirming n Response Confirming z Manual Flag Confirming z Ion Ratio Flag Confir
204. he Insert Sample icon to insert multiple sample rows The ToxLab Forms application inserts new empty samples above the selected sample Note You cannot insert samples into an empty batch You must have at least one sample to select before you can use this icon To copy a sample 1 Select the sample you want to copy 2 Right click and choose Insert Copy Sample from the shortcut menu The ToxLab Forms application adds a copy of the sample above the selected sample Figure 36 Completed Development Batch Filename Sample name Comment Vial position Injection volume Instrument Method 10 0 Pesticides and Herbicides x T bho e 9 M Pesticides and Herbicides m Pesticides and Herbicides ees NN Oo l j 1 File SLM ie i n s Pesticides and Herbicides Pesticides and Herbicides Wes h Thermo Scientific ToxLab Forms 3 1 User Guide 155 4 Using the Method Development Mode Working with Development Batches Editing Samples in a Development Batch 156 A development batch requires fewer parameters than a real batch but the mechanism for managing the information is the same For detailed instructions about using the Copy Down or Fill Down commands to enter column values see Appendix B Using Copy Down and Fill Down Follow these procedures S ToxLab Forms 3 1 User Guide To enter column values To resize or reorganize the columns To remove selected samples f
205. he Save button is not enabled either you have entered a name that is already used or you have not selected a subproject Click Save To add samples to the list Right click the sample list pane and choose Add Sample from the shortcut menu or use the Add Sample icon to add multiple sample rows Add Sample icon The ToxLab Forms application adds the specified number of new empty samples to the end of the sample list Thermo Scientific 5 Using the Production Mode Working in Batch View To insert samples into the list 1 Select the sample above which you want to insert empty samples 2 Right click the sample list pane and choose Insert Sample from the shortcut menu or use the Insert Sample icon to insert multiple sample rows sample type Sample level Sample ID kro o mm a cal std 20 rigzuL ca std 20 Lal Std To import samples into the list 1 Click Import The Sample Import Tool dialog box opens Sample import tool Import fram a file csv or ml repertis etenim appended to the end af the list From this dialog box you can import samples from a csv file or xml file 2 Click Browse and select a csv or xml file that contains the samples you want to import 3 From the Imported Samples Will be list select Appended to the End of the List or Inserted at the Selected Row 4 Click Import The Sample Import Tool dialog box closes and the ToxLab Forms appli
206. hod Report Level Page number A Reports sample Standard Reports Page 10 of 36 ToxLab Forms 3 1 User Guide 289 A Reports sample Standard Reports 290 Method name EC25B 8level 322010 a EPAMethod8270B 8level Master method name EPAMethod8270B 8level Current calibration file EC25B 8level 322010 a calx Assay type Robustness lon range calc method Inj vol 1 000 Instrument method TargetsSplit Tune Breakdown method DFTPPSplit Report options Quan report options Report concentration Decimal places to be reported Show chromatogram on Quantitation report Display valid compound only Qual options Sort Qual results by Enable limiting peaks Limit Peaks to User interface options Shade row when sample is outside of evaluation criteria Separate ion overlay display Use alternative calibration report format Show quan flags and legend ToxLab Forms 3 1 User Guide Always True True Reverse Search Index True Top 10 by Height True True True True Method Report Page number Level 4 EnviroLab Forms settings Quan flags Flag values below LOD Flag values below LOQ Flag values above LOR Flag values above ULOL Flag values above Carryover Flag values between LOD and LOQ Correct for surrogates option Correct for surrogates False False False False False True False Page 11 of 36 Thermo Scientific A Reports sample Stand
207. hod name EC25B_8level_322010_a_EPAMethod8270B_8level Page number Page 26 of 36 Master method name EPAMethod8270B 8level Current calibration file EC25B 8level 322010 a calx Assay type Robustness lon range calc method Level 4 Inj vol 1 000 Instrument method TargetsSplit Tune Breakdown method DFTPPSplit QAQC Matrix Spike Compound Theo Conc Min Recovery 96 Max Recovery 96 Max RPD N Nitrosodimethylamine 0 000 0 00 0 00 0 00 Pyridine RCRA 0 000 0 00 0 00 0 00 2 Picoline 0 000 0 00 0 00 0 00 N Nitrosomethylethylamine APP9 0 000 0 00 0 00 0 00 Methyl methanesulfonate 0 000 0 00 0 00 0 00 2 fluorophenol sur 0 000 0 00 0 00 0 00 N Nitrosodiethylamine APP9 0 000 0 00 0 00 0 00 Ethyl methanesulfonate 0 000 0 00 0 00 0 00 phenol d5 sur 0 000 0 00 0 00 0 00 Phenol CCC 0 000 0 00 0 00 0 00 Aniline 0 000 0 00 0 00 0 00 Bis 2 chloroethyl ether 0 000 0 00 0 00 0 00 Pentachloroethane 0 000 0 00 0 00 0 00 2 chlorophenol 0 000 0 00 0 00 0 00 1 3 Dichlorobenzene 0 000 0 00 0 00 0 00 1 4 Dichlorobenzene CCC 0 000 0 00 0 00 0 00 Benzyl alcohol 0 000 0 00 0 00 0 00 1 2 Dichlorobenzene 0 000 0 00 0 00 0 00 2 methylphenol 0 000 0 00 0 00 0 00 Bis 2 chloroisopropyl ether 0 000 0 00 0 00 0 00 N Nitrosopyrrolidine APP9 0 000 0 00 0 00 0 00 3 Methylphenol amp 4 methylphenol 0 000 0 00 0 00 0 00 Acetophenone 0 000 0 00 0 00 0 00 N Nitroso di N propylamine SPCC 0 000 0 00 0 00 0 00 o toluidine APP9 0 000 0 00 0 00 0 00 Hexachloroethane 0 000 0 00 0 0
208. hromatogram pane The mass spectrum for the peak is displayed in the spectrum pane In the spectrum pane pause the cursor over the m z value for an ion A red box around the ions m z value indicates that the ion is selected Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 3 Right click to display the shortcut menu 4 Pause the cursor over Set This Mass as Quan Mass and choose one of the following commands Dont Update Ion Ratios Update Ion Ratios Using this Reference Spectrum Quan peak m z155 82 Original quan peak mass ity baolute Intens 4 8 5 0 5 2 5 4 RTimirn NL 656115 BP 200 78 Detect Relative Intensity E o Apply background subtrackion to peak and set as reference speckrum Update confirming ion ratios with this spectrum Don t update ian ratios Update ion ratios using this reference spectrum New quan peak mass 4 8 5 0 RT min Spectrum 7 NL 656115 BP 200 78 E m Relative Intensity hi o ToxLab Forms 3 1 User Guide 107 4 Using the Method Development Mode Working with Master Methods To add ions together to get an accumulated signal 1 Pause the cursor over the m z value for an ion in the Spectrum pane A red box around the ion s m z value indicates that the ion is selected 2 Right click and choose Add This Mass to Existing Quan Mass Range from the shortcu
209. ick Open Instrument Method on the Instrument View task pane An instrument method browser opens 2 In the browser select an instrument method from the list and open the file The selected method opens in the Thermo Xcalibur Instrument Setup You can edit this method and save the changes or you can save this method to another name This example instrument setup shows multiple configured instruments EA untitled Thermo Xcalibur Instrument Setup File TRACE Help So 31735 3000 25 u GS O Ha aa aa a 000 O20 O40 060 O80 100 120 140 160 1 80 200 220 240 260 280 3 00 TSU Quantum W TRACE GC Ultra Oven Enable Cryo Max Temp C 350 Post Hun Conditions Temperature 9 Time min o Pressure Left psi 05 Pressure Right psi s Acquisition Time mir Oven Runtime 500 1605 Hamps Hate Temp Hold Time Emin PC minutes Initial 40 Frep Hun Timeout min 10 00 E quilibratian Time min 0 50 C Specific Time Note Io open Help for any of your configured instruments click Help on the instrument page 152 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Development Batches Working with Development Batches In the Development Batch view you can test your instrument method in real time by creating and acquiring test samples Development batches let you test diff
210. ie Hane Table 7 Select Compound Datastore parameters Parameter Description Compounds Lists the datastores you have created for this technology Default The default datastore defined for this technology File Name File name for the new datastore Save Writes the new datastore to the specified folder Add Folder Adds a new folder where you can save the datastore Cancel Closes the dialog box and makes no changes to the datastore To remove a compound or a compounds transition information 1 In the Compound Datastore view select the row you want to delete You can remove either of the following Anentire compound including all associated transition information e A row of transition information 2 Click the Remove Transition icon E g1 or right click and choose Remove Transition from the shortcut menu 3 If you are sure you want to delete the selected row at the prompt click Yes The selected row and all items within it are deleted Tip If you add a row of compound or transition information and do not complete all the required values you can right click and choose Cancel to remove the entire row You can cancel only incomplete compound or transition rows 34 ToxLab Forms 3 1 User Guide Thermo Scientific 3 Using the Configuration Mode Compound Datastore To filter the compound list 1 To display a filtered list of compounds click the funnel icon in the column header For each column filterabl
211. ilure C Carryover Linearity limit D Detection limit Q Quan limit POS Cutoff n Negative b Solvent blank H Hydrolysis Thermo Scientific ToxLab Forms 3 1 User Guide 279 A Reports sample Standard Reports High Density Sample Report 2 Long High Density Sample Report 2 Long Lab name Thermo Fisher Laboratory Page 1 of 1 Instrument Thermo Scientific Instrument Method Drug_A_Drug_A User AMER jamie humphries Drug_A Batch Drug_A Cali File Drug_A calx Int_Std Drug_A Quan m z 380 20 Quan m z 371 20 Total Area 678044 Total Area 227568 Peak Area 678044 Peak Area 227568 RT 1 93min 1 94 RT 1 95min 1 95 Amount 15 000 ng mL Amount 5 581 ng mL TAmount 6 000 ng mL Relative Intensity Relative intensity Qual m z 473 20 Area 62641 Ratio 27 53 Range 22 33 33 49 Qual m z 479 20 Area 134976 Ratio 19 91 Range 15 69 23 54 Relative intensity Relative intensity Flag legend LOD lt J lt LOQ I lon ratio failure C Carryover Linearity limit D Detection limit Q Quan limit POS Cutoff n Negative b Solvent blank H Hydrolysis 280 ToxLab Forms 3 1 User Guide Thermo Scientific High Density Sample Report 3 Lab name Thermo Fisher Laboratory Instrument Thermo Scientific Instrument User AMER jamie humphries Batch Drug_A High Density Sample Report 3 Method Drug A Drug A Drug A Cali File Drug A calx A Reports sample Standard Reports Page 1 of 1
212. ime after injection at which the compound elutes The total time that the compound is retained on the GC column Compound The compound name call calz User defined calibration levels for the compound Manage Calibration Defines values for each of the calibration level values for the levels selected compound Shortcut menu Copy down Copies the selected column value to all rows in that column For detailed instructions about using the Copy Down command see Appendix B Using Copy Down and Fill Down ToxLab Forms 3 1 User Guide 115 4 Using the Method Development Mode Working with Master Methods Table 25 Calibration levels parameters Sheet 2 of 2 Parameter Description Display retention time Displays or hides the RT column in the compound list column Delete compound from Removes the selected compound from the current master method method QC Levels Use the QC levels page for a master method to define the standards for QC levels You can edit QC levels for master methods only The contents of this page are read only when you are editing a local method To specify OC levels and concentrations 1 Select the compound whose QC levels percentage test values and concentrations you want to define Compound Acetamiprid 1 Methyldodecylamine 2 In the QC Levels area type a name for the first QC level The ToxLab Forms application adds a new empty QC level row beneath the edited row 3 Type a value for
213. iption The injection volume in microliters of sample to be injected Minimum value 0 05 When you are using an autosampler you can set the default injection volume in the autosampler dialog box in the Instrument View The minimum and maximum injection volumes that you can use depend on the autosampler you configure The usable range depends on the injection mode and might be smaller than the range displayed Dilution applied to the injected concentration A user defined comment for the sample Adds a single empty row to the sample grid Inserts a single empty row to the sample grid above the selected row Copies the currently selected row and inserts a copy above the row Creates a copy of the selected sample and appends INJ001 to the file name Additional re injections of the same sample are numbered INJ002 INJ003 and so forth Removes selected samples from the sample grid Opens the Sample Import Tool Follow the instructions To import samples into the list on page 165 Submits all selected samples to be acquired or processed Submits all samples in the batch to be acquired or processed Opens a dialog box where you can select a raw data file to use for the selected sample row You can also browse in multiple raw data files to create multiple samples ToxLab Forms 3 1 User Guide 173 5 Using the Production Mode Working in Batch View Submitting a Batch In Batch view you can submit an entire batch or only
214. iption Specifies the High ICIS peak detection algorithm Highest peak uses the highest peak in the chromatogram for component identification Nearest RT uses the peak with the nearest retention time in the chromatogram for component identification Determines the degree of data smoothing to be performed on the active component peak prior to peak detection and integration The ICIS peak detection algorithm uses this value Range Any odd integer from 1 through 15 points Default 1 The noise level multiplier used to determine the peak edge after the location of the possible peak The ICIS peak detection algorithm uses this value Range 1 through 500 Default 5 The noise level multiplier used to determine the potential peak signal threshold The ICIS peak detection algorithm uses this value Range 1 through 1000 Default 10 The ToxLab Forms application looks for a local minima over this number of scans The ICIS peak detection algorithm uses this value Range 1 through 500 Default 40 Constrains the peak width of a component during peak integration of a chromatogram You can then set values that control when peak integration is turned on and off by specifying a peak height threshold and a tailing factor Selecting the Constrain Peak Width check box enables the Peak Height 96 and Tailing Factor options ToxLab Forms 3 1 User Guide 103 4 Using the Method Development Mode Working with Master Methods 104
215. is mass as quan mass command 110 Shade row when sample is outside of evaluation criteria parameter 157 Show chromatogram on Quantitation Report parameter 137 Showing parameter 235 Smoothing parameter Genesis 99 ICIS 103 Solvent Blank page Master Method View 126 Solvent sample type defined 197 Specify default ion ratio ranges parameter 145 Specimen sample type defined 197 Specimen Qual sample type defined 197 Spectra page 215 ToxLab Forms 3 1 User Guide 323 Index T Spectra page Peak detection settings 215 Spectrum page Master Method View 106 SRM data exporting 148 standard reports listed 4 Standard type parameter 113 starting ToxLab Forms 8 Starting vial number parameter 186 Status indicators 200 Status parameter 236 Stepoff value parameter 78 Supervisor role 26 supported file types defined 2 supported software and hardware vii system requirements vii T Tailing factor parameter Genesis 100 ICIS 104 Technician role 26 Technology selection parameter 40 Template Layout parameter 186 templates method 139 Theoretical amount parameter 237 Thermo Xcalibur Instrument Setup dialog box 73 Threshold Lower Limit parameter 127 Total batch rows parameter 186 Total response parameter 236 Trace parameter Detection 96 Tune file lifetime parameter 138 U ULOL Linearity limit parameter 120 Unextracted sample type defined 197 Units parameter 113 Update confirming ion ratios with this spectrum command 110 Uppe
216. kes the evaluation by comparing the quality check standard results for each compound in the sample to the initial calibration using values defined on this page On the Quality Control report the ToxLab Forms application flags the calculated values for internal standard compounds that exceed these limits For linear and quadratic modes the maximum difference for the calculated concentration in the QC Check sample versus the theoretical value is set on the QC levels page of the Compounds page Figure 26 OC Check page General Compounds Want Group T ie FL Ls as Weal AT Compound Mas AF Diff 2 Min RF 1 Methylene Chloride 20 00 0 000 2 4 Arsine 20 00 0 000 Table 29 QC Check parameters Parameter Description RT Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Compound The compound name Max RF Diff The maximum deviation between the response factor RF of the QC sample and the average response factor from the calibration when in average RF mode Min RF The minimum response factor for the QC sample when in average RF mode Shortcut menu Copy down Copies the selected column value to all rows in that column For detailed instructions about using the Copy Down command see Appendix B Using Copy Down and Fill Down Display retention time Displays or hides the RT column in the compound list column
217. ks with signal to noise values greater than this value are integrated Range 0 0 to 999 0 Uses the valley detection approximation method to detect unresolved peaks This method drops a vertical line from the apex of the valley between unresolved peaks to the baseline The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak The expected peak width parameter in seconds This parameter controls the minimum width that a peak is expected to have if valley detection is enabled With valley detection enabled any valley points nearer than the expected width 2 to the top of the peak are ignored If a valley point is found outside the expected peak width the ToxLab Forms application terminates the peak at that point The application always terminates a peak when the signal reaches the baseline independent of the value set for the expected peak width Range 0 0 to 999 0 Constrains the peak width of a component during peak integration of a chromatogram You can then set values that control when peak integration is turned on and off by specifying a peak height threshold and a tailing factor Selecting the Constrain Peak Width check box enables the Peak Height 96 and Tailing Factor options ToxLab Forms 3 1 User Guide 99 4 Using the Method Development Mode Working with Master Methods Table 20 Detect parameters for Standard Genesis Sheet 2 of 3 Parameter
