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Chromeleon/MSQ Plus Operator`s Guide

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1. Chromeleon MSQ Plus Operators Guide 1 4 13 Starting a Sequence MSQ Mass Spectra Data Extraction Integration and QNT Editor Views Background Subtraction In some circumstances it may be useful to subtract the background ions out of the spectra Subtracting the background ions may make it easier to identify what masses are attributed to your sample versus those attributed to the solvents There are two ways to subtract the background spectra 1 via the MS tab in the QNT editor 2 via Mouse Clicks on the chromatogram To Enable Background Subtraction via MS Tab Peak Spectrum Bunch v Enable Background Subtraction Width specta Background Subtraction f Peak Dependent Background Subtraction Left Region Bunch Width i za spectra Right Region Bunch Width i spectra t Fixed Background Subtraction Ranges 4 A Calibration A Spectra Library Screening ASST AMS la The MS tab defaults to background subtraction disabled To activate background subtraction 1 Click the box next to Enable Background Subtraction 2 Two options appear for background subtraction a Peak Dependent The software will average a user defined amount of spectra points to the left and right of each peak Automatically calculated for each peak in the chromatogram b Fixed Background Subtracts two specific time segments from the chromatogram Typically the time points are set at t
2. TRUE DENSSOURCE Ms new grading ICS3000 MSQ 11 5 Batch Report Ckrl R MS iodate pam ICS3000_MS 11 MS L pgm ICS3000_MSQ 11A Print Table MS BrO3 pam ICS3000 MSQ 11 5 MS Br pgm ICS3000 MSQ 11 1 MS pam ICS3000 MsQ 11M ONLY pgm ICS3000_MS 41142 Show History fault qnt 11 21 Properties Alt Enter gt m Type Pos ny Vol OREN 1 12 13 06 default J equilibration Blank 30 100 0 IC MS new grad2 TEMP default 2 03 25 08 deFault 3 equilibration Blank 30 100 0 IC MS new grad2 TEMP default 3 03 25 08103 25 08 3 water blank Unknown 31 100 0 IC MS new grad2 TEMP defaut 4 SLG SHENDAYLAP_ 420080311 1ppb Standard 32 100 0 IC MS new grad2 TEMP default 5 SLG ASHENDAYLAP 120080312 2ppb Standard 33 100 0 IC MS new grad2 TEMP default 6 030708lDef ault Sppb Standard 34 1000 IC MS new grad2 TEMP default 7 A51 8 OA ESIneg F5 0 7 B 10ppb Standard 35 1000 IC MS new grad2 TEMP default 8 A518 OA ESIneg 0 7 20ppb Standard 36 100 0 IC MS new grad2 TEMP default n 35ppb Standard 37 100 0 IC MS new grad2 TEMP default Exit 38 100 0 IC MS new grad2 TEMP default J M5020602_local a 31 100 0 IC MS new grad2 TEMP default MSTC A local a equilibration 30 100 0 IC MS new grad2 TEMP default Other Templates B equilibration 30 100 0 IC MS new grad2 TEMP default T a a water blank 31 100 0 IC MS new grad2 TEMP default ia Mini zin 8 32 1000 IC MS new grad2 TEMP default training customer data 0 IC MS
3. Extemal f nternal f nternal Esternal Internal Standard Options Use sample amount as reference Variable Internal Standard Cancel Help 9 The last step is to link the analytes of interest to the internal standard a Double click on the standard column for the analyte of interest b In the dialog box select Internal and in the pull down list for Associated ISTD Peak choose the name of the internal standard Standard Method for Cmpd B Evaluate amounts by the following standard method External Associated ISTO Peak f nternal t nternal E sternal 10 When complete standard type for the UV Conductivity as External the SIM monitored analyte as Internal referencing the internal standard peak and the internal standard labeled as ISTD Internal Ret Time Window Standard Int Type HE Re Comment 1 Total mmm Ge0504G Internal ISTD A 2 Autogenerated 2 367 min 0 083 AG JSTO internal Area Ho Feak Hame Ret Time Autogenerated Autogenerated Peak Tracking A MS Tracking A Calibration A Spectr 4 4 12 Chromeleon MSQ Plus Operator s Guide el N F MSQ Starting a Sequence Mass Spectra Data Extraction Integration and QNT Editor Views Amount Table Tab The amount table is used to define the concentration of the standards 1 Double click on the column labeled Amount As long as standa
4. The program and quantification Files will be imported copied inta the new sequence Browse Preferred Reporting Options Preferred Report Preferred Channel EDI N F X Chromeleon MSQ Plus Operator s Guide 3 21 Chromeleon Software Sequences MSQ Chromeleon Sequence Wizard Step 5 of 5 Saving the Sequence Saving the Sequence Specify where to save the sequence Press Finish to save it Name amp Title Remember to enter a new sequence name unless you want to overwrite an old sequence Sequence Name Title Location Datasource SHENDAYLAP local Directory m Browse Cancel Help Modifying an Existing Sequence In order to modify an existing sequence open the previous sequence in the Browser Recall Sequences are identified by the blue folder icon next to their names 1 Open an existing sequence 2 From the File Menu select Save As 3 Specify a new name for the sequence about to be created 4 Click Save File Edit Tools Window Help e ie 15920190 local SHENDAYLAP local IV CS12A MS qnt CS124 MS 11 8 2007 9 14 27 A MSQ J Analyst V AS16 qnt 11 7 2007 6 02 20 P MSQ za M AS51615 mM KOH 1 4S16 15 mM KOH 0 25 mL min Anions 11 13 2007 3 49 24 MSQ J AUDIT fij 11022007 BACKGROUND TEST fm 11062007 SINGLE ION STANDARDS Cat NoJNam Type Pes Inj Vol Method Inj ffi 11062007 SIN
5. MSQ 2 0 SP1 Read me Figure 1 Install NIST 2 0 from Xcalibur 2 0 Installation CD The default installation folder for the NIST MS Search program is C Program Files NISTMS MSSEARCH 8 7 Download and Install NIST MS Search Program Upgrade 1 Download the upgrade from this link as shown in Figure 2 http chemdata nist gov mass spc Srch v1 7 index htmlNIST 02 MS Library UPDATE 2 Savethe upgrade program on your local PC hard drive e g desktop the default file name is V17 20 UPG 8 4 Chromeleon MSQ Plus Operator s Guide EDI N F MSQ Establishing NIST 2 0 Anion Library Download and Install NIST MS Search Program Upgrade MS Search Program v 2 0 UPGRADE This upgrade installs version 2 0 of the NIST MS Search Program This upgrade will not replace your NIST MS Search Program v 1 6 or 1 7 but it will upgrade any previously distributed version 2 0 files Please refer to readme v20 txt included in the zip file below for more details This software upgrade should not be applied to the software accompanying the NIST 02 MS Library UPGRADE INSTRUCTIONS Detailed instructions are included in readme v20 txt in the zip file Please read this document before downloading the complete zip file For this upgrade to work properly it is important that the MS Search Program is not open when the files are extracted Download MS Search Program v 2 0 Upgrade Figure 2 Download MS Search program upgrade Close the NIST MS