218. lication when user security is enabled 1 Enter your assigned user name Before you can log on to the ToxLab Forms application a system administrator must set up a user account for you The administrator assigns you a user name and password and gives you permission to access specific modes 8 ToxLab Forms 3 1 User Guide Thermo Scientific 2 Getting Started Installing the ToxLab Forms Application 2 Enter your password If your user name and password do not match the system reports this error La rr Login Invalid username or password Correct the user name or password or contact your system administrator 3 Click Login The ToxLab Forms dashboard opens See ToxLab Forms Dashboard on page 14 4 To exit the ToxLab Forms application without logging on click Exit ToxLab Forms IMPORTANT If you are the administrator logging on with user security enabled use Administrator Password as the username password Figure 1 Toxlab Forms logon screen fA Thermo ToxLab Forms Welcome ww username and password 5 Exit ToxLab Forms SCIENTIFIC Table 1 Logon screen parameters Parameter Description Username The users assigned user name Password The assigned password for the user name Login Verifies the user name and password and displays the dashboard Exit ToxLab Forms Quits the ToxLab Forms application Thermo Scientific ToxLab Forms 3 1 User Guide 9 2 Getting Started Installin
219. list Moves all reports from the Displayed Reports list to the Installed Reports list Opens a browser where you can choose a report file to add to the Installed Reports list Returns the report selections to their original state when you first opened this page Applies the current selections and reminds you that you must restart the application before the report selections are available for the Method Development and Production modes ToxLab Forms 3 1 User Guide 45 3 Using the Configuration Mode Application Configuration Custom Reports Use the ToxLab Forms application to configure and import custom reports Follow these procedures To specify which custom reports are available o import new custom report types To specify which custom reports are available 1 Click the Custom Reports tab The Custom Reports page opens See Custom Reports page on page 47 2 Use the directional arrows to move reports from the Installed Reports pane to the Displayed Reports pane Tip Use the CTRL or SHIFT keys to select multiple reports All reports in the Displayed Reports pane are available to users in the Method Development and Production modes 3 To create a single report for an entire batch rather than separate reports for each sample select the Batch Level Report check box for the report type Rather than creating separate reports for each sample the application uses data from only the last sample to
220. list of compounds you want to identify Follow these procedures To add calibration data to the calibration file To identify specific compounds or groups of compounds To add calibration data to the calibration file 1 To add calibration data from another batch to the current calibration file click Extend Calibrations The Select a Calibration File to Use dialog box opens The dialog box lists only calibration batches that use the same master method as the current batch Select a calibration file to use Batches with calibration Files Calibration batch Date Methad2UB 3152010 e 3 15 2010 10 30 15 AM 194 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Batch View Select a calibration file to append to the current calibration file and click OK The ToxLab Forms application appends the selected calibration file to the current file mets gE Methad2DB 3152010 e gt Method2Ub6 3152010 g Extend Calibrations To save calibration data from both files into a single file for this batch click Create New When you are finished with the Calibration and Compound Selection page click Next The Finish page opens See Submitting the Batch on page 192 To identify specific compounds or groups of compounds In the Compound Groups area select the groups that include the compounds you want to identify in the samples In the Included Compounds area select the
221. ll and type a new name To display a filtered list of compounds use the Show list box Thermo Scientific ToxLab Forms 3 1 User Guide 83 4 Using the Method Development Mode Working with Master Methods 84 Table 16 Identification parameters Sheet 2 of 2 Parameter Description Compound type Compound types are Target Compound or Internal Standard The ToxLab Forms application uses target compounds and internal standards in quantitative analysis Active Identifies each compound to be included in data review and reporting By default all added compounds are set to active CAS No The Chemical Abstract Service CAS number that the ToxLab Forms application matched with each compound To change or add a number click the CAS No cell and enter a new number Use as RT Reference When performing peak detection with retention time standards the ToxLab Forms application first identifies those compounds identified as retention time standards and then uses their observed retention times to adjust any associated target compound Reference compound Reference compound to be used for retention time adjustment for a compound This list includes all compounds that are selected in the Use as RT Reference column Detection Use the Detection page to customize peak detection and integration for any ions that define peaks and compounds On the Detection page you can configure how characteristic ions for targeted compounds are detected and integr
222. loro 3 methylphenol CCC Safrole APP9 2 Methylnaphthalene Hexachlorocyclopentadiene SPCC 1 2 4 5 Tetrachlorobenzene 2 4 5 Trichlorophenol 2 4 6 Trichlorophenol CCC 2 fluorobiphenyl sur Isosafrole APP9 2 Chloronaphthalene Thermo Scientific EC25B 8level 322010 a EPAMethod8270B 8level EPAMethod8270B 8level EC25B 8level 322010 a calx Robustness 1 000 TargetsSplit DFTPPSplit Response Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Area Method Report lon range calc method Calibration Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Internal Curve type Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Average RF Avera
223. lues above LOR parameter 137 Flag values above ULOL parameter 137 Flag values below LOD parameter 137 Flag values below LOQ parameter 137 Flag values between LOD and LOQ parameter 137 Full name parameter 23 G General page Background subtraction range option 78 editing 72 Injection volume parameter 78 Instrument method parameter 78 Ion range calc method parameter 78 Number of scans to subtract parameter 78 Qualitative peak processing template parameter 78 Set chromatogram reference sample parameter 78 Set Reference sample parameter 78 Stepoff value parameter 78 General page Master Method View 72 Groups page Master Method View 128 ToxLab Forms 3 1 User Guide 317 Index H H Help command dashboard 14 Hydrolysis page Master Method View 127 Hydrolysis sample type defined 197 Identification page Master Method View 83 Import an Xcalibur Method dialog box 62 Import Compounds command 31 Import parameter custom 48 Import parameter standard 45 Import Xcalibur Processing Method parameter 62 Include compound peak spectrum as reference spectrum parameter 145 Include confirming ions parameter 145 Injection amount parameter 60 Injection concentration parameter 237 Injection Units parameter 237 Injection volume parameter 78 Installed Reports parameter custom 47 Installed Reports parameter standard 44 installing NIST and QED libraries 10 ToxLab Forms 8 Instrument method parameter General page 78 Meth
224. ly applicable data and interpret the data but you do not manipulate the data A QAQC user is responsible for these tasks Reviewing data from the mass spectrometer Understanding the results and who ran and passed along the results before giving intermediate approval and sending the data to management Receiving instructions for new sets of samples for the ToxLab Forms application to analyze after finishing the current analysis Note A user in the role of a QAQC technician cannot submit batches for acquisition from the Production mode Thermo Scientific ToxLab Forms 3 1 User Guide 2 3 Using the Configuration Mode Project Administration Project Administration In the role of Manager or IT Administrator you can create and manage projects and subprojects in the Project Administration view of the Configuration mode Follow these procedures To open the Project Administration view o create projects or subprojects To delete projects or subprojects To open the Project Administration view 1 Click Configuration from the dashboard or the navigation pane 7 Configuration The Configuration navigation pane opens 2 In the Configuration navigation pane click Project Administration Project Administration A The Project Administration view opens ProJect Administration Projects Project e Subproject 3 batches zig Project Subproject 7 batches ug Project e Subprojechh
225. m the shortcut menu or click the Remove Sample icon m The ToxLab Forms application removes the selected samples from the Samples list To edit sample values For each sample click the Sample Type column and select a sample type from the list Available TLF sample types Negative Solvent QC Specimen Qual Calibrator Hydrolysis Specimen Unextracted For each Calibrator or QC sample click in the Sample Level cell and select a level from the list The sample levels were defined in the master method If there is nothing to select in the Sample Level list do the following a Return to the Method Development mode b Open the method c Click the Compounds tab d Click the Calibration Levels tab e Add the levels f Savethe method g Return to the Production mode and begin this batch again You must close your original batch without saving and start a new batch For detailed instructions see Chapter 4 Using the Method Development Mode Optional Type a sample ID sample name or comment To add multiple samples of the same type In the Repeat Sample Count column type the number of samples you want to create for this sample type When you use this template to create a batch the batch will contain this number of individual samples of the specified type To specify report options To specify the type of report output to create for each report type select the check box in the appropriate c
226. mL Sample Conc 5 581 na mL Retention time 1 95 E Area Quan 227568 i Heiaht Quan 226730 i Qual ratio 1 Pass Qual ratio 2 Pass aaa ATimin Qual lon 1 473 20 Ratio 27 53 Range 22 33 33 49 100 ied aun 0 7 50 E 50 E an 30 20 10 18 15 19 201 2m 1 2 1 85 2 0 RT mim Qual lon 2 488 20 MS Data Ratio 14 0996 Range 11 43 17 1496 cal 1 Drug A 1 95 100 Relate Interiby Relative Intensity 1 85 RTTImI Zu 1 60 1 85 2 00 RT mim MS METHOD 31140 Relative Intensity Relais Intensity Thermo Scientific ToxLab Forms 3 1 User Guide 273 A Reports sample Standard Reports High Density Calibration Report High Density Calibration Report Lab name Thermo Fisher Laboratory Page 1 of 10 Instrument ThermoFisher Instrument Method EC25B 8level 322010 a EPAMethod8270B 8level User AMERYessie butler EPAMethod8270B 8level Batch EC25B 8level 322010 a Cali File EC25B 8level 322010 a calx N Nitrosodimethylamine Pyridine RCRA 2 Picoline Average RF 0 67458 RSD 6 0474 Average RF 1 44628 RSD 9 7152 Average RF 1 74213 RSD 10 9084 0 75 u 164 B u u s J o 1 0 70 1 54 18 a 0 65 g a a n 14 T L O vo o JU 0 60 34 m 16 m u 0 55 12 8 Ja J 144 0 50 1 1j 1 pes p pia S 09 s u 040 wc L 1 S 0 35 S 5s 4 S J 8 0 30 gg 06 1 er 054 0 6 0 20 24 0 15 J 044 034 J 0 10 024 024 0 05 0 1 1 0 00 ee lir e
227. me 2 Click the icon for the instrument you want to use for the method 3 Edit the values on the instrument page 4 From the main menu on Thermo Xcalibur Instrument Setup choose File gt Save As The Save As dialog box opens 150 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Instrument Methods Save As Save in C methods gt de jt EEE accelal meth le instrumenti meth My Recent Documents My Computer File name accelaz meth hu Network Save as type Methods meth Places Header Information Monday January 04 2010 4 35 44 PM Monday February 15 2010 10 19 26 AM Last saved by Number of saves 1 Comment Mew Method 5 Select an instrument method name to overwrite or type a new name for the instrument method and click Save The File Summary Information dialog box opens File Summary Information Header Created Monday February 15 2010 10 40 50 AM Last saved by Humber of saves Hot changed Comment This is a comment about my new instrument method Cancel Help 6 Optional Type a comment about the new instrument method 7 Click OK The ToxLab Forms application saves the new instrument method in the following folder Xcalibur methods Thermo Scientific ToxLab Forms 3 1 User Guide 151 4 Using the Method Development Mode Working with Instrument Methods To open an instrument method 1 Cl
228. me Quan Mass Response Inj Conc Inj Units Sample Conc Sample Units Description Retention time for the quan mass The time after injection at which the compound elutes The total time that the compound is retained on the GC column Mass range for the quan peak Sum of all Quan Peak Response values for the compound Calculated amount as the sample was injected with no conversion applied Injection units specified on the Calibration page in Method Development mode See Calibration on page 113 Calculated amount multiplied by the conversion factor Sample units specified on the Calibration page in Method Development mode See Calibration on page 113 Table 61 Calibration Curve Report Active View values Column Curve Type Average RF Average Response AO Al R 2 Thermo Scientific Description The type of curve used when calibrating the compound linear quadratic or average response factor The average response factor Applicable if curve type is Average RF The average response for the internal standard across all calibration points Applies only to Internal Standard sample types The value with no X Applies only to linear and quadratic curves The X value Applies only to linear and quadratic curves The X 2 value Applies only to quadratic curves The minimum correlation coefficient r for an acceptable calibration when in linear or quadratic mode ToxLab Forms 3 1 User
229. mine SPCC 20 00 0 50 0 990 20 000 o toluidine APP9 20 00 0 00 0 990 20 000 Hexachloroethane 20 00 0 30 0 990 20 000 nitrobenzene d5 sur 20 00 0 00 0 990 20 000 Nitrobenzene 20 00 0 20 0 990 20 000 N Nitrosopiperidine 20 00 0 00 0 990 20 000 Isophorone 20 00 0 40 0 990 20 000 2 Nitrophenol CCC 20 00 0 10 0 990 20 000 2 4 Dimethylphenol 20 00 0 20 0 990 20 000 Bis 2 chloroethoxy methane 20 00 0 30 0 990 20 000 2 4 Dichlorophenol CCC 20 00 0 20 0 990 20 000 1 2 4 Trichlorobenzene 20 00 0 00 0 990 20 000 Naphthalene 20 00 0 70 0 990 20 000 p Chloroaniline 20 00 0 01 0 990 20 000 2 6 Dichlorophenol 20 00 0 00 0 990 20 000 Hexachloropropene APP9 20 00 0 00 0 990 20 000 Hexachlorobutadiene CCC 20 00 0 01 0 990 20 000 N Nitroso di N butylamine 20 00 0 00 0 990 20 000 4 Chloro 3 methylphenol CCC 20 00 0 20 0 990 20 000 Safrole APP9 20 00 0 00 0 990 20 000 2 Methylnaphthalene 20 00 0 40 0 990 20 000 Hexachlorocyclopentadiene SPCC 20 00 0 05 0 990 20 000 1 2 4 5 Tetrachlorobenzene 20 00 0 01 0 990 20 000 2 4 5 Trichlorophenol 20 00 0 20 0 990 20 000 2 4 6 Trichlorophenol CCC 20 00 0 20 0 990 20 000 2 fluorobiphenyl sur 20 00 0 00 0 990 20 000 Isosafrole APP9 20 00 0 00 0 990 20 000 2 Chloronaphthalene 20 00 0 80 0 990 20 000 Thermo Scientific ToxLab Forms 3 1 User Guide 291 A Reports sample Standard Reports Method name Master method name Current calibration file Assay type Inj vol Instrument method Tune Breakdown method QAQ
230. ming z Ion Ratio Confirming z Range Retention Time Quan mass Response Injection concentration Injection Units Sample Concentration Sample Units Qlon RT Manual Integration reports m z Method RT Method Peak Height Description Retention time for the quan peak Theoretical amount of the compound Reports N A when not applicable Mass of the confirming peak Response of the confirming peak Indicates a manually integrated confirming peak Indicates that the ion ratio is out of range Actual ratio of the confirming ion response to the quan ion response Acceptable range for the confirming ion The time after injection at which the compound elutes The total time that the compound is retained on the GC column The mass to charge ratio used to determine the peak area and peak height of the compound Sum of all Quan Peak Response values for the compound Calculated amount as the sample was injected with no conversion applied Injection units specified on the Calibration page in Method Development mode See Calibration on page 113 The injected concentration multiplied by the conversion factor Sample units specified on the Calibration page in Method Development mode See Calibration on page 113 Mass range for the quan peak Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Mass to charge ratio f
231. modes From the Reports page you can configure standard reports or custom reports This section includes configuration instructions for the following reports Standard Reports Custom Reports To open the Reports page of the Application Configuration view 1 Click Configuration from the dashboard or the navigation pane The Configuration navigation pane opens 2 Click Application Configuration The General page of the Application Configuration view opens 3 Click the Reports tab The Reports page of the Application Configuration view opens 42 ToxLab Forms 3 1 User Guide Thermo Scientific Standard Reports Thermo Scientific 3 Using the Configuration Mode Application Configuration The ToxLab Forms application supplies standard reports Example PDFs of standard report formats are located in the following folder C Thermo Shared ExampleReports Follow these procedures S To specify which standard reports are available To import new standard report types To specify which standard reports are available Click the Standard Reports tab The Standard Reports page opens This page is the default when you first open the Reports page See Standard Reports page on page 44 Use the directional arrows to move reports from the Installed Reports pane to the Displayed Reports pane Tip Use the CTRL or SHIFT keys to select multiple reports All reports in the Displayed Reports pane are a
232. ms 3 1 User Guide Level Max recovery 96 150 00 150 00 150 00 150 00 150 00 150 00 Page number Min RT min 0 25 0 25 0 25 0 25 0 25 0 25 Max RT min 0 25 0 25 0 25 0 25 0 25 0 25 Page 21 of 36 Thermo Scientific A Reports sample Standard Reports Method Report Method name EC25B_8level_322010_a_EPAMethod8270B_8level Page number Page 22 of 36 Master method name EPAMethod8270B 8level Current calibration file EC25B 8level 322010 a calx Assay type Robustness lon range calc method Level 4 Inj vol 1 000 Instrument method TargetsSplit Tune Breakdown method DFTPPSplit QAQC Solvent Blank Compound Method Upper Limit 96 N Nitrosodimethylamine None Pyridine RCRA None 2 Picoline None N Nitrosomethylethylamine APP9 None Methyl methanesulfonate None 2 fluorophenol sur None N Nitrosodiethylamine APP9 None Ethyl methanesulfonate None phenol d5 sur None Phenol CCC None Aniline None Bis 2 chloroethyl ether None Pentachloroethane None 2 chlorophenol None 1 3 Dichlorobenzene None 1 4 DICHLOROBENZENE D4 IS None 1 4 Dichlorobenzene CCC None Benzyl_alcohol None 1 2 Dichlorobenzene None 2 methylphenol None Bis 2 chloroisopropyl ether None N Nitrosopyrrolidine_APP9 None 3 Methylphenol amp 4 methylphenol None Acetophenone None N Nitroso di N propylamine SPCC None o toluidine_APP9 None Hexachloroethane None nitrobenzene d5 sur None Nitrobenzene None N Nitrosopiperidine None Isophorone No
233. n Mode Working in Batch View To simplify the sample list Select the Quick Mode check box In Quick Mode the Batch Specification page displays only the following columns Sample Type Sample ID Injection Volume e Conversion Factor Note The shortcut menu and its functions are not available when Quick Mode is selected To add samples to the batch 1 Right click and choose Add Sample from the shortcut menu or click the add sample icon Tes The ToxLab Forms application adds a new Specimen sample to the end of the sample list 2 In the Filename column for each sample type a file name Note Alternately you can right click and choose Browse in Raw File from the shortcut menu Follow the instructions To browse in a raw data file on page 190 3 Select a sample type from the Sample Type list box for each sample Available TLF sample types Negative Solvent QC Specimen Qual Calibrator Hydrolysis Specimen Unextracted For a detailed description of sample types see Specifying Sample Types on page 197 4 For each Calibrator or QC sample select a level from the Sample Level list The sample levels are defined in the master method If there are no levels to select from the Sample Level list a user with Supervisor or Manager permissions must edit the method and specify the levels For detailed instructions about defining sample levels see Chapter 4 Using the Method Development Mode 5 In th
234. n linear or quadratic mode Relative standard deviation Applies only to internal standards and targets calibrated with an average RF curve The column specifies the level name the field value specifies the data point used in calibration This field can be Response Factor for external calibration Response Ratio for internal linear or quadratic or Relative Response factor for Internal Average RE There will be one column for each level in the curve If the batch uses an extended calibration there might be more columns than calibration standards in the current batch Thermo Scientific Thermo Scientific 5 Using the Production Mode Working in Report View Table 63 High Density 1 and High Density 1 Long Report Active View values Column Description m z Mass to charge ratio for the quan peak Total Response The sum of all Quan Peak Response values for the compound Quan Peak Response Response of the quan peak Quan Peak RT Retention time for the quan peak T Amount Theoretical amount of the compound Reports N A when not applicable Conc Calculated injected amount Table 64 High Density 2 and High Density 2 Long Report Active View values Column m z Total Response Quan Peak Response Quan Peak RT T Amount Conc Confirming 1 Mass Confirming 1 Response Confirming 1 Manual Flag Confirming 1 Ion Ratio Flag Confirming 1 Ion Ratio Confirming 1 Range Description Mass to charge ratio for the quan peak Sum o
235. n range calc method Method Report Theo Conc 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 40 000 Level Min Recovery 96 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 80 00 Page number Max Recovery 96 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 120 00 A Reports sample Standard Reports Page 32 of 36 Max RSD 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 20 00 2
236. n the selected peak and library entries Search index method used to search the NIST library Reverse search index method used to search the NIST library Match probability Library compound that matches the identified peak ToxLab Forms 3 1 User Guide 229 5 Using the Production Mode Working in Report View Working in Report View Use the Report View to display the reports for the batch currently selected in the Data Review view or to display the Active View for the reports 4 To open the Report View 1 Click Production from the dashboard or the navigation pane Production The Production navigation pane opens 2 From the Production navigation pane click Report View Report View E From the Report View you can access the following pages Displaying the Report View Page Displaying the Active View Page Displaying the Report View Page Use the Report View page to select a report and navigate the report display 4 To display the Report View page Click the Report View tab The Report View page is the default page To display a report 1 Select a report type from the Select a Report list Only the report types created for the current batch are displayed in the list 2 Optional When the report type includes separate reports for each sample select a sample file ala r Calibration Report x Sample file AP UT k Note All report types create separate reports for each sample except the standard
237. n view in Configuration mode is hidden and cannot be edited Note By default user security is not enabled IMPORTANT If you are the administrator logging on with user security enabled use Administrator Password as the username password Immediately create an account with Manager or IT Administrator permissions for yourself To specify a datastore to use in method development 1 In the Compound Datastore Selection area select the Enable Compound Datastore check box Note By default the Enable Compound Datastore option is not selected 2 Click Select The Select Compound Datastore dialog box opens Select Compound Datastore EEE COS CDS2 Default Cancel 3 Select a compound datastore from the list 4 Do one of the following e To use the selected datastore for all methods click Select Or To close the Select Compound Datastore dialog box and keep the currently specified datastore click Cancel 5 In the Application Configuration view click Apply 38 ToxLab Forms 3 1 User Guide Thermo Scientific 3 Using the Configuration Mode Application Configuration 6 When you are prompted to restart your application click Yes When the application restarts the following changes are implemented The application displays the Acquisition List page on the Compounds page in the Master Method View See Editing the Compounds Page on page 79 The application displays the Compou
238. nal Standards 2 At the bottom of the Groups area click Add Group The Add a New Group dialog box opens 3 Type a name for the new group and click OK The new group appears in the Groups area 4 Drag a compound from the Compounds area onto a group name as if you were moving files into a folder 5 To remove all the compounds from a group rename the group or delete it right click the group name and choose from the shortcut menu H Quan Group a Empty group oo Alac Rename group Delete group 6 To remove a single compound click the compound name in the group right click and choose Remove from Group from the shortcut menu 128 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 31 Groups page Calibration file last used Z2 Juan compounds General Compounds l Com pour d Methylene Chloride F Quan Group Arsine 0 0 Phenol 3 methyl Phenol 3 methyl Q rine BH Purin b ane 1 7 dihwdra E Ir Target Group o Chloroaniline eo Hydrogen bromide Naphthalene 2 methy Q Diethyl Phthalate Benzene 1 2 4 5 tetrachlora I ISTO Group Biphenylene CO Methylene Chloride Biphenvlene 2 TM Naphthalene z maethul Hydrogen bromide Add Group Table 35 Groups parameters Parameter Description Compounds Lists all available compounds Groups Lists all available groups Add Group Opens the Add a New Grou
239. nd Datastore task pane on the Configuration mode navigation pane See Compound Datastore on page 30 The application enables the Export SRM Data command in the Method Development mode See Exporting SRM Data on page 148 To specify a default laboratory name instrument name and mass precision 1 In the Defaults area type the name of your laboratory in the Lab Name box When you create a method this default laboratory name is used for the Laboratory Name value on the General page of the Master Method View This laboratory name is also used in the headings of reports Note This default laboratory name is not applied to previously created methods By default the laboratory name is ThermoFisher Laboratory 2 In the Defaults area type the name of your instrument in the Instrument Name box When you create a batch this default instrument name is used for the Instrument Name value This instrument name is also used in the headings of reports Note This default instrument name is not applied to previously created batches By default the instrument name is T hermoFisher Instrument 3 In the Defaults area in the Display Mass Precision box set the mass precision decimal places value to an integer from 0 through 5 The default mass precision is 2 The ToxLab Forms application uses this mass precision value in the following locations Reports Confirmation report data spectra library spectra quan ion displ
240. nd graphical values displayed in the Qual Mode pane The Flags column in the Samples list displays a caution flag if the sample is not in compliance with the method criteria Method cal batch cal test Instrument Thermofisher Was Status Flags Filename Sample type Sample level Sample ID 2 Q A ums oma Cealte Sark sample flags Status indicators To open a dialog box with a list of problems found in the sample click the caution flag The dialog box does not list compounds that are not found in Specimen sample types Status Indicators Status indicators show the current status of each sample during the acquisition and processing Orange for samples that are currently acquiring Blue for samples that have not been acquired Yellow for samples that have been acquired and not processed Green for samples that have been acquired and processed 200 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 5 Using the Production Mode Working in Data Review Sample Flags Sample flags are displayed when compounds within the samples have an error Sample caution flags remain static when you switch between compounds for chromatogram review until a change is completed for example when a compound is manually integrated and no longer falls outside the accepted criteria Sample caution flags list a summary of all compound indicator messages within the sample when you pause the cursor over the flag
241. nd in the sample to a specified range If all of your target compounds are set to external calibration mode or you have not identified any compounds as internal standards this page does not show any values Figure 28 STD page General Compounds Qar Groups I Reports I Limits Calibration OC Check Negative eee ee HT Compound Min recovery Z Max recovery z Min AT min Mas AT mir 1 151 Methylene Chloride 50 00 150 00 025 025 k 2 46 78 Naphthalene 2 methul p 25 Table 31 ISTD parameters Sheet 1 of 2 Parameter Description RT Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Compound The compound name 124 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 31 ISTD parameters Sheet 2 of 2 Parameter Min recovery 96 Max recovery 96 Min RT min Max RT min CV Test 96 Shortcut menu Copy down Display retention time column Delete compound from method Description The minimum and maximum percent recoveries for the internal standards to define an acceptable range For check standards the ToxLab Forms application compares the response of each internal standard in each sample to a
242. ne 2 Nitrophenol CCC None 2 4 Dimethylphenol None Bis 2 chloroethoxy methane None 2 4 Dichlorophenol CCC None 1 2 4 Trichlorobenzene None NAPHTHALENE D8 IS None Naphthalene None p Chloroaniline None 2 6 Dichlorophenol None Hexachloropropene_APP9 None Hexachlorobutadiene CCC None N Nitroso di N butylamine None 4 Chloro 3 methylphenol CCC None Safrole_APP9 None 2 Methylnaphthalene None Hexachlorocyclopentadiene SPCC None 1 2 4 5 Tetrachlorobenzene None 2 4 5 Trichlorophenol None 2 4 6 Trichlorophenol CCC None 2 fluorobiphenyl sur None Isosafrole APP9 None 2 Chloronaphthalene None 2 Nitroaniline None 1 4 Naphthoquinone APP9 None Thermo Scientific ToxLab Forms 3 1 User Guide 295 A Reports sample Standard Reports 296 Method name Master method name Current calibration file Assay type Inj vol Instrument method Tune Breakdown method QAQC Surrogates Compound phenol d5 sur nitrobenzene d5 sur 2 4 6 tribromophenol sur p terphenyl d14 sur EC25B 8level 322010 a EPAMethod8270B 8level EPAMethod8270B 8level EC25B 8level 322010 a calx Robustness lon range calc method 1 000 TargetsSplit DFTPPSplit ToxLab Forms 3 1 User Guide Level Theo Conc 40 000 40 000 40 000 40 000 Page number Min Recovery 96 70 00 70 00 70 00 70 00 Page 25 of 36 Max Recovery 96 130 00 130 00 130 00 130 00 Thermo Scientific A Reports sample Standard Reports Method Report Met
243. ne Breakdown method QAQC Lab Control Compound N Nitrosodimethylamine Pyridine RCRA 2 Picoline N Nitrosomethylethylamine APP9 Methyl methanesulfonate 2 fluorophenol sur N Nitrosodiethylamine APP9 Ethyl methanesulfonate phenol d5 sur Phenol CCC Aniline Bis 2 chloroethyl ether Pentachloroethane 2 chlorophenol 1 3 Dichlorobenzene 1 4 Dichlorobenzene CCC Benzyl_alcohol 1 2 Dichlorobenzene 2 methylphenol Bis 2 chloroisopropyl ether N Nitrosopyrrolidine_APP9 3 Methylphenol amp 4 methylphenol Acetophenone N Nitroso di N propylamine SPCC o toluidine APP9 Hexachloroethane nitrobenzene d5 sur Nitrobenzene N Nitrosopiperidine Isophorone 2 Nitrophenol CCC 2 4 Dimethylphenol Bis 2 chloroethoxy methane 2 4 Dichlorophenol CCC 1 2 4 Trichlorobenzene Naphthalene p Chloroaniline 2 6 Dichlorophenol Hexachloropropene_APP9 Hexachlorobutadiene CCC N Nitroso di N butylamine 4 Chloro 3 methylphenol CCC Safrole_APP9 2 Methylnaphthalene Hexachlorocyclopentadiene SPCC 1 2 4 5 Tetrachlorobenzene 2 4 5 Trichlorophenol 2 4 6 Trichlorophenol CCC 2 fluorobiphenyl sur Isosafrole APP9 2 Chloronaphthalene 2 Nitroaniline 1 4 Naphthoquinone APP9 Dimethyl phthalate 1 3 Dinitrobenzene app9 2 6 Dinitrotoluene EC25B 8level 322010 a EPAMethod8270B 8level EPAMethod8270B 8level EC25B 8level 322010 a calx Robustness 1 000 TargetsSplit DFTPPSplit 298 ToxLab Forms 3 1 User Guide lon range calc method
244. ng the noise than the INCOS Noise algorithm but the analysis takes longer The minimum number of scans required in a peak The ICIS peak detection algorithm uses this value Range 0 to 100 scans Default 3 The minimum separation in scans between the apexes of two potential peaks This is a criteria to determine if two peaks are resolved The ICIS peak detection algorithm uses this value Range 1 to 500 scans Default 10 Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 21 Detect parameters for High ICIS Sheet 3 of 3 Parameter Area tail extension Area scan window RMS Description The number of scans past the peak endpoint to use in averaging the intensity The ICIS peak detection algorithm uses this value Range 0 to 100 scans Default 5 The number of allowable scans on each side of the peak apex A zero value defines all scans peak start to peak end to be included in the area integration Range 0 to 100 scans Default 0 Specifies that the ToxLab Forms application calculate noise as RMS By default the application uses Peak To Peak for the noise calculation RMS is automatically selected if you manually determine the noise region ToxLab Forms 3 1 User Guide 105 4 Using the Method Development Mode Working with Master Methods Spectrum Use the Spectrum page to store a reference mass spectrum for a quan peak or compound Foll
245. nu Sheet 1 of 2 Command Method integration settings Manual integration settings Add peak Remove peak Cancel add peak Description Displays method integration settings Displays manual integration settings Adds a peak removes a peak or cancels an add peak Operation in progress ToxLab Forms 3 1 User Guide 211 5 Using the Production Mode Working in Data Review Table 50 Quantification Peak shortcut menu Sheet 2 of 2 iption Confirming ion list Selects the confirming ions to be viewed Peak labels Displays or hides the peak labels Label Area Label Retention Time Label Height or Label Signal to Noise Show peak info Displays peak information for the selected compound For example methyltestosterone Reset scaling Resets the original scaling after a zoom operation Peak detection settings Opens the Peak Detection Settings dialog box for the selected compound See Peak Detection Settings on page 213 212 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Data Review Peak Detection Settings Use the Peak Detection Settings dialog box to adjust detection settings that were specified in the method Peak detection settings 2 Propyn 1 amine N methyl DuanPeakl Quan peak Confirming peak 1 Confirming p e o ug c gc k Go G tc C m GE GC GC m l m m c em c cm Lr em rl Relative Intensity iho Las tn o
246. o remove a peak Right click the chromatogram plot and choose Remove Peak from the shortcut menu The ToxLab Forms application removes the peak displayed in the Qual Peak pane AII data for this peak is removed from the Qual Mode panes To switch between method and manual integration modes Right click the chromatogram view and choose Method Integration or Manual Integration from the shortcut menu Initially the method and manual integration settings that are stored for a compound and file are identical and when you select one mode it does not affect the saved result set However when manual data are available the chromatogram plots and the result set update as you switch between method and manual modes As you switch between modes the changes are reflected in each pane The generated reports for this data identify the manual modifications To change the displayed information for detected peaks 1 Right click the chromatogram plot and pause the cursor over Peak Labels 2 Choose to display labels for the peak retention time peak height peak area or signal to noise The label types in the list are selected for displayed labels and cleared for labels that are not displayed 3 To remove a label select the label type again and clear it Label settings are globally applied to qual peaks confirming peaks and internal standard peaks Note The labels do not always update on all peak displays To update all labels selec
247. od Forge 60 Instrument Name parameter 41 Instrument view 149 instruments supported vii Ion Overlay page 219 Ion Overlay page Peak detection settings 219 Ion range calc method parameter 78 Ionization parameter Acquisition List 81 Compound datastore 35 ISTD matching min parameter 147 ISTD page Master Method View 124 ISTD parameter 113 IT Administrator role 25 L Lab name parameter 77 Laboratory Name parameter 41 Lens parameter Acquisition List 82 Compound datastore 36 Level parameter 118 Limit library hits parameter 145 318 ToxLab Forms 3 1 User Guide Limit the retention time range parameter 145 Limits page Master Method View 119 Load Compound Datastore command 31 Local Method view 248 LOD Detection limit parameter 119 Log Off command 14 logging on to EnviroLab Forms 8 Login parameter 9 logon screen 9 LOQ Quantitation limit parameter 119 LOR Reporting limit parameter 119 m z parameter Detection 97 Manager role 25 Manual Flags parameter 236 Manual injection parameter 60 Master Method View Acquisition List page 79 Blank page 123 Calibration Levels page 114 Calibration page 113 Compounds page 79 Detection page 84 General page 72 Groups page 128 Hydrolysis page 127 Identification page 83 ISTD page 124 Limits page 119 QAQC page 119 QAQC page Calibration page 121 QC Check page 122 QC Levels page 116 Ratios page 111 Reports page 130 Solvent Blank page 126 Spectrum page 106 Max Amt Diff p