6. Protocol field on the left side of the box 4 Notice the Panel Tabset appears without the tab for the MSQ 5 Right click on the grey space to the right of the last tab and select Add Panel 6 Click the Up One Level icon on the pop up screen until you get to the Datasource name 7 Open the Dionex Templates folder This folder typically has a red lock next to the name 8 Browse to and open the Panels folder inside Dionex Templates 9 Once inside the Panels folder open the LC MS folder 10 Double click on the MS SIM Mode panel 11 The panel is added to your tabset 12 Save the tabset in a location you will later be able to find 13 The next time this tabset is open it will include the MSQ tab Chromeleon Panel Tabset File Edit View Workspace Qualification Control Batch Window Help 0 X D c d A P b e m m Sud BDI N M LLL Chromeleon MSQ Plus Operators Guide 1 3 3 Chromeleon Software Creating Modifying the Panel Tabset Connect to Chromeleon Serve Computer bly Computer i Chromeleon Server 4 Bg Network Neighborhood Protocol x Enter connection information manually or select a Chromeleon Server from the list on the right Cancel Help Ehramalean Panel Tabet FE Fie Edt View Workspace Guilfication Control Batch Wika Help OGM De Se ete eh Sud ay ED 11 14 43 AM User SHenday trem SHENMDAYLAFP has
7. t Off Normalize time C Shift Stretch Normalize signal Offset Arrangement m om Overlay m Overlay Selen Overlay with peak decoration Mixed Overlay with right signal asis C amp utopurification Mirror chromatogram cone Arey He 5 2 Chromeleon MSQ Plus Operator s Guide BDI ONEA MSQ Backing Up Exporting Data Files Mass Spectra Data Extraction Integration and QNT Editor Views Backing Up Exporting Data Files In order to store the complete data or e mail the data to a Dionex representative the following steps must be followed 1 Inthe Browser screen single click on the name of the sequence Do not click anywhere else If for instance you click on the name of a sample then only that specific sample will be stored 2 Go up to File and select Export Backup Choose Backup Chromeleon MSQ20190_local ICS3000_MSQ 2_Data UNH 1 1 20 07 CURVE Browser UE File Edit View Workspace Qualification Batch Tools Window Help D Mew Ctrl N Open Cctrl O Close Y Save s utdown_MS and IC pgm linear ramp 7 60 LEMP hi 4 producibility check pam linear ramp 7 61 ANDI Chromatography AIA Wear ramp 0 23 Import Restore gt Electronic Signature gt np 4 pgm Preferences MS new grad3 pqm linear ramp 7 61 anne brit Kali sin id se deii i ICS3000 MSQ 11 1 MS rad2 i
8. 9 2 Adding a Chromeleon MS spectra to an Existing Library esses 9 3 9 3 Create Your Own Library and Add Entries sse 9 4 IV Chromeleon MSQ Plus Operator s Guide EDI N M MSQ Chromeleon MSQ Plus Operator s Manual Introduction Chromeleon MSQ Plus Operator s Manual 1 1 Introduction The intent of this manual is to familiarize users with basic concepts of MSQ operation under Chromeleon control Users should already be comfortable with the hardware of the front end ion chromatograph IC or liquid chromatograph LC MSQ Plus and with basic Chromeleon functions This manual should not be used as a substitute for formal Chromeleon training 1 2 Conventions The figures and call outs used in this manual are to aid the user in performing Directions and actions Directions to be performed in an ordered sequence Alternate ways of performing a given task Commonly used commands icons for Mass Spectrometry Important Notes and Cautions Caution Always turn power OFF EID ONEA Chromeleon MSQ Plus Operator s Guide 1 1 MSQ The Chromeleon Server Monitor Starting the Server The Chromeleon Server Monitor 2 1 Starting the Server When the computer is initially started the Chromeleon Server is not running In order to establish communication with the devices including the mass spectrometer open the Server Monitor 1 Locate the Server Monitor in the task bar 2 Id
9. There are several factors that will affect the probe temperature a Solvent composition b Flow rate c The thermal labile properties of your sample 3 The probe temperature will have to be optimized for each application B In the lower portion of the screen define the scan functions 1 Name FSI in the name field indicates the parameter fields are for a full scan event 3 12 Chromeleon MSQ Plus Operator s Guide BDI N f X MSQ Chromeleon Software Program Files 2 Mass Range Enter the range of atomic mass units amu for the detector to scan The software for the MSQ Plus is calibrated to scan from 23 1972 amu 3 Time Range Define the time in minutes for the run to be collecting the data 4 Peak Format Sets the scan function for how data is collected a Centroid The most common way to collect full scan spectra Nearby masses are averaged into a shape resembling sticks b Profile Collects data that visually resembles chromatographic peaks Yields a great deal of information about the mass of your specific analyte but takes a lot of memory on the computer 10x more hard drive space is required when using Profile mode over Centroid mode HAN MS Method Editor Per Method Parameters Description ISetpoint g lonization Mode ES NUM Probe Temperature C 400 00 w Show Method Options All Scans 100 Full Scans SIM Scans 90 Parameters a0 Scans gt 70 veyor MSO Add Full 3 60 Add
10. matrix Hed the selected device from the list diversion valves external water for IC systems EC on Program Wizard Relay and State Devices Options MS Start Retention Time min State 94 Open State Open 94 Closed SHEE Pump gece av Duration MS Start Help Inserts the selected device mto the list Nest gt Cancel Help 3 10 Chromeleon MSQ Plus Operator s Guide BDI ONEA MSQ EDIONEX Chromeleon Software Program Files a If the first few minutes of a run are not important enter the delay time here b If the run is to be synchronized with the inject command enter 0 01 minutes into the blank 3 Set the duration to 20 seconds 4 Click Add Program Wizard Relay and State Devices Options MS Start Retention Time 0 01 min B lg State ga Open Duration 20 d 011 53333 30 s 4 Closed sem PUSH erit Noi Stmte Duration Help Enter the retention time in industry minutes Back Cancel Help Program Wizard Relay and State Devices Options MS Start Retention Time 0 01 mir lo State g Open Duration 20 0 01 59999 90 g Closed cui rea MMS Start Open 0 010 MS Start Closed Help Inserts the selected device into the list lt Back Next gt Cancel Help Chromeleon MSQ Plus Operators Guide 1 11 3 11 Chromeleon Software Program Files MSQ Upon completion o