248. of Cutott ka 1 00 B Naphthalene Z methyl Concentration 0 000 Table 30 Blank parameters Sheet 1 of 2 Parameter Description RT Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Compound The compound name Thermo Scientific ToxLab Forms 3 1 User Guide 123 4 Using the Method Development Mode Working with Master Methods Table 30 Blank parameters Sheet 2 of 2 Parameter Description Method The evaluation process used for comparing the calculated concentration You can specify no maximum a specific concentration or a percentage of the cutoff LOR LOD or LOQ Percentage The percentage of the cutoff LOR LOD or LOQ if you are using the percentage approach Max Conc The maximum concentration if you are using an absolute value Shortcut menu Copy down Copies the selected column value to all rows in that column For detailed instructions about using the Copy Down command see Appendix B Using Copy Down and Fill Down Display retention time Displays or hides the RT column in the compound list column Delete compound from Removes the selected compound from the current master method method ISTD Use the ISTD page to review the response and retention time of internal standards if available The ToxLab Forms application makes the evaluation by comparing the area and retention time results for each internal standard compou
249. of the calibration curve Calibrants are weighted by the inverse of their response or response ratio 1 Y 2 Specifies a weighting of 1 Y 2 for all calibration data points during the least squares regression calculation of the calibration curve Calibrants are weighted by the inverse of the square of their response or response ratio Response via Specifies if the ToxLab Forms application uses area or height in response calculations 146 ToxLab Forms 3 1 User Guide Area Specifies that the application use this peak area value in response calculations Height Specifies that the application use this peak height value in response calculations Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 39 Method Template Editor parameters Sheet 3 of 3 Parameter Description Qualitative Peak Processing ISTD matching Excludes all the target compounds found in the method and does min not list these compounds in the TIC Report or in the Qual Mode view in the Data Review Exclude matching quan Compares the retention time of the internal standard in the peaks method to the found retention time of the internal standard in the library search and excludes peaks outside the range Thermo Scientific ToxLab Forms 3 1 User Guide 147 4 Using the Method Development Mode Working with Master Methods Exporting SRM Data In the ToxLab Forms application you can export your selected reaction moni
250. oject ewell i level levels Select a reference sample from the right panel and click Dpen Note If you are using a ToxLab Forms 2 5 method you will not see any reference samples here You must first create and save a batch using the ToxLab Forms 2 5 method 3 Select a project from the list of projects 4 Select a subproject from the list of subprojects 5 Select a batch from the list of batches The ToxLab Forms application displays only batches that were created using the same master method as the current batch 6 Select a sample from the list of processed samples The ToxLab Forms application displays all the processed samples in the selected batch To use a sample as a reference sample it must have been acquired and processed with the current master method 7 Click Open The selected sample is displayed as the chromatogram reference sample in the Master Method View Tip To clear the reference sample from the master method click Set Chromatogram Reference Sample and select None from the list 16 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 11 General page Lab name ThermoFisher Laboratory ECT TESI Assay name Injection volume 10 Instrument method Qualitative peak pr ing template eS Ee BEE Mone Humber of scans to subtract Background subtraction range option vi v
251. olumn Thermo Scientific 5 Using the Production Mode Working in Batch View 2 To duplicate the output type for all reports click the cell to select it then right click and choose Copy Down from the shortcut menu Print Create PDF Create ML All check boxes in the column below the selected cell duplicate the selected or cleared state of the selected cell By default all report output types are cleared To specify active compounds 1 In the sample table click anywhere in the sample row to select the sample for which you want to specify active compounds Compound selections are specific to a sample You can select different compounds for each of the samples even if they are the same sample type 2 In the Compound Active Status area select the Active check box for each compound you want to identify in the selected sample If you have created compound groups you can make the entire group active or inactive Right click and choose the group from the list Compound Active Status All uan Group Quan Group Mon Quan Group Mon Quan Group Inactive groups Active groups Active wem m Amina All N Atrazine DE Al dochlor All Quan Group Quan Group Target Group Target Group Inactive groups Active groups Figure 43 Batch Template Editor Thermo Scientific ToxLab Forms 3 1 User Guide 181 5 Using the Production Mode Working in Batch View B
252. olumn values for the samples See Specifying a Batch on page 187 There is no confirming message Immediately exits the Batch Wizard and does not save the batch From the Batch Specification page you must enter either a sample ID sample name or comment You can also add or remove samples from the sample list or edit the column values for the samples The batch template might contain many samples that you do not want to use for your batch If you do not enter a sample ID sample name or comment for these samples the ToxLab Forms application discards them when you save the batch S l To enter a sample ID sample name or comment In the Sample ID column type an identifier The identifier can be any text string In the Sample Name column type a name The name can be any text string In the Comment column type a comment The comment can be any text string Note The ToxLab Forms application requires at least one of these fields to acquire a sample When the batch begins acquisition it discards any sample that does not have a value in at least one of these fields Follow these procedures Thermo Scientific To simplify the sample list To add samples to the batch To remove samples from the batch To insert samples into the batch To copy a sample To move a sample up or down in the sample list To browse in a raw data file ToxLab Forms 3 1 User Guide 187 5 Using the Productio
253. ompound name Compound type QAQC flags Quan flags Manual flags 240 ToxLab Forms 3 1 User Guide Description The status of the reported compound A yellow caution sign indicates one of the following conditions The compound was manually integrated Any of the confirming peaks was manually integrated The compound has quan flags The compound has a QAQC failure A green check mark indicates that none of these conditions exist When the compound is an internal standard warning flags are displayed only on the internal standard report Alphanumeric name assigned to the compound Target Compound Internal Standard or Surrogate Indicates that the QAQC check for the sample failed Quan flags include Limit of Detection LOD Limit of Quantitation LOQ Limit of Reporting LOR Values between the limit of detection and the limit of quantitation known as the J flag Upper Limit of Linearity ULOL Quan flags do not apply to the following sample types Calibrator QC Negative or Solvent This column is not included on the Calibration report This column is not included on the Calibration Curve report Indicates manually integrated peaks M indicates a manually integrated quan peak mindicates a manually integrated confirming peak Thermo Scientific 5 Using the Production Mode Working in Report View Table 60 Blank Report Active View values Column Retention Ti
254. on Security Groups v User Listing lt All groups Username Role IT Administrator mama Account Humber Phone Number Email Address Enabled Manage u IT Admiristrator ee Technician M Wem emm 1 1 Tg Tenn LRL Thermo Scientific IT Administrator Table 5 User Administration parameters Sheet 1 of 2 Security Groups User Listing Username Role Account Number Phone Number Email Address Enabled User Username Role Password Full name Account number All permission levels defined in the ToxLab Forms application For detailed descriptions of user permissions see User Roles on page 25 User logon names The security group that defines user permissions User account numbers User telephone numbers User e mail addresses Available or unavailable status for the user account Logon name for this user Security group that defines this users permissions Logon password for this user The users actual name Optional account number for this user ToxLab Forms 3 1 User Guide 23 3 Using the Configuration Mode User Administration 24 Table 5 User Administration parameters Sheet 2 of 2 Parameter Phone number Email address Enabled Icon Function Add user Remove user F ea Edit user Save changes Cancel changes ToxLab Forms 3 1 User Guide Description Optional telephone number for this user E mail address for this user Used
255. on The Identification page lists the compounds that are targeted for analysis reporting and other compound specific values To filter the displayed compounds From the Show list box select the type of compounds you want to display in the compounds list Show Quan compounds Juan compounds Target compounds Internal Standards Compound Type Description Quan compounds Displays only quan compounds such as target compounds and internal standards Target compounds Displays only target compounds Internal Standards Displays only internal standard compounds Figure 13 Identification page Compounds LAE Groups Reports Identification Detechon Calibration Calibration levels evels General Acquisition List HI Compound Compound type A amp clve CAS No Use as HT Reference Reference compound 2 1 4 Dichlorobenzene Internal Standard m HM Table 16 Identification parameters Sheet 1 of 2 L Parameter Description RT Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column RT and Window values are used to determine the start and stop time for the acquisition Range 0 00 to 999 00 Start time RT Window 2 Stop time RT Window 2 Start and stop range 0 00 to 999 00 Compound A list of compounds that have been identified To customize the compound names click the ce
256. on level security Technology selection Defaults to Gas Chromatography GC 40 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 3 Using the Configuration Mode Application Configuration Table 9 General configuration parameters Sheet 2 of 2 Parameter Compound Datastore selection Defaults Lab name Instrument name Display mass precision Chromatogram Intensity Scale Description Enable compound datastore Enables the Acquisition List page on the Compounds page in the Master Method View and displays the Compound Datastore task pane on the Configuration mode navigation pane Select Opens a browser where you can select a saved datastore xml file Specifies the default laboratory name used for methods Default ThermoFisher Laboratory Specifies the default instrument name used for batches Default ThermoFisher Instrument Specifies the number of decimal places used to display mass precision Valid values any integer between 0 and 5 inclusive Specifies the type of chromatogram display in data review and reports ToxLab Forms 3 1 User Guide 41 3 Using the Configuration Mode Application Configuration Specifying the Reports Configuration In the Application Configuration view of the Configuration mode as a user in the role of Manager or IT Administrator you can configure a list of reports that are available to users when they generate reports from the Method Development or Production
257. or the quan peak Apex retention time for the method integrated peak Height of the method integrated peak ToxLab Forms 3 1 User Guide 237 5 Using the Production Mode Working in Report View Table 58 Active View parameters Sheet 4 of 4 Parameter Method Peak Area Manual RT Manual Peak Height Manual Peak Area Internal Standard reports Std Response Minimum Response Maximum Response Sample Response Std RT Min RT Max RT Sample RT Graphical data Quan Peak 1 Calibration curve Spectra Confirming Ions ToxLab Forms 3 1 User Guide Description Area of the method integrated peak Apex retention time for the manually integrated peak Height of the manually integrated peak Area of the manually integrated peak Average of the internal standard s response as found in the calibration file Minimum response time as specified on the ISTD page in Method Development mode See IS TD on page 124 Maximum response time as specified on the ISTD page in Method Development mode See ISTD on page 124 Area found in the sample Average retention time as found in the calibration file Minimum retention time as specified on the ISTD page in Method Development mode See ISTD on page 124 Maximum retention time as specified on the ISTD page in Method Development mode See ISTD on page 124 Retention time found in the sample Displays a graphical view of the calibration curve for the select
258. or the raw data file Defines the retention time and window for a quan peak See Times on page 95 Defines the detector and its parameters used to display each chromatogram trace See Signal on page 96 Defines the peak detection algorithm and its options See Detect on page 98 Defines a reference mass spectrum for a quan peak or compound See Spectrum on page 106 Defines the criteria for evaluating confirming or qualifying ions See Ratios on page 111 Thermo Scientific Thermo Scientific Times 4 Using the Method Development Mode Working with Master Methods Use the Times page to define the retention time and window for a quan peak Figure 15 Times page QuanPekl Quan peak 465 30 gt 419 76 0 23 Relative Intensity j Lo E ot o oo 82 Oo Oo QG a 0 2 Times Signal RT min 0 4 0 6 Expected AT min Window SEC M EI width mir I Table 18 Times parameters Parameter Expected RT min Window sec View width min Description Expected retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Width of the window in seconds of how far around the expected retention time the system will look for a peak apex Viewable size of the ion chromatogram display Changing the view width does not affect the process of peak detection the ToxL
259. ore specified for the gas chromatography technology Select compounds to add App 2 Select the check box for each of the compounds you want to add to the method and click Apply The ToxLab Forms application adds the compounds to the Acquisition List and Compounds pages of the Master Method View 80 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 12 Acquisition List page General Compounds Acquisition List Identification Reports Calibration Calibration levels OIC level Table 15 Acquisition List parameters Sheet 1 of 2 Parameter Function Icon Compound parameter Compound Name Category Ionization Chemical Formula Thermo Scientific Description Opens the Select Compounds to Add dialog box that lists all the compounds defined in the compound datastore specified for the gas chromatography technology Deletes the selected compound transition The icon is unavailable when no row is selected If you have used the filters to display a subset of compounds the selected compound might not be visible in the Acquisition List page Alphanumeric name assigned to the compound Optional Alphanumeric identifier Optional Alphanumeric identifier Valid values ESI APCI EI CI APPI Optional Alphanumeric chemical identifier ToxLab Forms 3 1 User Guide 81 4 Using the Method Development Mode Working wi
260. orms 3 1 User Guide 0 23 E 0 59 0 2 0 4 0 6 Confirming peak 1 465 30 420 38 nr je Relative Intensity amp om c o D O28 D o1 La D Signal Detect Ratios e Standard Genesis Smoothing SAN threshold I Enable valley detection Expected width sec 0 00 MH Constan peak width Peak height Tailing factor Min peak height 5 M Peak 5 M cutoff LT 3 el 3 Valley S N H background sc Report noise as BNE Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Table 20 Detect parameters for Standard Genesis Sheet 1 of 3 Parameter Sensitivity Detection method Smoothing S N threshold Enable valley detection Expected width sec Constrain peak width Description Specifies the Standard Genesis peak detection algorithm Highest peak Uses the highest peak in the chromatogram for component identification Nearest RT Uses the peak with the nearest retention time in the chromatogram for component identification Determines the degree of data smoothing to be performed on the active component peak prior to peak detection and integration The ICIS peak detection algorithm uses this value Range Any odd integer from 1 through 15 points Default 1 Current signal to noise threshold for peak integration Peaks with signal to noise values less than this value are not integrated Pea
261. ou can also select an appropriate combination of method and batch template Column values 182 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Batch View Table 43 Batch Template Editor parameters Sheet 2 of 2 Parameter Sample type Sample level Sample ID Sample name Comment Repeat sample count Standard Report Name Print Create PDF Create XML Custom Report Name Print Create XLS Batch Level Report Name Print Create XLS Compound Active Status Compound name Active Description Defines how the ToxLab Forms application processes the sample data Each sample is classified as one of the following sample types Negative Calibrator QC Specimen Specimen Qual Solvent Hydrolysis Unextracted The level defined for a calibration sample or quality control sample A user defined alphanumeric string that identifies a sample A user defined name that identifies a sample A user defined comment for the sample Number of samples to create for this sample type The name of a report Reports to be sent to the printer Reports to be saved as PDF files Reports to be exported in XML format The name of a report Reports to be sent to the printer Reports to be exported in XLS format The name of a report Reports to be sent to the printer Reports to be exported in XLS format List of all compounds for the method Identifies compounds to identify in the
262. out using the Copy Down command see Appendix B Using Copy Down and Fill Down Displays or hides the RT column in the compound list Removes the selected compound from the current master method ToxLab Forms 3 1 User Guide 127 4 Using the Method Development Mode Working with Master Methods Editing the Groups Page Use the Groups page of the Master Method View to organize compounds into functional or logical groups You can use these groups for creating a subset of target compounds for quantitative processing See Groups page on page 129 For quantitative processing the ToxLab Forms application processes all compounds in the method and stores the complete result set but only those in the selected group are visible in the Production mode Limiting the displayed compounds to those in the selected group can be useful when working with a master method containing a large list of compounds only some of which are required for analysis in certain samples In that case the application requires only a single method and can reduce the results To display only those compounds to be used in quantitative processing select Quan Compounds from the Show list box You can create as many groups as you want and the same compound can be included in multiple groups 4 To create a group 1 From the Show list box select the type of compounds you want to view Show Guan compounds Quan compounds Target compounds Inter
263. ow these procedures S S 106 ToxLab Forms 3 1 User Guide To apply or remove the background subtraction To update confirming ion ratios To change the quantitation mass used for a quan peak To add ions together to get an accumulated signal To add a quan peak to an existing compound To add one or more confirming ions to an existing compound To zoom in the chromatogram or spectrum displays To apply or remove the background subtraction Right click the Spectrum pane and choose Apply Background Subtraction to Peak and Set as Reference Spectrum from the shortcut menu The ToxLab Forms application replaces the normal reference spectrum with a background subtracted reference spectrum To remove the background subtracted reference spectrum right click the Spectrum pane and choose Remove Background Subtracted Reference Spectrum from the shortcut menu The ToxLab Forms application removes the applied background subtracted reference spectrum and returns to the normal reference spectrum When there is no spectrum annotated at the beginning the application displays no data To update confirming ion ratios Click a peak in the quan peak chromatogram pane The mass spectrum for the peak is displayed in the Spectrum pane Right click the Spectrum pane and choose Update Confirming Ion Ratios with this Spectrum from the shortcut menu To change the quantitation mass used for a quan peak Click a peak in the c
264. p dialog box where you can create a new group Shortcut menu Empty group Removes all compounds from the selected group Rename group Changes the name of the selected group Delete group Removes the selected group and all the compounds in it Remove from group Removes the selected compound from its group Thermo Scientific ToxLab Forms 3 1 User Guide 129 4 Using the Method Development Mode Working with Master Methods Editing the Reports Page Use the Standard Reports and Custom Reports pages to specify how you want to save or print your reports For the Quantitation Report type you can modify quan report user interface quan flag and surrogate correction options in the Report Options pane This section includes instructions for the following tasks Specifying Report Formats Specifying Report Flag Options Specifying Report Formats For each standard report you generate you can create a hardcopy printout a PDF file or an XML file In addition to the report type you can specify a report title for each of your reports The default report title is the report name For each custom report you generate you can create a hardcopy printout or an XLS xlsm file You cannot specify a report title for a custom report Follow these procedures To specify standard report types and output formats To specify custom report types and output formats To specify standard report types and output formats 1 Click the Standard
265. peak 3 Right click and choose Add this Mass as New Confirming Ion from the shortcut menu The ToxLab Forms application adds the confirming ion to the quan peak QuanPeakl QuanPeak2 Quan peak Confirming peak 1 Confirming peak 2 miz 169 04 m z148 88 m z182 04 You can use the shortcut menu on the spectrum pane for this new confirming ion to perform any of the tasks you could perform on the original confirming ions To save the new method 1 Choose File gt Save The Save Master Method dialog box opens 2 Do one of the following Type a new name for the master method and click OK Ore Select a method name to overwrite and click Overwrite The ToxLab Forms application saves the new method data in the following folder Thermo IoxLab Forms Methods 92 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Figure 14 Detection page General Compounds m sic Reports Identification Detection Calibration Calibration levels temewd na 1 1 3 Bichlorobenzene Quan peak Confirming peak 1 1 4 Dichlorabenzene muz 28 00 1 4 Diichloroherizerie 1 2 Dichlorobenzene 5 12 Heachloroethane 100 hb c DIM did in irrabenzene cd gt m 1 2 4 Trichlorobenze me 70 E t M aphthalene d8 B E B g sp Hexachloropropene a au lt 40 Hexachlorobutadiene e Pentachloroethan
266. peaks by relative height or area and the percentage of the highest peak that will result in compound selection Displays a specific number of the largest peaks by height or area Lists the libraries you can search Specifies the number of hits returned when the system searches a spectrum against the selected libraries Specifies how to sort the library searches Valid values Search Index Reverse Search Index Match Probability Specifies the number of confirming ions which are other ions in the spectrum whose ratio is compared to the quantitation ion to identify the compound This value defaults to 2 because you typically perform a 3 ion experiment with one quan mass and two confirming ions Enables the ion ratio range features Ion coelution specifies the maximum difference in retention time between a confirming ion peak and the quantification ion peak Window type specifies an Absolute or Relative calculation approach for determining the acceptable ion ratio range Window specifies the acceptable ion ratio range Includes the peak spectrum in the processing method Use this setting to perform a spectra comparison in Production Specifies an internal or external calibration method Specifies a linear quadratic or average RF curve type ToxLab Forms 3 1 User Guide 145 4 Using the Method Development Mode Working with Master Methods Table 39 Method Template Editor parameters Sheet 2 of 3 Parameter Descri
267. plate on page 139 Thermo Scientific ToxLab Forms 3 1 User Guide 57 4 Using the Method Development Mode Working with Master Methods 5 Select the Name the Master Method check box and type a name for your master method You can enter an existing method name and overwrite it when you create the method If you do not specify a name the method is named for the raw file used to create the method 6 Ensure that the Automatically Create the Master Method check box is not selected 7 To select a raw data file click the browse button and locate the file 8 To manually create the master method click OK or Overwrite The Master Method View displays a list of possible matches in the Library Results pane The ToxLab Forms application displays the best match in the Compound Name list and displays the peak spectrum for that compound level level2 Peaks 1 Peak spectrum A NL 51035136 BP 188 09 K s 2 6 Cuclohexadien 1 one 4 4 a 0 2 5 cyclohesa I s 153 09 E cC Relative Intensity tn c 50 01 94 03 65 95 99 94 118 07 132 03 146 04 IPB Library results 2 5 Cyclahexadien 1 one 4 4 on0 2 5 cpclohexadier1 ylidene MAINLIB Fal 845 SI 323 MP Tr DD 93 00 39 00 51 00 66 00 77 00 gs og 117 00 26 00 12 00 2400 28 00 38 00 24 0 79 00 81 00 58 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 9 To use a compound other than th
268. plays only internal standard compounds To add compounds to the method 1 Click the Compounds tab 2 Click the Detection tab General Compounds Reports Identification Detection Calibration Calibration levels UL levels Eompaund oo The Detection page shows an empty Compound list 3 From the main menu choose Master Method gt Associate a Raw Data File The Associate a Rawfile dialog box opens Associate a Raw data file x Update target ion ratio values No L ve Automatically set reference spectrum No ve Cancel 4 Browse to a raw data file to associate with the method and open the file Thermo Scientific ToxLab Forms 3 1 User Guide 85 4 Using the Method Development Mode Working with Master Methods 5 To update the target ion ratio values when you associate this raw data file click Yes 6 To set a reference spectrum do one of the following Click Yes Or Click Yes with Background Subtraction This feature is available only when you have set background subtraction values on the General page of the Master Method View See Editing the General Page on page 72 7 Click OK The ToxLab Forms application displays the chromatographic and spectrum data for the compoundis in the selected raw file JEF c Full ms 35 00 500 00 5 96 l 12 52 14 26 Absolute Intensi 15 66 16 96 p047 5459775 0 CixcaliburvdataiLabForms Raw Filesilevell raw 116 84 xp
269. port WuantitationA eport Steroid nalysish eport Undo changes Table 11 Custom Reports parameters Sheet 1 of 2 Standard Reports Displays all available standard reports Custom Reports Displays all available custom reports Installed reports All reports listed in the Installed Reports pane are potentially available for this application but are not selected for the Method Development or Production modes Displayed reports All reports listed in the Displayed Reports pane are selected for the Method Development and Production modes By default the application displays all reports gt gt Moves all reports from the Installed Reports list to the Displayed reports list gt Moves the selected reports from the Installed Reports list to the Displayed Reports list Thermo Scientific ToxLab Forms 3 1 User Guide 47 3 Using the Configuration Mode Application Configuration Table 11 Custom Reports parameters Sheet 2 of 2 Parameter Description Moves the selected reports from the Displayed Reports list to the Installed Reports list Moves all reports from the Displayed Reports list to the Installed Reports list Batch level report Creates a single report for the entire batch by using data from only the last sample rather than creating separate reports for each sample Batch level reports are prepended with a B to differentiate them Import Opens a browser where you can choose a report file
270. pound type level 1 level 2 level 3 Int_Std 678044 689630 599115 Drug_A L 0 336 0 875 9 659 Curve Type A Average RF L Linear Q Quadratic l Internal standard Note Amounts displayed for internal standards represent the ISTD Response Calibration flags D RSD F Response factor RZR 2 A Amount X Excluded X ISNF Excluded because ISTD wasn t found Manually integrated Thermo Scientific ToxLab Forms 3 1 User Guide 263 A Reports sample Standard Reports Lab name Thermo Fisher Laboratory Instrument Thermo Scientific Instrument User AMER jamie humphries Batch Drug_A Sample ID Filename cal 1 6 ng mL cal_1 cal2 15ng mL cal 2 Calibration Report Method Drug A Drug A Drug A Cali File Drug A calx Level Sample Name File Date Comment level 1 4 17 2008 5 05 47 PM level 2 4 17 2008 5 06 13 PM Page 3 of 3 cal 3 176 ng mL cal 3 level 3 4 17 2008 5 06 39 PM Curve Type A Average RF L Linear Q Quadratic l Internal standard Note Amounts displayed for internal standards represent the ISTD Response Calibration flags D RSD F Response factor R R42 A Amount X Excluded X ISNF Excluded because ISTD wasn t found Manually integrated 264 ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports Chromatogram Report Chromatogram Report Lab name Thermo Fisher Laboratory Page 1 of 1 Instrument Thermo Scientific Instrument Method Drug_A_Drug_A User AMER jamie
271. pounds that are found in the processed samples samples List Compounds pane Method lib cal test Instrument ThermaFisher Instrument W Status Flags Filename Sample lupe Sample level Sample ID _ Compounds WB 1 2 4 5 Tetrachlorobenzene Q o ons 5 Calirator cast S noL P 1 2 4 Trichlorabenzene je Spedmenual II en WS Hesachlorobutadiene MNN WEE een EET EE Quan Peak 1 BED spectra Confirming lons 1 3 Dichlorabenzene RT 4 38 RT 4 38 leveld RT 4 38 level RT 4 38 RT 4 38 RT 4 23 AA 20239420 11 Arc 18174603 22 AA 8953539 78 AH 21283268 25 AH 13295232 30 AH 6483744 30 5 N 25478 20s E 5N 8318 05g N 4633 pm 2100 E 100 3100 5 aD 60 gp E 2 2 60 60 5 en qi qi qi amp 4n E an T 40 20 20 20 45 4 5 4 5 RT min RT min RT min m z 111 00 10 00 70 00 Apex HT 4 33 Apex AT 4 38 Quantification Peak pane Qualification pane In addition to the Samples List the Quan Mode view uses the following panes Compounds Pane Quantification Peak Pane Qualification Pane Compounds Pane In Quan Mode the Samples list works with the Compounds pane to select a unique sample and compound combination which then has its textual and graphical values displayed in the Quan Mode pane The list of compounds that are available for a specific method is displayed in the Compounds pane The Compounds
272. ption Origin Specifies that the origin is ignored forced or included in the generated calibration curve Ignore Specifies that the origin is not included as a valid point in the calibration curve when the curve is generated When you select Ignore the calibration curve might or might not pass through the origin Force Specifies that the calibration curve passes through the origin of the data point plot when the calibration curve is generated Include Specifies that the origin is included as a single data point in the calculation of the calibration curve When you select Include the calibration curve might or might not pass through the origin Weighting Specifies the weighting for the calibration data points Equal Specifies that the origin is included as a single data point in the calculation of the calibration curve When you select Equal the calibration curve might or might not pass through the origin 1 X Specifies a weighting of 1 X for all calibration data points during the least squares regression calculation of the calibration curve Calibrants are weighted by the inverse of their quantity 1 X 2 Specifies a weighting of 1 X 2 for all calibration data points during the least squares regression calculation of the calibration curve Calibrants are weighted by the inverse of the square of their quantity 1 Y Specifies a weighting of 1 Y for all calibration data points during the least squares regression calculation
273. r Description And Requires that all filter criteria must be met conditions Or Requires that any of the specified filter criteria be met conditions Add a Adds a new empty condition to the filter criteria condition Delete Deletes the selected condition Click the box at the left of the row to select condition the condition Operator The mathematical function applied to the operand Operand The arguments to which the operator is applied 314 ToxLab Forms 3 1 User Guide Thermo Scientific S M index Symbols csv defined 2 meth defined 2 pmd defined 2 raw defined 2 xml defined 2 background scans parameter 101 Test parameter 118 A Account Number parameter 23 Acquire a new raw data file parameter 60 Acquisition List page Master Method View 79 Active parameter Identification 84 Active View page 234 Add a condition parameter 314 Add a mass as new confirming ion command 111 Add Compound command 32 Add Folder parameter 34 Add Group command 129 Add this mass to existing quan mass ranges command 110 Add to CDS command 63 Add Transition Information command 32 Add user parameter 24 Amount parameter 113 And conditions parameter 314 Application Configuration view 37 Area noise factor parameter 103 Area scan window parameter 105 Area tail extension parameter 105 Assay type parameter Batch Wizard 186 General page 77 Associate a Raw Data File dialog box 65 Associate a Raw Data File parameter 65 automat
274. r Limit parameter 126 127 Use alternate calibration report format parameter 137 Use an existing raw data file parameter 60 Use as RT Reference parameter 84 Use autosampler parameter 60 Use Method Forge parameter 54 Use the default template parameter 60 Use these libraries parameter 145 user accounts creating 20 User Administration view 20 324 ToxLab Forms 3 1 User Guide user roles and permissions 25 user roles defined 25 User Security parameter 40 Username parameter 9 23 V Valley rise parameter 101 Valley S N parameter 101 Vial position parameter 60 View width parameter Detection 95 views Application Configuration 37 Batch 163 Compound Datastore 30 Data Review 198 Development Batch 153 Instrument 149 Local Method 248 Method 53 Project Administration 28 Report View 230 User Administration 20 W Weighting parameter Calibration 115 Method Template Editor 146 Window parameter Acquisition List 82 Compound datastore 36 Detection 95 workflow general 7 Thermo Scientific
275. r the confirming ions See Ratios on page 111 4 To replace a quan mass 1 Click the pane for the quan mass that you want to replace 2 In the raw file spectrum pane pause the cursor over a peak The red box indicates the selected peak NL 484023856 BP 188 10 ity 100 50 Relative Intena 267 93 2093 02 150 200 250 300 8561 88 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific L 4 Using the Method Development Mode Working with Master Methods Right click and choose Set This Mass as Quan Mass from the shortcut menu Choose either Don t Update Ion Ratios or Update Ion Ratios Using This Spectrum You can see the updated ion ratios on the Ratios page for the confirming ions See Ratios on page 111 To add a mass to the existing quan mass ranges In the raw file spectrum pane pause the cursor over a peak The red box indicates the selected peak Right click and choose Add This Mass to Existing Quan Mass Ranges from the shortcut menu Choose either Don t Update Ion Ratios or Update Ion Ratios Using This Spectrum The ToxLab Forms application adds the selected mass to the existing quan mass ranges to increase the signal If you chose to update the ion ratios you can see the updated ion ratios on the Ratios cc 55 page for the confirming ions See Ratios on page 111 To add a quan peak In the raw file spectrum pane pause the cursor over
276. range around the average of the responses of that compound in all of the calibration standards For all other samples the application calculates the comparison range around the check standard responses if a check standard is available in the batch If no check standard is available the application tests against the initial calibration The minimum and maximum drift in minutes for the internal standards to define an acceptable range For check standards the ToxLab Forms application compares the retention time of each internal standard in each sample to a range around the average of the retention times of that compound in all of the calibration standards For all other samples the application calculates the comparison range around the check standard retention times if a check standard is available in the batch If no check standard is available the application tests against the initial calibration Coefficient of Variation test Copies the selected column value to all rows in that column For detailed instructions about using the Copy Down command see Appendix B Using Copy Down and Fill Down Displays or hides the RT column in the compound list Removes the selected compound from the current master method ToxLab Forms 3 1 User Guide 125 4 Using the Method Development Mode Working with Master Methods Solvent Blank Use the Solvent Blank page to view or edit QC values for solvent reporting The evaluation is made by compa
277. restore the method default view right click the chromatogram plot and choose Reset Scaling from the shortcut menu To change the displayed information for detected peaks Right click the chromatogram plot and pause the cursor over Peak Labels Choose to display labels for the peak retention time peak height peak area or signal to noise The label types in the list are selected for displayed labels and cleared for labels that are not displayed To remove a label select the label type again and clear it Label settings are globally applied to quan peaks confirming peaks and internal standard peaks Note The labels do not always update on all peak displays To update all labels select a different compound then reselect the compound whose labels you changed ToxLab Forms 3 1 User Guide 217 5 Using the Production Mode Working in Data Review To display the peak information window 1 Right click the quantification and confirming ion chromatogram plots 2 Choose Show Peak Info from the shortcut menu Information in this window includes the data stream processed for this ion consisting of a particular detector filter if applicable and trace For example an MS detector might show a filter of c Full ms 35 00 500 00 and a Mass Range trace This window also shows the peak area and height along with the retention times of the peak integration and the peak apex Table 52 Confirming lons