11. 18 KB Customer ata IC MS new grad6 p 27 min run 5mM 0 10 10 20 5 47mM 20 ICS3000 MSQ 11 27 2007 6 08 33 SHenday 18 KB AUDIT MR IC MS new grad5 P 27 min run 5mM 0 10 10 20 5 47mM 20 ICS3000 MSQ 11 27 2007 10 24 3 SHends 3 KB 11022007 B MR IC MS new grad4 T 27 min run 5mM 0 10 10 20 5 47mM 20 ICS3000 MSG 11 28 2007 2 25 20 SHend 11062007 SI MP IC MS new grad4 T 27 min run 5mM 0 10 10 20 5 47mM 20 ICS3000_MSQ 11 29 2007 3 26 42 SHend 11062007 SI MP IC MS new grad3 p linear ramp 7 60 IcS3000_MSg Dz 3 03 Heng G 11132007 BF P IC MS new grad2 eM Te ty ETUR S oe ETUR 11142007 BE VI default2 ant Sal FINAL DATA V default qnt 12 T7407 4 29 36 SHend Sros Mome ie fros mi Vol Program Method o Dionex Template Blank Blank 1 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 2 23 58 1 0000 HPLC A Dionex water blank Unknown 1 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 3 00 44 1 0000 IC A Dionex water with ISTD Unknown 2 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 3 35 25 1 0000 IC MS 4 f 1ppb Standard 3 100 0 IC MS new grad4 TEMP default2 Finished 41 29 2007 4 10 03 1 0000 Other Templates ff 2ppb Standard 4 1000 IC MS new grad4 TEMP default2 Finished 11 29 2007 4 44 43 1 0000 E THERMO E7508E 8 m Sppb Standard 5 1000 IC MS new grad4 TEMP defautt2 Finished 11 29 2007 5 19 23 1 0000 HUND ft 10ppb Standard B 100 0 IC MS new grad4 TEMP defaul
12. 449 Bromate RT 6 75 min NL 1 53E3 T 0 3 c ESI corona sid det 1400 00 SIM ms 126 75 127 25 70 00 1 342 127 0 Bromate RT 6 89 min NL 5 79E3 T 0 3 c ESI corona sid det 1400 00 SIM ms 126 75 127 25 70 00 127 0 Bromate RT 7 05 min NL 2 10E3 T 0 3 c ESI corona sid det 1400 00 SIM ms 126 75 127 25 70 00 m z DE LIS UAE a a TS ee c ccEUUN PEG ICI STE pum Ze 126 750 126 800 126 900 127 000 127 100 127 200 127 250 To remove the retention spectra i 2 3 4 5 EDI N F X Chromeleon MSQ Plus Operator s Guide 1 3 Right click on the spectra side of the screen Select Decoration Go to the Peak Spectra tab Uncheck the boxes next to Retention spectra Front 1 and Tail 1 Click OK Report Definitions Removing the Retention Spectra eee MSQ 6 At this point if the spectrum does not appear in the spectra screen select the portion of the chromatogram where you would like to look at the spectra Chromeleon MSQ20190_local ICS3000_MSQ 2_Data UNH 11 16 07 26 35 ppb CD_1_Total MSQ20190_local ICS3000_MSQ 2_Data UNH 11 16 07 26 35 ppb CD 1 Total A File Edit view Table Workspace Qualification Window Help 8 X Dc k sirg K k Eod WI OL AG IK uz c 71M e amme a B Ate EU 11 16 07 26 35 ppb CD_1_Total 440 Bromate RT 6 75 min NL 1 53E3 T 0 3 c ESI corona sid det 1400 00 SIM ms 126 75 127 25 70 00 1 200 50 How to What s thi
13. Data Extraction Integration and QNT Editor Views Duplicate column Ret Time Channels Delete Channels Fill mode Copy contents from original C Setto default values OK Cancel Help Select Channel ADD SIM 2 SI Ul UD 1 IED Total Pump 2 Pressure mind m3 7 In complicated analysis compound identification may be easier if separate SIM channels are created for each analyte of interest 8 Locate the Standard column a Chromeleon defaults to list the Standard as External b Double click on the word External in internal standard row Select Use this peak as Internal Standard ISTD Click OK e p The color of the row shades in yellow when internal is selected ls Peak Hame Ret Time ndow Standard Int Type Cal Type Peak Type Comment LI nl umm 1533mn x 0 050 AG External Area Lin Auto Autogeneraled 1933mn v O 067 46 External Area Lin Auto Autogenerated 2 Cmpd B S STD A a gt General A Detection Peak Table A Arnoun EDIONEX 2 367 min 0 083 AG External Area Lin Auto Awtogenerated Tracking A MS Tracking Calibration Chromeleon MSQ Plus Operators Guide 1 1 1 4 11 Starting a Sequence MSQ Mass Spectra Data Extraction Integration and QNT Editor Views Evaluate amounts by the following standard method
14. Dwell CD_1_Total 2 LINDA AND CARY 6 time corre oted by 0 180 min OA stds Dwell SIM 01 lt a x13 LINDA AND CARY 6 time corrected by 0 180 min DA stds Dwell SIM 02 4 LINDA AND CARY 6 time corrected by 0 180 min OA stds Dwell SIM 03 lt E 15 LINDA AND CARY 6 time corrected by 0 180 min DA stds Dwell 8IM 04 NDA A AR 6 time cortacted by if td h M Of 34 8 H 10 11 269 m How to What s this Tools gt SB1 3 2 92 49 8581 22 2709 P 4 448 7 4387 10 299 i UV Background Subtraction gt MS Background Subtraction gt 4 1 250 000 A 3 JA Full Size Autoscale 376 000 4 Detection Parameters gt Export Ld 0 0 1 0 2 0 3 0 4 0 5 0 6 0 70 8 0 9 0 10 0 11 0 12 0 13 0 Load Report Definition 5 Locate the Comparison tab Uncheck Signal Offset if you would not like to see the baseline of the runs shifted up but at the same level Play with all of these parameters to see which one best fits your needs Including the arrangement section of the menu EDI N EX 0 LLL Chromeleon MSQ Plus Operators Guide _____SSSSSSSSSSSSSS 5 1 Overlaying Data Channels or Multiple Injections M SQ Mass Spectra Data Extraction Integration and QNT Editor Views Chromatogram Decoration Colors Fractions Peak Calipers Frame amp Anes Time Sale T Caption Peak Decoration Feal Label Compr Hormalization At peak
15. MS Library and how to use the Anion MS Library to perform spectra search for unknown analytes The Anion MS Library currently contains single quadrupole MS spectra of eighty four common anions and organic acids It is not intended to explore the complete functionalities and features of the NIST 2 0 MS Search For detailed information on how to use the NIST 2 0 MS Search and additional information please refer to the NIST User s Manual which can be downloaded from this link http www nist gov data WebGuide nist01 Ver20Man pdf 8 2 Parameters Used to Acquire Standard Spectra EDIONEX Ion Chromatography ICS 2000 Reagent Free lon Chromatography RFIC Column System AS20 P N 063065 or AS11 HC P N 052961 hydroxide selective column 2 x 250 mm ASRS 300 P N 064555 external water mode Assistant make up 0 2 mL min acetonitrile delivered by an AXP MS pump P N flow 060684 Static mixing tee P N 063143 for combining IC and organic make up flow Suppressed conductivity and MSQ Plus mass spectrometer Mass Spectrometry MSQ Plus single quadrupole mass spectrometer lonization interface Electrospray ionization ESI Probe temperature 450 C Chromeleon MSQ Plus Operator s Guide 8 1 Establishing NIST 2 0 Anion Library MSQ System Requirements Needle voltage 1500 V Nebulizer gas Nitrogen at 85 psi All MS spectra were obtained from chromatographically separated peaks to eliminate interfe