278. rigin Force Specifies that the calibration curve passes through the origin of the data point plot when the calibration curve is generated nclude Specifies that the origin is included as a single data point in the calculation of the calibration curve When you select Include the calibration curve might or might not pass through the origin 142 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 4 From the Weighting list select one of the following Equal Specifies that the origin is included as a single data point in the calculation of the calibration curve When you select Equal the calibration curve might or might not pass through the origin 1 X Specifies a weighting of 1 X for all calibration data points during the least squares regression calculation of the calibration curve Calibrants are weighted by the inverse of their quantity 1 XN2 Specifies a weighting of 1 X 2 for all calibration data points during the least squares regression calculation of the calibration curve Calibrants are weighted by the inverse of the square of their quantity 1 Y Specifies a weighting of 1 Y for all calibration data points during the least squares regression calculation of the calibration curve Calibrants are weighted by the inverse of their response or response ratio Y 2 Specifies a weighting of 1 Y 2 for all calibration data poin
279. ring the calculated response for each compound in the sample to the maximum response defined on this page On the Solvent Blank report the ToxLab Forms application flags the calculated values for target compounds that exceed these limits Figure 29 Solvent Blank page Groups i Reports General Compounds ot 21 HT Compound Method Upper Limit 141 51 Methylene Chloride None 2 1444 Arsine All lon RT w 1 3 44 3 Phenol 3 rmethul Quanlon AT w zu Table 32 Solvent Blank parameters Parameter Description RT Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column Compound The compound name Method The evaluation process to use as a response for the quan ion only Quan Ion RT or a summed response for the quan ion and any confirming ions All Ion RT To deactivate the solvent blank test for a specific compound select None Upper Limit Specifies an upper limit for each compound in the sample if an evaluation process is selected These values are not concentrations they are raw response values Shortcut menu Copy down Copies the selected column value to all rows in that column For detailed instructions about using the Copy Down command see Appendix B Using Copy Down and Fill Down Display retention time Displays or hides the RT column in the compound list column Delete compound from Removes
280. rom the list To remove all samples from the list To enter column values Double click the Filename column and type a file name for the raw data file Optional Enter values for the Sample Name Sample ID or Comment columns Enter a vial position for each sample Enter an injection volume for each sample The minimum injection volume value allowed is 0 05 pL To enter an instrument method for each sample click the down arrow in the Instrument Method column and select a method from the list This list contains all the available instrument methods To resize or reorganize the columns To resize a column drag the header separator on the right side of the column To move a column drag the column header You cannot move the Filename column Thermo Scientific 4 Using the Method Development Mode Working with Development Batches To remove selected samples from the list 1 Select the samples you want to remove Ensure that the first column indicates that the samples are selected Filename Sample ID Sample name Comment sample Selected samples 5 sample2 samples CAN 2 Right click and choose Remove Selected Samples from the shortcut menu To remove all samples from the list 1 Click New Sample List in the Development Batch task pane 2 One of the following happens Ifthe samples in the current batch have all been acquired the list is cleared f the samples in the current list h
281. rt copy sample Copies the currently selected row and inserts a copy above the row Remove selected samples Removes selected samples from the sample list Move sample up Moves the selected sample up one row in the sample list Move sample down Moves the selected sample down one row in the sample list Thermo Scientific ToxLab Forms 3 1 User Guide 191 5 Using the Production Mode Working in Batch View Submitting the Batch 192 ToxLab Forms 3 1 User Guide Table 45 Batch Specification parameters Sheet 2 of 2 Parameter Description Browse in raw file Opens a dialog box where you can select a raw data file to use for the sample row You can also browse in multiple raw data files to create multiple samples Fill down Enters sequential values in the column starting with the value in the selected row and ending with the last row in the column For detailed instructions about using the Fill Down command see Appendix B Using Copy Down and Fill Down From the Finish page you can change the name of the batch access the Calibration and Compound Selection page to edit the calibration file or edit the list of compounds to identify or save the batch and open it in Batch View Follow these procedures S S To change the name of the batch To save the batch To edit the calibration file To identify specific compounds or groups of compounds To change the name of the batch Edit the name in the Batch Name box
282. rt3Long QuantitationReport ToxLab Forms 3 1 User Guide 253 A Reports Report Flags Report Flags When generating or viewing a report you might see one of the following quantification or calibration flags listed on the page Table 75 Quantification flags Flag b I or D Q POS Definition Compound was observed at a concentration in a Negative sample above the specified limit Compound was observed at a response in a solvent blank sample above the specified limit Compound was observed at a concentration above the limit of detection but below the limit of quantitation Confirming qualifying ion ratio for acompound was observed outside the target ratio range or the coelution between quantification and confirming qualifying ion was larger than acceptable limit Compound was observed at a concentration above the specified carryover limit Compound was observed at a concentration above the specified linearity limit Compound was observed at a concentration below the specified limit of detection Compound was observed at a concentration below the specified limit of P P quantitation Compound was observed at a concentration above the specified cutoff Table 76 Calibration flags Flag D X Definition Calibration for this compound exceeded the specified maximum percent relative standard deviation RSD Response factor for this compound was below the specified minimum response factor Min RF
283. s Int Std None N A Negative Summary Sample ID Compound Criterion Max Value Calc Amt Flags negative Int Std Concentration 0 000 N A Compound Report Compound IS Mean Response ISTD Recovery RT Quan Mass 1st Qual Ratio Range 2nd Qual Int Std 1 94 380 20 479 20 0 0096 0 0096 Drug A 2205925 1102962 3308887 1 95 371 20 473 20 22 3396 33 4996 488 20 Compound 3rd Qual Ratio Range 4th Qual Ratio Range 5th Qual Ratio Range Int Std Drug A 479 40 22 2296 33 3396 380 40 12 69 169 0396 371 40 80 0096 120 0096 Calibration Flags A Amount Quan Flags Legends of Abbreviations C Carry Over Linearity Limit D Detection Limit Q Quan Limit H Hydrolysis A IS Area Range R IS RT Range lon Ratio Failure n Negative b Solvent M Quan ion manually integrated m Qualifier ion manually 258 ToxLab Forms 3 1 User Guide Ratio Range 11 4396 17 1496 Thermo Scientific Report Generated Quantitation Report Compound Name Data File cal_1 Int_Std cal_2 cal_3 negative hydrolysis qc 40 specimen 1 specimen 2 specimen 3 specimen 4 qc 125 Batch Name Method Cali File Operator Instrument ID 6 17 2010 8 41 37AM Sample ID cal 1 6 ng mL cal 2 15 ng mL cal 3 176 ng mL negative hydrolysis qc 40 6 ng mL specimen 1 specimen 2 specimen 3 specimen 4 qc 125 18 75 ng mL Compound lon Ratios Data File 479 20 380 20 cal_1 19 91 cal_2 19 22 cal_3 19 72 negative h
284. s views where you can review batches batch data reports and local methods 5 View and print reports in the Report View of the Production mode Use the Report View to view or print the reports for the currently selected batch Installing the ToxLab Forms Application Follow these instructions to install start and log on to the ToxLab Forms application To install the ToxLab Forms application 1 Follow the instructions on the included CDs to install the Xcalibur 2 1 data system and your instrument drivers 2 Install the driver for your GC device and autosampler 3 Insert the ToxLab Forms 3 1 CD in the drive and follow the on screen instructions If the install windows do not automatically open navigate to the Xinstall exe file and launch it To start the ToxLab Forms application 1 Configure your instruments You cannot configure your instruments while the ToxLab Forms application is running 2 Double click the ToxLab Forms 3 1 application icon on your desktop or go to Start gt All Programs gt Thermo ToxLab Forms 3 1 gt Thermo ToxLab Forms 3 1 By default user security is not enabled and the application does not require a password To enable user security follow the instructions To enable user security on page 38 IMPORTANT If you are the administrator logging on for the first time with user security enabled use Administrator Password as the username password To log on to the ToxLab Forms app
285. save a datastore Click Save Compound Datastore in the Compound Datastore task pane The database is stored as Ihermo IoxLab Forms Databases foldername filename xml If the datastore contains any compounds that do not have an associated transition the Compounds That are Missing Quans dialog box opens listing the compounds Compounds that are missing Quans Item Compound Name Field Value Error Message Result UU 0 Unconazole 2 Do one of the following Thermo Scientific To remove the listed compounds from the datastore and save the datastore click Continue Or To keep the listed compounds and return to the datastore click Cancel Note You cannot save a compound that does not have an associated transition To save a datastore to a new name Click Save As Compound Datastore in the Compound Datastore task pane The Save Compound Datastore dialog box opens See Save Compound Datastore dialog box on page 34 Enter a file name for the new compound datastore ToxLab Forms 3 1 User Guide 33 3 Using the Configuration Mode Compound Datastore 3 Optional Click Add Folder and enter the name for a new folder to be created in the Ihermo IoxLab Forms Databases folder 4 Click Save The database is stored as Thermo ToxLab Forms Databases foldername filename xml Figure 4 Save Compound Datastore dialog box Save Compound Datastore H
286. ser Guide 55 4 Using the Method Development Mode Working with Master Methods When the acquisition completes Method Forge performs peak detection datastore searching and characteristic ion and reference spectrum identification Method Forge then loads this information into a new master method This process occurs immediately if you selected a previously acquired raw file If the compounds in the raw data file you used to create the method are not in the Compound Datastore the ToxLab Forms application displays the compounds in the Edit Compound Dependent Parameters dialog box Edit compound dependent parameters 8 Continue to Method Add to CDS 10 11 12 13 56 ToxLab Forms 3 1 User Guide Optional Select the compounds that you want to add to the compound datastore and click Add to CDS The selected compounds are added to the current compound datastore Note To add these compounds to the datastore you must use the Add to CDS command before you continue to the method To use these compounds in your method and close the dialog box click Continue to Method All compounds found in the raw data file are used in your method The ToxLab Forms application displays the General page of the Master Method View From the Instrument Method list on the General page select an instrument method To save the new method choose File Save from the main menu For a detailed description of how to modify a ma
287. ses the text in a red box Enlarges the report text by the specified scale factor ToxLab Forms 3 1 User Guide 233 5 Using the Production Mode Working in Report View Displaying the Active View Page 234 Use the Active View page to view quantitative data for each sample ina report Data in Active View are labeled with flag information These flags are based on a comparison of the batch data to criteria defined in the master method 9 ToxLab Forms 3 1 User Guide To display the Active View page Click the Active View tab The Active View page displays quantitative data and QAQC error flags for each sample See Active View page on page 235 To display a report Select a report type from the Select a Report list Only the report types created for the current batch are displayed in the list Optional When the report type includes separate reports for each sample select a sample file To filter which compounds to display E 2 TE Ni Calibration Report Sample file Felis UT Toggle the Showing button to display either all compounds or only compounds that are flagged for failing a QAQC test Showing All Compounds ee Flagged Compounds Only Thermo Scientific 5 Using the Production Mode Working in Report View Figure 52 Active View page Steers eren High Density Sample Report 1 Long ea Unknown 0312101564543 Report View eve View Total Rowe 2 Showing All Compounds ia St
288. shortcut menu Sheet 1 of 2 Command Method integration settings Manual integration settings Add peak Remove peak Cancel add peak Range Calc method Manual Range calc level Target ratio Window type Window Peak labels Show peak info 218 ToxLab Forms 3 1 User Guide Description Displays method integration settings Displays manual integration settings Adds a peak removes a manually added peak or cancels an add peak operation in progress Selects the method used to calculate the ion ratio range windows Manual Average Weighted Average or Level Specifies the range based on the calibration level Specifies the theoretical ratio of the confirming ion s response to the quantification ions response Specifies the Absolute or Relative calculation approach for determining the acceptable ion ratio range Specifies the acceptable ion ratio range Displays or hides the peak labels Label Area Label Retention Time Label Height or Label Signal to Noise Displays peak information for the selected compound For example methyltestosterone Quan ion m z 267 10 285 20 Integration mode Left RT 1 87 Area Apex RT als Fight RT 2 20 Data File Thermo Scientific Thermo Scientific 5 Using the Production Mode Working in Data Review Table 52 Confirming lons shortcut menu Sheet 2 of 2 Command Description Reset scaling Resets the original scaling after a zoom operation Peak
289. specify an absolute or relative calculation approach for determining the acceptable ion ratio range select Absolute or Relative from the Window type list c To specify the acceptable ion ratio range set a value in the Window 96 box 3 To include the peak spectrum in the processing method select the Include Compound Peak Spectrum as Reference Spectrum check box Use this setting to perform a spectra comparison in Production mode To calibrate the compounds Calibrate the compounds Calibration method Weighting w Origir Ignore v Response via Area bul 1 From the Calibration method list select Internal or External 2 From the Curve type list select one of the following Linear All other settings are available with this exception When Include is selected in the Origin list all weighting values are unavailable except for Equal Quadratic All other settings are available with this exception When Include is selected in the Origin list all weighting values are unavailable except for Equal Average RF No selections in the Weighting or Origin lists are available The Weighting list is set to Equal and the Origin list is set to Ignore 3 From the Origin list select one of the following Ignore Specifies that the origin is not included as a valid point in the calibration curve when the curve is generated When you select Ignore the calibration curve might or might not pass through the o
290. splayed in a list box On all list boxes you can choose to filter by All Blanks NonBlanks or by custom filter criteria Other filter criteria are specific to the individual columns Choose the type of compound you want to display For example if you choose All in the Compound Name column the ToxLab Forms application displays all compounds if you choose Blanks in the Compound Name column the application displays only blank compound types Optional To create a custom filter based on compound values in a specific column choose Custom from the column list box For detailed instructions about creating a custom filter see Appendix C Using Filter Criteria ToxLab Forms 3 1 User Guide 19 4 Using the Method Development Mode Working with Master Methods To delete a compound from the list 1 Select the compound to remove from the list or right click and choose 2 Click the Remove Compound Transition icon Remove Compound Transition from the shortcut menu A confirmation dialog box opens listing the compound to be removed 3 To confirm the deletion click Yes The selected compound is removed from the acquisition list To add a compound transition to the list 1 Click the Add Compound Transition icon ry or right click and choose Add gt E Compound Transition from the shortcut menu The Select Compounds to Add dialog box opens listing all the compounds defined in the compound datast
291. stem uses a batch centric approach and tools to automate and speed up the processes of method creation loading samples automatically generating data manually reviewing and editing results and finalizing the data review and reporting process The ToxLab Forms software package includes data acquisition processing reviewing and reporting capabilities designed to assist analysts in environmental and food safety applications The application has a fully automated acquisition mode and a manual review mode You can use the data acquisition system to create and submit batches and monitor real time review of results The ToxLab Forms application uses a comprehensive processing method to provide improved handling of ion ratio calculations reviewing and reporting In addition the application provides a mass spectral comparison capability and an integrated connection between the processes of data review and reporting Key features include the following Role based authorization for Manager IT Administrator Supervisor Technician and QAQC quality assurance roles Configuration mode with user administration project administration datastore administration and application administration Method Development mode with instrument method editor processing parameters QAQC parameters and reporting options Production mode with batch views data review local method views and report views Database capable method development Qu