16. SEG ASHENDAY LAP _ iu MS manual Program LC MS 800 psi Sequence 124 07 EH Injector Elapsed Program Time j ICS 2000 span Total Program Time i iv Connected Startup down Show Plot Load e T me Inject 124 07 Injector Settings ICS 2000 Column Heater t d Temperature Heater Settings 0 306 uS Suppressor On 5m Detector Se ICS 2000 Detector 1 2 it a i a i a ae ii Scan ia ccc a 0 0 2 0 4 0 6 0 8 0 12 0 14 9 min 11 6 pS SHenday IC MS Acquisition Familiarize yourself with the menus and toolbars at the top of the screen to navigate between these windows Chromeleon Panel DET FE File Edit View Workspace Qualification Control D S RE 3 2 Chromeleon MSQ Plus Operator s Guide BDI ONEA MSQ Chromeleon Software Creating Modifying the Panel Tabset 3 4 Creating Modifying the Panel Tabset Your Dionex Service Representative should have created a custom Panel Tabset for your system A link to this tabset should be found in your Browser To create your own Panel Tabset 1 Click on the shortcut to the Panel Tabset icon or as in the yellow box Click on the Shortcut to Panel Tabset icon 2 To connect to the Chromeleon Server click on the by My Computer 3 Click on the Chromeleon Server to populate the Computer and
17. disconnected from Limpia u Ic MS T1243 AM User SHenday from SHEMDAYLAP has connected bo bimebase IC MS 111249 AM User SHenday fem SHENDATLAP has acquired contra over timebase lc MS Program Elapsed Program Time gMCS 2000 Syetan m Total Program Time E Connected Startup Shutdown Show Plot beadPosition Load Inject Injector Settings i Heater Settings 0 068 pS Are om Detector Settings 3 4 Chromeleon MSQ Plus Operator s Guide iE VT TT BL Umm 1 iri i a 11 12 43 AM Uggi Hentay from SHENDAYLAF has connected bo bimebase li MS al MSQ m fa fx A E EDIONEX MSQ Chromeleon Software Creating Modifying the Panel Tabset Up One Level Browse Look in E MSQ201790_local d P Templates al REFLOW RATE TT EicsasonnECD Mame J Flow Rate JiCS 3000 M50 Cancel JMS 20602_local Object of type Control Panel Hel MSTC local elp ili Mame Object of type Control Panel f Help MS SIM MODE zl Cancel Object of type Control Panel m Help Chiremalggn Panel Fabel EE Fle Ei vem Workspace Gualficetion Coin dutch Window Help D ak va PW bo er EF eee LE IM E IC ME IC5 2300 System IC H5 SHENOATLAP Sequence Conna Sista TC MS sairon Tease IC H3 on SHEHDATLAP courte Ne Virriehaese KMS l alaritr na Do
18. from the Tool drop down menu Gs onn xleis from the top tool bar 3 As shown in Figure 4 click on the 2 tab of the dialog window named Libraries From the left side of the window click ic ms anions from available libs and click gt gt Add gt gt to Included libs 814 Spectra in 2 ries in 4 Click on the nistdemo from the Included libs and click on the di P delete button located next to Included libs to delete the NIST Spectrum search z Demo library which contains GC EI MS spectra not applicable to IC MS applications Click OK to save the settings OK Cancel Help Figure 4 Specify the Search Library NOTE If multiple applicable libraries are available for example a Dionex IC MS Anions and a user customized library both libraries can be added to the Included Libs The libraries selected will be searched sequentially and if a representative compound is in one or more libraries it may appear multiple times in the results of a search This can be used to an advantage for instance if a compound was run twice with different parameters the search will return the closest matches ranking the selected spectra with the best fit to the searched spectrum 8 6 Chromeleon MSQ Plus Operator s Guide EDI ONEX MSQ Using the NIST MS Search with Chromeleon Search Chromeleon MS spectrum against NIST Libraries Using the NIST MS Search with Chromeleon 9 1 Search Chrome
19. it is necessary to extract mass spectra data for a LC peak For this to occur full scan data must be acquired Hopefully the m z of this known or unknown peak falls within the range of the full scan THIS IS TYPICALLY THE FIRST STEP WHEN IDENTIFYING THE m z OF A KNOWN OR UNKNOWN SAMPLE Chromeleon MSQ Plus Operator s Guide BDI N f X MSQ la File Edit View Table Workspace Qualification Window Help Dc He 09 18 06 16 ACT MIX UV_VIB_ 1 4 Peak 2 AV 1 57 1 61 min 2 NL 3 78E5 T 0 2 c ESI corona sid 75 00 det 1200 00 Full ms 40 00 1000 00 35 0 WVL 254 nm 235 7 2 1 592 EDIONEX Starting a Sequence Mass Spectra Data Extraction Integration and QNT Editor Views To extract mass spectrometer data Open the data file by double clicking on the finished sample in the Browser Go to the View Menu gt Show Mass Spectra or click the Show Mass Spectra icon on the toolbar The screen will change to show the CD UV data on the left side of the screen and the mass spectra data on the right side of the screen Select the spectra tool from the toolbar Single left click the apex of the UV CD peak or to average the spectra across the peak hold the left mouse key down and drag across the width of the peak R Let bN A ESAR W Keo e 388 3 451 3 646 3 7260 808 8 858 9 056 Gn z nk eh Atl it Bt hi 400 500 600 700 800 900 1 000 M N 0 P Q R The mass spectra data on the right side
20. new grad2 TEMP default Stacy 0 IC MS new grad2 TEMP default ia 07 23 07 0 IC MS new grad2 TEMP default AIL 0 IC MS newv grad2 TEMP default LINDA AND CARY LO IC MS new grad2 TEMP default E 5G O IC MS new grad2 TEMP default 4 Selecting Backup opens a menu Hit the Browse button to identify where the backup file should be stored and to name the file 5 Make sure to check the boxes for a Include MS spectra raw files b Include linked objects c Compress Data EDI N EX 0 LLL Chromeleon MSQ Plus Operators Guide ______ SSS 6 1 Backing Up Exporting Data Files Mass Spectra Data Extraction Integration and QNT Editor Views Selected item s MSQ20790_localSICSS000_MSQ 2_DataSUNH411 20 0 CURVE seq Destination CAD acuments and Sethngsshenday Desktop backup cmb Default Path C Documents and Settingssshendau s used for empty paths Options Title I Include 3D fields Iv Include MS spectra raw files Remark Signed sequences are always stored completely including all channels 3D fields and M5 files Iv Include linked objects w Compress data ee Delete original Cancel Help MSQ 6 If by accident Delete original is checked do not worry Chromeleon will perform a safety check function to make sure that all backed up data is complete and correct before deleting your data 7 Press Start 8 Asthe data is backed up a menu will show th
21. spectrometer enters standby mode the high voltages heater and nitrogen gas flow turn off Shutdown Parameters Depending on the configuration the hardware and software requirements to place the system into standby mode will differ Things to remember to turn off on the front end are e Flow to the column e UV lamp e Ovens e Fluent generator suppressors CR TCs for IC customers The easiest way to create a shutdown program is to modify an existing program to include the shutdown parameters and save this file under a different name Creating a Shutdown Program for the Mass Spectrometer EDI N F Qhromeleon MSQ Plus Operators Gude 1 393 15 Chromeleon Software Shutdown Programs While it is difficult to create a specific example of a shutdown program that will apply to all customers the following steps are required to shutdown the mass spectrometer at the end of the sequence 1 Open an existing program by double clicking on the file name In this example open the program file associated with the sequence Ug File Edit View Workspace Qualification Batch Tools Window Help D c bel 2 EH db R sme mooka ume O v me eme esumme meas sg SHENDAYLAP local gt A shutdown MS and linear ramp 7 50 TEMP AT 35C ICS3000_MS 11 16 2007 2 03 36 SHenday 1KB Analyst MR IC MS new grad p 27 min run 5mM 0 10 10 20 5 47mM 20 ICS3000_MS 11 27 2007 6 08 55 SHenday
22. 15 b Lower span values generally offer more sensitivity but may be less robust A slight shift in mass could cause the scans to be on the peak shoulder not centered on the apex 3 14 Chromeleon MSQ Plus Operator s Guide BDI N f X MSQ Chromeleon Software Shutdown Programs 5 Time Range Enter the time range in minutes to scan for this mass in your chromatographic run a When running several scan functions consider specific time ranges for each SIM channel b Staggering the time range for each peak minimizes the total analytical cycle time and optimizes the signal to noise 6 Dwell Time The time spent in seconds on scanning this specific mass Dwell time is critical for optimizing signal to noise on the peak This parameter must be optimized for each application b Its value also depends on how many channels of data you are acquiring from the mass spectrometer Be wary with total analytical cycle time with respect to dwell time c Calculate to measure at least 10 measurements across the chromatographic peak 7 Polarity Positive or negative polarity anionic or cationic species Cone Voltage Analyte specific this value is user optimized to determine maximum peak sensitivity and the desired CID 3 6 Shutdown Programs At the end of the run the system should be placed into standby mode In this mode the eluent flow is either turned off or diverted away from the mass spectrometer When the mass
23. 3 2007 3 49 24 MSQ 19 KB E 11022007 BACKGROUND Ku 11062007sINGEIONsT No Name TT T CN TNNNNNNNENICECENNNE E CE a 11062007 SINGLE ION ST mE n DI Water Standard 20 000 4516 15 mM KOH 10 min Sa 11132007 BACKGROUND 2 fj DI Water Standard 20 000 AS16 15 mM KOH 10 min Finished Hill 11142007 BACKGROUND fj 10 ppm Chloride Standard 20 000 AS16 15 mM KOH 10 min Finished El FINAL DATA 4 ffj 10 ppm Chloride Standard 20 000 4516 15 mM KOH 10 min Finished 11 13 2007 4 33 50 Nm oh 2 The fastest way to create a method is to type a name in the column and hit enter 3 Click F9 to add the same method name down the entire column vug ww yu me ee MEIN od ek Em at 7 ustomer Data M AS16 15 mM KOH 1 AS16 15 mM KOH 0 25 mL min Anions 11 3 2007 3 49 24 MSQ 19 KB fa 11022007 BACKGROUND Eu 11062007 SINGLE ION sT No Name Type Pos inj Vol Program Method Status _ In E 11062007 SINGLEIONST 1 fj DI Water Standard 1 20 000 AS15 15 mM KOH 10 min a 11132007 BACKGROUND f DI Water Standard 1 20000 AS16 15 mM KOH 10 min fill 11142007 BACKGROUND 10ppm Chloride Standard 2 20000 AS16 15 mM KOH 10 min Finished 11 1 I CS124 MS qnt C3124 MS 11 8 2007 9 14 27 A MSQ 10 KB t AS15 qnt 11 7 2007 6 02 20 P MSQ 21 KB VP AS1815 mM KOH 1 4518 15 mM KOH 0 25 mL min Anions 11 13 2007 3 49 24 MSQ 13 KB 5 The software alerts you that there is no method file with the name you ente
24. 4 6 Chromeleon MSQ Plus Operator s Guide EDI ONEA MSQ Starting a Sequence Mass Spectra Data Extraction Integration and QNT Editor Views Detection Tab Ret Time Param Name Param Value Channel min 0 000 Minimum Ares 0 001 Signal m AES ee cs All Channels CD 4 CD 1 Total Pump 1 Pressure Pump 2 Pressure SIM 01 SIM 2 v 4 A General ADetection A Peak Table A Amount Table A Peak Tracking A MS Tracking A Calibration The Detection tab defines the criteria for identifying peaks There are over twenty five parameters available to define a peak in the chromatogram These parameters are unique for each application and must be user customized for the analysis NOTE To see a complete list of the parameters along with explanation of the parameter double click the parameter name field Not the title but the name of the parameter Edit detection parameter Parameter Value Default 0 001 Retention Time Farameter Name O oo min Id aximum Area Reject Minimum Height Range 0 0 1 0E 15 Maximum Height Reject oo ice ENT Maximum Peak Height a cme mi Miniman Width E Masinum Width Rider Threshold M asimum Rider A atio Rider Skimming Peak Shoulder Threshold Explain Param Front Riders to Main Peaks Help Determines the minimum area For peak detection and integration This parameter has ta be activated before the pea