292. ster method see Editing a Master Method on page 70 Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To manually select compounds to create a method 1 From the Method View task pane click Create Method Method View 2 L Create method BE Open method amp Export SRM data Recent Files The Create Master Method dialog box opens Create Master Method Method Forge Use Method Forge Performs peak detection against a raw data file n Performs library lookup if requested Import Xcalibur Processing Method Import Xcalibur Processing Method Imports a previously created processing method finding configured compounds and reference spectra Associate Haw Data File i Creates a blank master method and associates a Associate a raw data file raw data file allowing manual peak selection Select Compounds from a compound datastore Creates a blank master method and displays the configured compound datastore allowing compound selection Select compounds from CDS 2 Select Use Method Forge 3 Click OK The Method Forge dialog box opens See Method Forge on page 59 4 In the Method Forge dialog box do one of the following e Select the Use the Default Template option Or Select Select a Custom Template and highlight your custom template in the Method Template table For detailed instructions about creating a custom method template see Creating a Method Tem
293. t a different compound and then reselect the compound whose labels you changed 226 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Data Review Table 55 Qual peak shortcut menu Command Description Reset scaling Resets the original scaling after a zoom operation Method integration Displays method integration settings Manual integration Displays manual integration settings Peaklabels Displays or hides the peak labels Label Area Label Retention Time Label Height or Label Signal to Noise Remove peak Removes the peak displayed in the Qual pane Thermo Scientific ToxLab Forms 3 1 User Guide 227 5 Using the Production Mode Working in Data Review Spectra Pane reference and selected The Spectra pane displays the reference spectra and the spectra for the selected sample The top pane displays the reference spectra for the identified compound from the library the bottom pane displays the spectra for the selected peak 4 To zoom in on a peak 1 In the spectra plot drag the cursor to delineate a rectangle around the peak The delineated area expands to fill the view to help you examine the peak limits for enhanced review and confirmation 2 To restore the default view right click the chromatogram plot and choose Reset Scaling from the shortcut menu Qual Library 153 00 u Reference 80 spectra for ao Acenaphthene m 40 qu t 20 53 00 1400 39 00
294. t menu You can now update the ion ratios to adjust the confirming ion comparisons to the new summed quan peak signal 4 To adda quan peak to an existing compound 1 Click the peak in the Quan Peak chromatogram pane The mass spectrum for the peak is displayed in the Spectrum pane 2 In the Spectrum pane pause the cursor over the zz z value for an ion A red box around the ions m z value indicates that the ion is selected 116 835311889648 605679 3 Right click and choose Set This Mass as New Quan Peak from the shortcut menu The ToxLab Forms application adds this ion as a new quan peak New quan peak mass 5 18 5 33 4 8 5 0 5 2 5 4 RT min 108 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods To add one or more confirming ions to an existing compound 1 Click the peak in the chromatogram pane The mass spectrum for the peak is displayed in the Spectrum pane 2 In the Spectrum pane pause the cursor over the zz z value for an ion A red box around the ions m z value indicates that the ion is selected 3 Right click and choose to Add This Mass as New Confirming Ion from the shortcut menu The ToxLab Forms application adds the selected mass as a confirming peak for this quan peak QuanPeakl Quan peak Confirming peak 1 Relative Intensity w b mo Donoso 475 487 509 531 538 50 52 5 50 a2 RT min RT min Detect 5 ignal D
295. t QAQC Blank Compound Criterion Max value N Nitrosodimethylamine Concentration 0 500 Pyridine RCRA Concentration 0 500 2 Picoline Concentration 0 500 N Nitrosomethylethylamine APP9 Concentration 0 500 Methyl methanesulfonate Concentration 0 500 2 fluorophenol sur Concentration 60 000 N Nitrosodiethylamine APP9 Concentration 0 500 Ethyl methanesulfonate Concentration 0 500 phenol d5 sur Concentration 60 000 Phenol CCC Concentration 0 500 Aniline Concentration 0 500 Bis 2 chloroethyl ether Concentration 0 500 Pentachloroethane Concentration 0 500 2 chlorophenol Concentration 0 500 1 3 Dichlorobenzene Concentration 0 500 1 4 Dichlorobenzene CCC Concentration 0 500 Benzyl_alcohol Concentration 0 500 1 2 Dichlorobenzene Concentration 0 500 2 methylphenol Concentration 0 500 Bis 2 chloroisopropyl ether Concentration 0 500 N Nitrosopyrrolidine_APP9 Concentration 0 500 3 Methylphenol amp 4 methylphenol Concentration 0 500 Acetophenone Concentration 0 500 N Nitroso di N propylamine SPCC Concentration 0 500 o toluidine APP9 Concentration 0 500 Hexachloroethane Concentration 0 500 nitrobenzene d5 sur Concentration 60 000 Nitrobenzene Concentration 0 500 N Nitrosopiperidine Concentration 0 500 Isophorone Concentration 0 500 2 Nitrophenol CCC Concentration 0 500 2 4 Dimethylphenol Concentration 0 500 Bis 2 chloroethoxy methane Concentration 0 500 2 4 Dichlorophenol CCC Concentration 0 500 1 2 4 Trichlorobenzene Concentration 0 500 Naphthalene
296. t 4 0 0 2 Wu a a gets wl es tins 265 Compound Calibration Report ra 5 993 2a ner 267 Compound Calibration Report Alternate 269 Gonlrmation Repottss xouna 5 pune d Reese aub e bodas d abes 272 COnnimation Ropon sree gente ee eee MR MS 273 High Density Calibration Report 2 222 220 eeeeeeeene nenn 274 High Density Internal Standard Report 275 High Density Internal Standard Report Long 276 High Density Sample Report 1 27 High Density Sample Report 1 Long 278 High Density Sample Report eue d ost obse aene der vo DEP ES 279 High Density Sample Report 2 Long 280 Thermo Scientific Thermo Scientific Contents High Density Sample RepottDassihseais tits sen tecaduscie se 281 High Density Sample Report 3 Long 282 Internal Standard Summary Report 283 lon Ratio Iailgre Report 24425 qos trenit e So te dod ades 284 Manual Integration Report cactus niger es 285 Method Report sadi ober Ene par S Sau Don ead ipa bafis dob berg q 286 INSTALL VE DO gebear pihe reaa Va rbd de bus oO esq dob eei ded 301 Juantitation Repott cues o dabo e a 6 en s aes aa eae babeo 302 Quantitation Reporte 2 6 org e dore eb SIRE P Pau eee seeks 303 Quality Control Repite ee tesira a Bates A re eeu 305 bamplie REPON aau epe itd E
297. t Long High Density Sample Report 1 High Density Sample Report 1 Long High Density Sample Report 2 High Density Sample Report 2 Long High Density Sample Report 3 High Density Sample Report 3 Long Internal Standard Summary Report on Ratio Failure Report Manual Integration Report Method Report Negative Report Quantitation Report Quantitation Report 2 Quality Control Report Sample Report Sample Report Long Solvent Blank Report Tip To easily view reports in landscape format choose View Rotate View Clockwise from the Adobe Acrobat viewer menu 256 ToxLab Forms 3 1 User Guide Thermo Scientific A Reports sample Standard Reports O L 0001 LL ueuireds V N O L 0001 Ol u ulo ds V N O L 000 L 6 u ulo ds V N 0 L 0001 8 IenO u ullo ds Y N 0 L 0001 el jueAos V N 0 L 0001 l o0 SZL 1949 0 L 0001 Z 20 Or 1949 0 L 0001 S AlBeB N V N 0 L 000 L 9 sis oJp H Y N 0 L 0001 V 10jeJqieo 1949 0 L 0001 10jeJqieo c 1949 0 L 0001 C 0jeJqieo 1949 0 L 000L L pejoeJxeun Y N JUSWIWOD uonniiq 0A ful SOd ElA adh ejduieg 19491 sweu a dwes xies y Dnuq ei eo v Bniq v bniq v Bniq poujelw JO Bed Jod tui uojeg Batch Report r usw oads c usw oads c usw oads uawioeds JUSAJOS I GZ 8 S L ob Juu Bu 9 950p Ib an ye au s sAjoJpAy Tu Bu 9 Je quj Bu S Z je9 7w Bu 9 Jeo poejoeJxeun ai s dwes Nd 6v
298. t Parameters 63 Import an Xcalibur Method 62 Open Chromatograph Reference Sample 76 Open Compound Datastore 31 Save Compound Datastore 34 Select Compound Datastore 38 Select Compounds to Add 68 Thermo Library Manager 11 Thermo Xcalibur Instrument Setup 73 Thermo Xcalibur Roadmap 10 Display Mass Precision parameter 41 Display Quan flags and legend parameter 137 Display retention time column command Blank page 124 Calibration page 121 Hydrolysis page 127 ISTD page 125 Limits page 120 QC Check page 122 Solvent Blank page 126 Display valid compounds only parameter 137 Displayed Reports parameter custom 47 Displayed Reports parameter standard 44 Thermo Scientific Index D E Edit Compound Dependent Parameters dialog box 63 Edit user parameter 24 Email Address parameter 23 Enable peak threshold parameter 145 Enable tune time tracking parameter 138 Enable User Security command 38 Enable valley detection parameter 99 Enabled parameter 23 Energy Ramp parameter Acquisition List 82 Compound datastore 36 Example parameter 132 Exclude matching quan peaks parameter 147 Exit ToxLab Forms command 9 Expected RT parameter Detection 95 Expected width parameter 99 Export SRM data parameter 51 Extend Calibrations parameter 196 F feature summary 3 File Name parameter Save Compound Datastore dialog box 34 file types supported 2 Fill down command 309 Filter parameter Detection 96 Flag values above Carryover parameter 137 Flag va
299. t a subproject The Available Templates area lists all the templates in the specified subproject 3 Select a starting vial position The default is vial position 1 but you can choose to start your acquisition at any vial position 4 Optional To simplify the sample list select the Quick Mode check box Quick Mode limits the columns of information in the Batch Specification page to the following Sample Type Sample ID Injection Volume e Conversion factor 5 From the Available Templates list select a template that defines the layout you want to use The Template Layout area displays sample information in the selected batch template and a list of methods that use the same assay type as your template Available Templates Available Method BatchT emplate3 BatchTemplatez BatchT emplatel Maethad2b Template Layout Sample Sample ample Sample Repeat tune name rows Comment 6 Select an available method By default the method used to create the batch template is selected but you can choose any method in the Available Methods list 7 To go to the next wizard page click Next From the Batch Specification page of the wizard you can customize the batch Thermo Scientific ToxLab Forms 3 1 User Guide 185 5 Using the Production Mode Working in Batch View Figure 44 Batch Template Selection page Batch Wizard aiv ud Project IF ee Subproject 1A Starting vial position ite Total batc
300. tandard Quantitation Report or Quantitation Report 2 observe the active or report view for only the last sample in the batch For the custom Quantitation Report make the report a batch level report Injection units specified on the Calibration page in Method Development mode See Calibration on page 113 Calculated injection amount multiplied by the conversion factor Refer to the note in the Injected Concentration description Sample units specified on the Calibration page in Method Development mode See Calibration on page 113 Thermo Scientific 5 Using the Production Mode Working in Report View Table 73 Sample Report and Sample Report Long Active View values Column Description RT Retention time for the peak The time after injection at which the compound elutes The total time that the compound is retained on the GC column Ion Mass The mass range for the ion Response The total response time the sum of all quan peak response times for the compound Calibration Amount Target Range Ratio The ratio of the confirming ion response to the quan ion response Table 74 Solvent Blank Report Active View values Column Description RT Retention time for the quan peak The time after injection at which the compound elutes The total time that the compound is retained on the GC column Olon Mass range for the quan peak Response Sum of all Quan Peak Response values for the compound Method Method of evalua
301. ter Acquisition List 82 Compound datastore 36 Print parameter Batch Template Editor 183 custom reports 133 standard reports 133 Product Mass parameter Acquisition List 82 Compound datastore 36 Production command 14 Project Administration view 28 projects and subprojects creating 28 0 QAQC Flags parameter 236 QAQC page Master Method View 119 QAQC role 27 QC Check page Master Method View 122 QC Levels page Master Method View 116 QC1 QCn parameter 118 QED library installing 10 Qlon parameter 237 Qual Mode 198 Qualitative peak processing template parameter 78 quality check QC sample definition 197 Quan Flags parameter 236 Quan mass parameter 237 Quan Mode 198 Thermo Scientific Quan peak m z parameter 236 Quan peak response parameter 236 Quan peak RT parameter 237 Quick mode parameter 186 R 2 threshold parameter 121 Ranges parameter Detection 97 Ratios page Master Method View 111 Raw filename parameter 60 Real Time Status command 14 real time display 175 Recent Files parameter master methods 51 Reference compound parameter 84 reference spectra 228 Remove user parameter 24 Report concentration parameter 137 report flag options specifying 134 report formats specifying 130 Report Name parameter Batch Template Editor 183 custom reports 133 standard reports 132 Report noise as parameter 101 Report Title parameter standard reports 133 Report View 230 reports configuring 42 flags defined 254 listed
302. ters Sheet 1 of 2 Parameter Method template selection Use the default template Select a custom template Name the master method Automatically create the master method Raw file selection Use an existing raw data file Acquire a new raw data file Instrument method Raw filename Path Sample comment Manual injection Use autosampler Vial position Injection amount Function button Overwrite ToxLab Forms 3 1 User Guide Description Creates a new method with the default template Lists all the available method templates For detailed instructions about creating a custom method template see Creating a Method Template on page 139 The name for the new master method When the acquisition completes Method Forge performs peak detection library searching and characteristic ion and reference spectrum identification This information is loaded into a new master method This process occurs immediately when you specify an existing raw data file Enables the Raw Filename box where you can select a raw data file to use to create the master method Enables functions to acquire data to create a raw file to use to create the master method The saved method meth file to use for acquiring the data The file name where the ToxLab Forms application will write the raw data The location where the ToxLab Forms application will save the raw data file Optional Comment about the acquired s
303. ters Sheet 1 of 2 Parameter Method Instrument Column values Status Filename Sample type Sample level Sample ID Sample name Vial Position 172 ToxLab Forms 3 1 User Guide Description Method to use for acquiring or processing the batch Instrument specified in the method used for the batch Orange for samples that are currently acquiring Blue for samples that have not been acquired Yellow for samples that have been acquired and not processed Green for samples that have been acquired and processed Name of the raw data file that contains the sample data Defines how the ToxLab Forms application processes the sample data Each sample is classified as one of the following sample types Negative Calibrator QC Specimen Specimen Qual Solvent Hydrolysis Unextracted The level defined for a calibration sample or quality control sample A user defined alphanumeric string that identifies a sample A user defined name that identifies a sample The tray vial number used for the autosampler acquisition Thermo Scientific 5 Using the Production Mode Working in Batch View Table 41 Batch View parameters Sheet 2 of 2 Parameter Injection volume Dilution Comment Shortcut menu commands Add sample Insert sample Insert copy sample Reinject this sample Remove selected samples Import samples Submit selected samples Submit batch Browse in raw file Thermo Scientific Descr
304. th Master Methods Table 15 Acquisition List parameters Sheet 2 of 2 Parameter Precursor Mass Product Mass Collision Energy Lens Polarity RT min Window sec Energy Ramp 82 ToxLab Forms 3 1 User Guide Description The mass to charge ratio of a precursor ion The location of the center of a target precursor ion peak in mass to charge ratio m z units Default 0 0 Range 10 000 to 2999 999 The mass to charge ratio of the quan ion The location of the center of a target quan ion peak in mass to charge ratio m z units Default 0 0 Range 10 000 to 2999 999 The energy used when ions collide with the collision gas Range 250 to 250 Optional Range 400 to 400 positive or negative Retention time The time after injection at which the compound elutes The total time that the compound is retained on the GC column RT and Window values are used to determine the start and stop time for the acquisition Range 0 00 to 999 00 Start time RT Window 2 Stop time RT Window 2 Start and stop range 0 00 to 999 00 Acquisition window RT and Window values are used to determine the start and stop time for the acquisition Range 0 00 to 499 50 Start time RT Window 2 Stop time RT Window 2 Start and stop range 0 00 to 999 00 Optional Range 0 00 to 200 00 Thermo Scientific 4 Using the Method Development Mode Working with Master Methods Identificati
305. the units of both Response and IS Response are counts sec If the Response is specified as Height in the processing method the units of both Response and IS Response are counts IS Amt Amount of internal standard IS Resp Response of the internal standard Active Displays or hides a compound for a particular sample When a calibration standard is marked inactive the ToxLab Forms application no longer uses the data files calibration point for the calibration and removes it from the graphical view of the calibration curve displayed in the Qualification pane It is no longer part of the result set Excluded Turns a compound on or off in the Calibration curve of the Qualification pane Diff The calculated amount minus the expected amount divided by the expected amount and then multiplied by 100 RSD Standard deviation of the multiple samples of one level multiplied by 100 and then divided by the average of the multiple samples of that level This calculation is based on the calculated amounts CV Coefficient of Variation Standard deviation of the multiple samples of one level multiplied by 100 and then divided by the average of the multiple samples of that level This calculation is based on either the area or height of the peaks 204 ToxLab Forms 3 1 User Guide Thermo Scientific 5 Using the Production Mode Working in Data Review Quan Mode The Quan Mode displays quan peak and confirming ion information for selected com