25. Default E area and height percent repart E peak analysis report 75 E area and height percent report 2 plots H Peak Area Ratios CATION repart E peak summary report 50 E default E Trending Report 25 Name defltLCMS ien Channel Cancel 0 0 13 25 38 5 0 63 75 8 9 10 0 143 Object of type Report definition Help D E G Peakname Ret Time Area Amount Height min nC min nC 5 033 21 3569 116 980 8 9 600 35 4810 8 110 748 3 n a 11 300 29 4220 n a MB 74 993 4 n a 12867 31 1706 n a BM 78 691 Go to the View menu and select Printer Layout 6 Scroll through the tabs at the bottom of the screen to discover all of the different views 7 To customize a view a First the report definition must be saved outside of the Dionex Template folder This is done by right clicking on the page and selecting Save Report Definition SAVE THE FILE OUTSIDE OF THE LOCKED DIONEX TEMPLATE FOLDER b The chromatogram can now be customized as desired c To change the columns displaying integration values you must enter Layout Mode EDI N F X Chromeleon MSQ Plus Operator s Guide 1 1 Report Definitions How to make a report definition for MSQ several SIM channels on one page 1 2 i From the Edit Menu select Layout Mode ii In this mode you can change the parameters of the report columns by double clicking on the report column name This displays all available parameters Chrom
26. FINAL DATA Browser Sel 8 X MSQ EDIONEX MSQ Chromeleon Software Shutdown Programs 3 Modify the IC LC parameters to turn off the flow or divert the flow away from the mass spectrometer Chromeleon Program File IC M5 new prad4 TEMP 2 Commands Hi Die Ede view Workspace Qualification contra window pep Ax D ck sas QN k dicke sx m E 5d MM I NE ES on Hibru e om 5 Snaothing Gaussian SmeothingPointea F Pump l Curve 5 Pump Z PFlow 0 400 ml min Pump z Curve J Wait Column TC Temperaturegtate Wait Compartment TC Tnmneraturn amp tnatn i Suppressorl Carbanate U U muppressorl Bicarbonate 0 0 5Sunnepor MSO uppressori Hydroxide 50 0 Suppressorl Tetraborate U U Suppressorl other eluent i Suppressorl Recommended Current 50 Wait Banpleheady CDetl Autorero Concentration 2 00 mM Load Wait cyoleTimnestate Inject 4 Right Click on the icon for the mass spectrometer in the method Chromeleon Program File IC MS new grad4 TEMP 2 Commands d File Edit View Workspace Qualification Control Window Help D aw Ed EFE pu Title 27 min run 5mM 0 10 10 20 5 47mM 20 23 60mM Pr Smoothing Gaussian Fi SmoothingPoints 9 wet Pump 1 Curve 5 Commands Pump 2 Flow 0 400 ml min Pump Z Curve 5 Wait Column TC TemperatureState Wait Compartment TC Temperaturestate Surveyor MSQ Suppressorl Ce
27. GLE ION STANDARDS CA ea DI Water Standard 1 20 0 451615 mM KOH 10 min AS16 Finished 117 Sa 11132007 BACKGROUND TESTS Standard 1 20 0 AS18 15 mM KOH 10min AS16 Finished 11 fl 11142007 BACKGROUND TESTS 10 ppm Chloride Standard 2 200 ASIB15mMKOH 10min AS1B Finished 11 Gill FINAL DATA f 10ppm Chloride Standard 2 200 AS1615mMKOH10min AS16 Finished 11 fia STACY ia 22 05 28 QJ Dionex Templates J HPLC T sine 5 A new sequence is created All sample information not data from the old sequence is found in the new sequence therefore the calibration data files are not carried forward If you do not wish to run a new calibration curve for the day the Finished runs for the Standards would need to be copied from the old sequence and pasted into the new sequence 6 Rename the samples position in the autosampler and injection volume as relevant 3 22 Chromeleon MSQ Plus Operator s Guide BDI N f X MSQ en _ Chromeleon Software Familiarization with the Sequence Format 3 8 Familiarization with the Sequence Format Chromeleon Sequence1 tg File Edit view Workspace Qualification Batch Tools Window Help D aw bel EE S k nZ0190 local MDAYLAP local C5124 MS qnt CS5124 MS 11 8 2007 9 14 27 A MS 10 KB ads Wai amp S15 ant 11 7 2007 6 02 20 P MEG 21 KB MP ASTB 15 mM KOH 14516 15 mM KOH 0 25 mL min Anions 1153 2007 4824 MEG 18 KB ma 112007 Br B rival Pr
28. Guide BDI ONEA MSQ Chromeleon Software Program Files 5 Click through the pages of the wizard to define all parameters of the system e g gradient oven temperatures etc These values will be unique per application 6 Continue to complete the wizard settings for your application When you reach the Acquisition Options of the wizard pay close attention A Acquisition Time Information gathered from the length of your gradient This field is customizable for the length of time you would like the data collected B Channels Check the boxes next to the signals for which you would like to collect data 1 If you would like to collect MS data the box next to MS must be checked 2 If you would not like to collect MS data for this run IC LC only uncheck this box Program Wizard Acquisition Options Acquisition Time From 0 000 min T 30 000 min Select data acquisition channels devices iw Channel Pressure Select All Deselect All Back Cancel Help 7 Continue to follow the steps of the wizard to program the IC LC detector 8 Several steps later the wizard will ask for options on the mass spectrometer A Range Sets the scale of the signal to be plotted by the MSQ in Chromeleon B Smoothing Improves the signal noise chromatogram appearance and reproducibility of peak baselines by applying different digital filters to the raw data Once applied these filters cannot be
29. IN THE CONTENT HEREINOF WITHOUT OBLIGATION OF DIONEX CORPORATION TO NOTIFY ANY PERSON OR ORGANIZATION OF SUCH REVISION OR CHANGES TRADEMARKS Chromeleon is a registered trademark of Dionex Corporation MSQ Plus and Xcalibur are trademarks of Thermo Fisher Scientific Microsoft is a registered trademark of Microsoft Corporation PRINTING HISTORY e Revision 01 January 2009 e Revision 02 June 2009 e Revision 03 October 2009 The products of Dionex Corporation are produced under ISO 9001 accredited quality management systems Published by Technical Publications Dionex Corporation Sunnyvale CA 94086 EYDIONEN Passion Power Productivity Chromeleon MSQ Plus Operator s Guide EDI N M MSQ Chromeleon MSQ Plus Operator s Guide Chromeleon MSQ Plus Operator s Guide Table of Contents Chromeleon MSQ Plus Operator s Guide ssccsssssssccccccccsssssssssssssssssssccscscccccccscsssssssssssssess iii 1 Chromeleon MSQ Plus Operator s Manual eee eee eee eee eee eese eese ee eesosaus 1 1 1 1 rae 10 616070 sensan E AEE ARA aAa 1 1 1 2 X Conventions 20 ee ee cece eccccccecccccccccecccccuccecceuccccueccscaeccscueccscuecescaucescueceescuucescuuceescasseeseuscensens 1 1 2 The Chromeleon Server Monitor ccccccccscsscscssccscccccccccccccccccccccccccccccccccccccccccccccccccccccces 2 1 MEE AMUN IRIS 2 1 3 Chromeleon SoftWare scsecesecesecececececc