306. thod Or a In the Raw File Selection area choose Acquire a New Raw Data File b From the Instrument method list select a method meth file to use for acquiring the data c In the Raw Filename box type the name of the file where the ToxLab Forms application will write the raw data d In the Path box type a path or click the browse button and locate a folder where the application will save the raw data file e Optional Type a comment about the acquired sample or the data file 8 If you chose to acquire a new raw data file do one of the following Choose Manual Injection QOr Do the following a Choose Use Autosampler b In the Vial Position box type a vial position c In the Injection Volume box type an injection volume The minimum injection volume value allowed is 0 05 uL 9 To automatically create the master method click OK or Overwrite As the Method Forge creates the method it displays the following status steroids03 Note When you have a compound datastore enabled the Method Forge process searches the library and displays the identified compound names instead of peak times EE HT min Compound Name gt 1 9 Peak 1 99 c Full ms2 303 30Gcid4D Peak 3 18 c Full ms 315 20 amp cid40 00 100 1 Fea 210 cam I5 mes 133 Peak 1 39 c Full ms 331 20 amp cid40 00 100 Pekel bise Ellms aes eci aA Thermo Scientific ToxLab Forms 3 1 U
307. thod and associates a Associate a raw data file raw data file allowing manual peak selection Select Compounds from a compound datastore Creates a blank master method and displays the configured compound datastore allowing compound selection o Select compounds from CDS 2 Select Import Xcalibur Processing Method 3 Click OK The Import an Xcalibur Method dialog box opens ES Import an Xcalibur method l alx calibur method to import ac a EEE Raw data file ta associate ES LE Mass precision decimal places 62 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 4 To select an Xcalibur processing method file to import click the browse button for the Xcalibur Method to Import box 5 Browse to the Xcalibur processing method file and open the file The ToxLab Forms application imports the compound information from the Xcalibur method file 6 To associate a raw data file with this method click the browse button for the Rawfile to Associate box 7 Browse to the raw data file and open the file 8 Optional Change the number of decimal places in the Mass Precision box You can set the mass precision decimal places to any integer between 0 and 5 inclusive 9 Click OK fel Import an Xcalibur method ER calbur method to Import 2 amp callbur methods C_method prnd STRE Pta ms s L Wicaliburvdata LabFormns Raw Filesslevell rav
308. tion defined in the method Upper Limit Defined in the method Thermo Scientific ToxLab Forms 3 1 User Guide 247 5 Using the Production Mode Working in the Local Method View Working in the Local Method View A local method is a copy of a master method associated with a batch From the Local Method 248 View you can edit a local method or create a method template Follow these procedures ToxLab Forms 3 1 User Guide To open the Local Method View To create a method template To open the Local Method View Click Production from the dashboard or the navigation pane The Production navigation pane opens From the Production navigation pane click Local Method The Local Method View for the currently selected batch opens Local methods are named BatchName MasterMethod Name You can edit many of the method parameters in a local method just as you would edit a master method See Editing a Master Method on page 70 Enter any local changes to the method Choose File Save To process the batch or create new reports with the edited local method return to the Batch View and submit the batch Thermo Scientific 5 Using the Production Mode Working in the Local Method View Figure 53 Local Method View page Master method c Lab name ThermaFisher TCS aner NOME Injection v olurne 1 00 000 2 3 BE Onabolic Steroids Background subtraction range option Before peak al Number of s
309. tore opens in the Compound Datastore view Thermo Scientific Thermo Scientific QD ico co on kam 3 Using the Configuration Mode Compound Datastore To open a compound datastore 1 Click Load Compound Datastore in the Compound Datastore task pane The Open Compound Datastore dialog box opens Open Compound Datastore i Default TEES D fault quantum fe 1 2 To expand the folder click the plus sign before the folder name 3 Double click the name of the datastore you want to open The selected datastore opens in the Compound Datastore view See Compound Datastore view on page 35 4 To create a new compound datastore Click New Compound Datastore in the Compound Datastore task pane A new empty datastore opens in the Compound Datastore view You can import a file of compounds into the new datastore following the instructions lo import compounds or you can manually add compounds one at a time following the instructions lo add a single compound 4 To import compounds 1 Click Import Compounds in the Compound Datastore task pane 2 Browse to a csv or xml compounds file and click Open The ToxLab Forms application imports the compounds from the imported file adds them to any compounds already in the datastore and alphabetically sorts them ToxLab Forms 3 1 User Guide 31 3 Using the Configuration Mode Compound Datastore 32 ToxLab Forms 3 1 User Guide To add a single compound to th
310. toring SRM data to an XML file To export SRM data to an XML file 1 Open the master method from which you want to export SRM data 2 From the Method View task pane click Export SRM Data The ToxLab Forms application writes the data in the SRM table to the following file Thermo ToxLab Forms Methods wmethodname xm The data in this file matches the TSQ xml data and can be used in the instrument method editor when you use the TSQ application Note This command is available only when you check the Enable Compound Datastore option on the General page on the Application Configuration view See Application Configuration on page 37 SRM TSQ Quantum example ZA IDocument xml xml version 1 0 encading LITF 8 TsOQMassList TSQListitem ParentMass FroductMass V CollisionEnergy My startTime J My StopTime T Polarity Mame Wy TSQListltem J My ParentMass FroductMass CollisionEnergy StartTime J My StopTime Polarity Name 4 EE ERI ET EET E rl 148 ToxLab Forms 3 1 User Guide Thermo Scientific 4 Using the Method Development Mode Working with Instrument Methods Working with Instrument Methods An instrument method is a set of experiment parameters that define the operating settings for an autosampler gas chromatograph GC mass spectrometer and so on Instrument methods are saved as file type meth IMPORTANT Do
311. ts Jr HM Project a Project2 EH Project Lal Project E 3 Subproechh Click the minus sign or right click and choose Remove Project or Remove Subproject from the shortcut menu 3 At the prompt click Yes to remove the selected project or subproject Thermo Scientific ToxLab Forms 3 1 User Guide 29 3 Using the Configuration Mode Compound Datastore Compound Datastore 30 In the role of Manager or IT Administrator you can manage compounds definitions in the current datastore in the Compound Datastore view of the Configuration mode The current default datastore is the datastore specified for the current technology in the Application Configuration view See Application Configuration on page 37 Follow these procedures ToxLab Forms 3 1 User Guide To open the Compound Datastore editor To open a compound datastore To create a new compound datastore To import compounds To add a single compound To save a datastore To save a datastore to a new name To remove a compound or a compounds transition information To filter the compound list To open the Compound Datastore editor Click Configuration from the dashboard or the navigation pane The Configuration navigation pane opens Click the Compound Datastore task pane Import Compounds L Mew Compound Datastore fr Load Compound Datastore iz Save Compound Datastore m Save As Compound Datastore Recent Files The current datas
312. ts during the least squares regression calculation of the calibration curve Calibrants are weighted by the inverse of the square of their response or response ratio From the Response via list choose Area or Height Area Specifies that the ToxLab Forms application use this area value in response calculations Height Specifies that the ToxLab Forms application use this height value in response calculations To enter a note for the method Type in the Notes box or paste text from another application using CTRL V You can add a note to your method template so that there is a record of what makes this template unique To save the method template Choose File gt Save from the Method Template Editor menu The Save Method Template dialog box opens Do one of the following Typea new name for the master method and click OK Or Select a method name to overwrite and click Overwrite The ToxLab Forms application saves the new method template in the following folder Thermo ToxLab Forms Templates Methods ToxLab Forms 3 1 User Guide 143 4 Using the Method Development Mode Working with Master Methods Figure 35 Method Template Editor Method Template Editor lib File ior Find the peaks Handle confirming ions Sensitivity High ICIS Include confirming ions l Limit the retention time range Number of confirming ions Min AT min 0 00 apecify default ion ratio ranges Max RT min
313. uisition List Identification Detection Calibration Calibration levels HI Compound call cal cald E 5 DD amp cetamiprid 762 1 Methyldodecylamine EE 5 Repeat Step 4 for all calibration levels associated with the first compound 114 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 4 Using the Method Development Mode Working with Master Methods 6 To specify the same concentration values for all compounds select the value you want to copy right click and choose Copy Down from the shortcut menu Identification Calibration Calibration levels Acquisition List RT Compound cali ale eab ale 75 000 2 52 1 Methyldodecylamine 10 000 25 000 50 000 75 000 3 18 59 Alidochler 10 000 25 000 50 000 75 000 E 375 Acephate 10 000 25 000 50 000 75 000 Figure 22 Calibration Levels page General Compounds Reports gage Acquisition List Identification Detection Calibration Calibration levels AT Compound call cal cal cald 62_ 1 Mettyldodecslarine 10000 25000 sau 75000 2 fAlidochor TOD0 2500 5000 75000 ee I1 Ob BEE BE aont i6 40 Carbon dioxide 10 000 25 000 50 000 5 000 n F F c LT E d Manage Calibration levels ja ja a jo SIR Table 25 Calibration levels parameters Sheet 1 of 2 Parameter Description RT Retention time The t
314. und you want to make inactive 3 From the Samples list select or clear the Active check box Use the horizontal scroll bar at the bottom of the table to scroll to the Active column Filename IS Resp Active Excluded Compounds APN_001_09050 O Aprazolam mE Aprazalam D5 APN DO3 DSO50 m Nm F Inactive APN 45 D9050 Ll gt Paroxetine To exclude a calibration point From the Samples list select the Excluded check box for the sample When a value is no longer used for calibration it remains part of the calibration dataset and is displayed in the graphical view of the calibration curve Quantification Peak Pane The Quantification Peak pane displays the compound selected in the Samples list and Compounds panes You can store two peak value sets method and manual integration settings with each compound in each file These settings can result in a different set of stored values The method values were originally calculated based on the processing method parameters The manual values are a result of what has been viewed or altered When the sample contains an internal standard the chromatogram shows both the analyte and the internal standard in side by side panes Follow these procedures To zoom in on a peak To manually integrate a quantification or qualification ion To manually add a peak To remove a manually created peak To switch between method and manual integration modes To change the
315. using an autosampler you can set the default injection volume in the autosampler dialog box in the Instrument View The minimum and maximum injection volumes that you can use depend on the autosampler you configure The usable range depends on the injection mode and might be smaller than the range displayed Indicates whether the peaks have been manually integrated or integrated from the original method The distance from the peak maximum to the peak base measured perpendicular to the ordinate When the Resp Ratio is specified as Height this column is indicated with an asterisk Height The area obtained by integrating peak intensities from the start to the end of the peak When the Resp Ratio is specified as Area this column is indicated with an asterisk Area Actual retention time for the compound Retention time is the time after injection at which a compound elutes and the total time that the compound is retained on the GC column Expected retention time for the compound The amount present in the sample as determined using the calibration curve and the response ratio Theoretical amount of the compound expected in the sample ToxLab Forms 3 1 User Guide 203 5 Using the Production Mode Working in Data Review Table 49 Samples List parameters Sheet 3 of 3 Parameter Description Resp ratio The ratio of the Response value to the IS Response value If the Response is specified as Area in the processing method
316. vailable to users in the Method Development and Production modes Do one of the following To return the report selections to their original state when you first opened this page click Undo Changes ES To apply the current selections do the following a Click Apply A message reminds you that you must restart the ToxLab Forms application before your report selections are reflected in the reports available for the Method Development and Production modes b To restart the ToxLab Forms application now click Yes or to remain on the Reports page click No To import new standard report types Click Import In the browser locate a Crystal Reports dll file and open the file The application writes the imported report to the ToxLab Forms installation directory The Installed Reports pane displays the new report ToxLab Forms 3 1 User Guide 43 3 Using the Configuration Mode Application Configuration Figure 7 Standard Reports page Lustom Reports Installed reports Displayed reports High Density Internal Standard Report Batch Summary Report High Density Internal Standard Report Long Calibration Curve Report High Density Sample Report 2 Sample Report High Density Sample Report 1 Sample Report Long High Density Sample Report 2 Long Batch Report High Density Sample Report 3 Long Calibration Report High Density Sample Report 3 Chromatogranm Report High Density Sample Report 1 Long mn Compound Calibr
317. vel EPAMethod8270B 8level EC25B 8level 322010 a calx File Date Comment 3 1 2010 1 37 46 PM Lab name Thermo Fisher Laboratory Instrument ThermoFisher Instrument Method User AMERYjessie butler Batch EC25B 8level 322010 a Cali File Sample ID Filename Sample Name 10ng run04 Pentachlorophenol CCC m z 266 00 Method integration Apex RT f Height i Area 1035 1043 1051 1073 1080 Manual integration Apex RT Height Area g m E m E i T 1017 1035 1043 1051 1073 inm 10 4 10 8 RTimin Thermo Scientific 10 53 113493 124704 10 53 114006 142357 ToxLab Forms 3 1 User Guide 285 A Reports sample Standard Reports Method Report Method name Master method name Current calibration file Assay type Inj vol Instrument method Tune Breakdown method Compound identification Compound N Nitrosodimethylamine Pyridine RCRA 2 Picoline N Nitrosomethylethylamine APP9 Methyl methanesulfonate 2 fluorophenol sur N Nitrosodiethylamine APP9 Ethyl methanesulfonate phenol d5 sur Phenol CCC Aniline Bis 2 chloroethyl ether Pentachloroethane 2 chlorophenol 1 3 Dichlorobenzene 1 4 DICHLOROBENZENE DA IS 1 4 Dichlorobenzene CCC Benzyl alcohol 1 2 Dichlorobenzene 2 methylphenol Bis 2 chloroisopropyl ether N Nitrosopyrrolidine_APP9 3 Methylphenol amp 4 methylphenol Acetophenone N Nitroso di N propylamine SPCC o toluidine APP9 Hexachloroethane nitrob
318. w view to investigate and edit the quantification values in a batch To open the Data Review view 1 Click Production from the dashboard or the navigation pane Production The Production navigation pane opens 2 From the Production navigation pane click Data Review to open the Data Review view Data Review The Data Review view for the currently selected batch opens Data Review Panes The Data Review view uses a Samples list and one of two modes Quan Mode or Qual Mode The Qual Mode is available only for Specimen Qual sample types When you view the data for one of these sample types you can toggle between Qual Mode and Quan Mode Use the Samples list to select a particular sample Status indicators for each sample indicate if the sample is unacquired acquired acquiring or processed See Samples List on page 200 Method cal batch cal test Instrument ThermaFisher Man Status Flags Filename Euri lupe level Sample ID 3E 2 ass ee los Yea ater 198 ToxLab Forms 3 1 User Guide Thermo Scientific Thermo Scientific 5 Using the Production Mode Working in Data Review Use the Quan Mode and the associated Compounds pane to view quantitative information to complement the textual information for the selected sample See Quan Mode on page 205 Da Review lif Method lib cal test Instrument ThermoFisher Instrument Status Flags Filename S
319. xide MAIMLIB NL 888 BP 112 00 112 00 Optional In the Add New Compound dialog box make any of the following changes a Change the name for the compound in the Name of New Compound box b To use a compound other than the compound chosen by the ToxLab Forms application scroll to the spectrum for that compound and select the compound name in the header of the spectrum pane Thermo Scientific 4 Using the Method Development Mode Working with Master Methods v Purazine 1 4 dioxide MAINLIB Ask 40 SE 410 MP 1 select compound NL 999 BP 112 00 112 00 e amp ED D E E Bo E E E qi ra hz m 62 00 80 00 36 00 c c Click the Type of Compound to Add list and select a compound type 4 Click OK Thermo Scientific ToxLab Forms 3 1 User Guide 91 4 Using the Method Development Mode Working with Master Methods To replace a confirming ion 1 Click the pane for the confirming ion that you want to replace 2 In the raw file spectrum pane pause the cursor over a peak The red box indicates the selected peak 3 Right click and choose Set this Mass as New Confirming Ion from the shortcut menu The ToxLab Forms application replaces the confirming ion with the selected mass To add a mass as a new confirming ion 1 Click the pane for the quan mass to which you want to add a confirming ion 2 In the raw file spectrum pane pause the cursor over a peak The red box indicates the selected
320. ydrolysis qc 40 19 40 specimen 1 specimen 2 specimen 3 specimen 4 qc 125 Calibration Flags Quan Flags Thermo Scientific 18 77 21 42 19 23 20 89 21 68 18 92 21 32 A Amount Batch Summary Report Drug_A_ISTD_Test001 Drug_A_ISTD_Test001_Drug_A_IMPORTED_ISTD Drug_A_IMPORTED_ISTD Drug_A_ISTD_Test001 calx b ThermoFisher Instrument Diln Factor 1 00 1 00 1 00 1 00 1 00 1 00 1 00 1 00 1 00 1 00 1 00 Legends of Abbreviations ISTD Name Drug A Conc RT Quan Flags N A 1 93 N A 1 93 N A 1 92 N A 1 92 N A 1 92 N A 1 93 N A 1 92 N A 1 91 N A 1 92 N A 1 94 N A 1 92 Internal Std lon Ratios 473 20 488 20 l479 40 371 20 0 00 m 59 31 27 94 21 96 28 25 2 04 0 00 3974 53 28 86 20 33 28 37 57 59 28 38 22 11 28 07 0 00 27 72 20 30 25 71 113 14 27 82 20 01 C Carry Over Linearity Limit D Detection Limit Q Quan Limit H Hydrolysis A IS Area Range R IS RT Range lon Ratio Failure n Negative b Solvent M Quan ion manually integrated m Qualifier ion manually Page 2 of 3 380 40 371 20 371 20 371 20 A Reports sample Standard Reports 371 40 297 95 100 00 114 27 100 00 10 35 100 00 21180 20 100 00 94 95 100 00 296 89 100 00 114 96 100 00 0 01 100 00 93 63 100 00 597 96 100 00 93 84 100 00 ToxLab Forms 3 1 User Guide 259 A Reports sample Standard Reports 260 Report Generated Sample Tune Dates

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