30. MSO Plus Chromeleon MSQ Plus Operator s Guide Document No 065322 Revision 03 October 2009 _ 1 l D mE Now sold under the Thermo Scientific brand Thermo SCIENTIFIC Chromeleon MSQ Plus Operator s Guide MSQ 2009 by Dionex Corporation All rights reserved worldwide Printed in the United States of America This publication is protected by federal copyright law No part of this publication may be copied or distributed transmitted transcribed stored in a retrieval system or transmitted into any human or computer language in any form or by any means electronic mechanical magnetic manual or otherwise or disclosed to third parties without the express written permission of Dionex Corporation 1228 Titan Way Sunnyvale California 94088 3603 U S A The MSQ Plus Mass Spectrometer System is manufactured for Dionex by Thermo Scientific Instruments 355 River Oaks Parkway San Jose CA 95134 DISCLAIMER OF WARRANTY AND LIMITED WARRANTY THIS PUBLICATION IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND DIONEX CORPORATION DOES NOT WARRANT GUARANTEE OR MAKE ANY EXPRESS OR IMPLIED REPRESENTATIONS REGARDING THE USE OR THE RESULTS OF THE USE OF THIS PUBLICATION IN TERMS OF CORRECTNESS ACCURACY RELIABILITY CURRENTNESS OR OTHERWISE FURTHER DIONEX CORPORATION RESERVES THE RIGHT TO REVISE THIS PUBLICATION AND TO MAKE CHANGES FROM TIME TO TIME
31. SIM Preview Commands P 30 mp ECD CS 5000 10 Hide Per Method Parameters 0 0 00 250 5 00 7 50 10 00 12 50 15 00 17 50 20 00 22 50 25 00 27 50 30 00 Time minutes Pump ECD Thermo ICS 2000 Full Scan Events Name IMass Range Time Range min IPeak Format ean Time Polarity Eus V CJ FS 1 100 00 1000 00 0 00 30 00 Centroid 5 Scan Time The amount of time you give the detector to scan across the mass range Scanning within the range of 250 1000 amu second is ideal when using Full Scan mode Relay and State De ire 6 Polarity Positive or Negative If you would like to scan both positive and negative polarities add another full scan event with the opposite polarity 7 Cone Voltage The amount of energy applied to the source region of the mass spectrometer Attracts the ion beam into the analyzer but excess energy can cause the molecule to break apart or fragment Can cause Collision Induced Dissociations CID fragments in this region to help identify unknowns EDI N F Qhromeleon MSQ Plus Operators Gude 93 13 Chromeleon Software Program Files MSQ C To add another full scan event locate the Add Full command in the middle of the page Pressing this command line adds another full scan event to the list D To switch between the views of SIM and full scan events locate the grey bar at the bottom of the screen 1 In full scan mode the bar is o
32. Search program if it is already running 4 Extract upgrade files from the upgrade zip package V17 20 UPG to the default folder of the MS Search program i e C Program FilesNNISTMSNMMSSEARCH 5 Toensure the upgrade is properly installed Run the MS Search program from the Microsoft Start Menu gt Programs gt NIST MS Search and AMDIS gt MS Search v 2 0 NOTE For convenience you can also create a desktop shortcut of the program by right clicking the MS Search v 2 0 from start menu and select Send to gt Desktop create shortcut 6 After launching the MS Search program select the Librarian tab on the bottom of the screen shown in Figure 3 If the Create Library button shows up in the toolbar the upgrade has been successfully installed amp E NIST MS Search 2 0 Librarian mA File Search View Tools Window Help sjale ol xele sO Nlavar Aiittan 313 10 70 130 190 250 310 370 430 490 Spec List Mixed_Standard_ ppm AV 12 73 13 11 min 16 SB1 0 42 2 02 64 SB Nome Mixed Standard 1 ppm AV 12 73 13 11 min 16 SB1 0 42 2 02 64 SBA Formula E MW N A CAS N A NIST N A IDs 1 DB Spec List Other DBs None Comment T 0 1 c ESI lcorona sid 50 00 det 1 659 00 Full ms 15 00 500 00 10 largest peaks 145999 313206 22 120 2 47 2 158 Lib Search For Help press F1 Figure 3 Ensure the successful installation of the NIST MS Search Upgrade EDI N F X Ch
33. arbonate 0 0 Suppressorl Bicarbonate 0 0 Suppressorl Hydroxide 50 0 Suppressorl Tetraborate 0 0 NEN Suppressorl Other eluent 0 0 Pump 2 Suppressorl Recommended Current 5 DP 3000 Wait SampleReady A 0 000 CDetl Autozero u Concentration 2 00 mM Piman 1 Load 5 Select Remove MS Instrument Method from the context menu d File Edit view Workspace Qualification Control Window Help Dol He M2 E kN ZB we E HN T ow Title 37 min run Send 0 10 10 20 547m 20 23 0mM Data Collection Rate Temperature Compensation db y N c Title 27 min run 5mM 0 10 10 20 5 47mM 20 23 60mM c1 Prat Smoothing Gaussian JSuppressorl Type ASRZ Zmm Passe i cCurrentzet gt 20 mA eae n SmoothingPoints 9 Pump 1 Plew 0 100 ml min sees Pump 1 Curve 5 iy 0 0 i Commands dc 0 0 ti Pump Z Flow i 0 400 ml inu 0 0 4 Pump Z Curve moothing Gaussian West Column imoothingPoints 3 f How to a Pump d Curve 5 What s this Pump Z Plow 0 300 ml min Survevor N L3 Pump 2 Curve 5 y Eher eren alin Wait Coluen_TC Temperatureatate Eta 00 Wait Compartment TC Pemperaturedtate Buppreasarl Carhnnatre n n Suppressorl Buppressorl Bicarbonate 0 0 Xe Suppressorl Other eluent 0 0 Suppressor hydroxide 30 0 o Buppressorl Teteaborate Pump 2 Suppresso
34. c 99 heel vi Comment m Help ori Teu ET bori Oth borl Rec Wait TI Command 0 000 CDetl Autozero uL Concentration OK amp Prev OK amp Next Hep EGC_2 Load EG 3000 ii Click the by MS iii Scroll down the MS list to find a green icon next to the word Operation Click on the word Operation Retention Time Fl REL EIE 8I ED RE amp amp aggg ce BB Smoothing BB SmoothingPoints EB DemoFileName 93 AbortAcquisition omment wt Help Detector OK amp Prev OK amp Nex 3 18 Chromeleon MSQ Plus Operator s Guide BDI ONEA MSQ Chromeleon Software Shutdown Programs iv From the pull down list on the right for Operation select StandbyNoWarning v Click OK to add this command to the program Commands SIM_14 Retention Time min SIM 15 J SIM_16 Operation On StandbyNoWaming 6 SIM 17 Tm an ge StandbyNow arning BB Startup BB Operation E BB Range E Smoothing BB SmoothingPoints EE DemoFileN ame Q4 AbortAcquisition lt Comment Help Indicates the mass spectrometer s operational status See also Startup Command Operation 7 Save the program file 8 Adda sample to the end of your sequence with the following parameters e Name Shutdown e Type Blank e Inj Volume make sure this is specific for your system e P
35. ckground acquisition 6 Ifthe Ready Check is successful you will get a message of success 7 Ifthe Ready Check fails you will receive a list of errors and warnings If only warnings appear clicking OK will start the sequence To correct errors and warnings click Cancel and address the errors and warnings Perform another ready check 8 Press Start Start Batch on ic ms L Chromeleon Check Results Batch List Reporting Error Handling Transfer Ready check was successful however there are one or more warnings Operator Delayed Start D All samples in this sequence are already SS Cee Me meee SHenday F finished Remove Move Up Move Down Cancel Ready Check Help EDI N k X SC Chromeleon MSQ Plus Operator s Guide 4 1 Starting a Sequence Examining Data Files eee MSQ 4 1 Examining Data Files After the samples have been run the status changes from Single to Finished This section walks you through data analysis and how to examine finished samples A quantification method must be specified in the sequence before the data file can be opened To check if the sequence has a quantification file associated with the samples 1 Open the sequence If the column under Method is blank then there is no method associated with the sample Analyst lA AS16 gnt 11 7 2007 6 02 20 P MSQ 21 KB Fustomer Data MP ASTB15 mM KOH 1 AS16 15 mM KOH 0 25 mL min Anions 11 1
36. e hardware parameters for the chromatographic separation and detection The samples are run with program files in order to separate the individual analytes of the sample mixture To create a program start from either the Panel Tabset or the Browser page 1 Go to the File menu 2 Select New to create a new document Chromeleon SHENDAYLAP localMPLCM 2 4 07 Browser View Workspace Qualification Batch Tools Window Help Create a new document B Ctrl M B Control Panel Panel T abset Cancel Sequence using Wizard Sequence from LIMS Worklist Query using Wizard Method File Spectra Library 3 A menu appears select Program File 4 The Program Wizard automatically opens The first question requests the Timebase A timebase is a group of hardware modules that work in concert you may be more familiar with the definition system or pump detector oven etc Program Wizard Select Timebase Options The Program Wizard guides you through the creation of program files To start select the timebase where the program will run Timebase lI MS Computer SHENDAYLAP Protocol hy Computer Enter connection information manually ar pick a timebase from the list at right My Computer Com Favorites Network Neighborhood Cancel Help 3 6 Chromeleon MSQ Plus Operator s
37. e i Desai mo miri Ho blank run subtraction f Subtract recent blank run sample in corresponding sequence 0 200 i 2nd Detector MS ag 19 C Subtract a fixed sample Browse ard Detector k Moner Se cone ran Enable matris blank subtraction 4 General Detection Peak Table A Amount Table Peak Tracking MS Tracking Calibration A Spectr Dimension of amounts Units for the analysis e g ppm ug mL Global calibration settings Defines which points are to be used to generate the calibration curve Leave as the default Total with Auto Recalibrate checked 2 Detector Delay It is important to match the retention times of the UV CD data and the mass spectrometer The tubing and flow rate affect this value If they are changed reoptimize this delay time 1 Overlay the UV CD peak with the MS peak a With the UV CD data open press and hold the Ctrl key on the keyboard while using the mouse to click the Previous or Next Channel icon This overlays the multiple data channels of the same run b The data channels are organized alphabetically Manually calculate the difference in retention time between the LC and MS peaks Define 2 Detector as MS using the down arrow menu Click OK to the warning message that appears Enter the delay of time of MS data into the field P xd s S sd Ensure the maxima of both peaks are aligned adjust the value as required
38. e status Click OK when complete ER 9 The data is stored in Chromeleon format where it can only be opened on computers with Chromeleon software loaded To import simply double click the icon and Chromeleon will auto launch asking where to restore the file Chromeleon MSQ Plus Operator s Guide EIDIONEX MSQ BEN l Report Definitions Mass Spectra Data Extraction Integration and QNT Editor Views Report Definitions There are limitless options for arranging the data in the printer layout screen It may be easiest to start with the Dionex template 1 Open a data file 2 From the Workspace menu select Load Report Definition Browse the directories until you reach the locked Dionex Templates folder Open this folder and then select Reports Open defltLCMS 4 Click No to the option to save printer layout changes Chromeleon MSQ20190 localuCS3000 MSQWY2 DataWShireV03 25 08 14 100pmol u E File Edt View Table RICER Qualification Window Help D ap td S EE amp b OP Workspace BO PAA GF ke 3 x j 4 E Hn b Save Workspace As w Autosave Workspace 03 25 08 14 100pmol uL mono 160 nc Reads decoration and layout settings u C Save Report Definition 2 9500 aar I I eports m 1 ReportsldefitLCMS 2 OQ PQ Modular Validation mo E amount repart E defltdad 3 SHENDAYLAP localldefauk EE ANION CATION report E defi MSS ES 4 REPORTSIDEFAULT 3 EJ ANION repart E E Sign
39. eleon 8 Once the report definition is customized as desired right click and again save the report definition 9 For advanced customization options please consider attending a Dionex training course 7 1 How to make a report definition for several SIM channels on one page 10 Open a finished sample run At the top of the screen go to the View Menu Select Printer Layout On the printer layout screen go to the Workspace Menu Select Load Report Definition In the browsing window that opens scroll up to the Dionex Templates folder Open this folder and then select the Reports folder Inside the reports folder select Peak Summary Report The screen will open back up to the integration view Go back to the View menu and select Printer Layout Go up to the Workspace menu Select Save Report Definition and save this report somewhere outside of the locked Dionex templates folder Go up to the Edit menu and select Layout Mode Once the report is in layout mode you will see little tabs in the corners of the headers Right click on the column for Retention Time Select Report Column Properties from the menu list In the menu box that appears focus on the boxes in the lower portion of the screen Since all of the SIM channels are linked to a specific analyte change a The Peak box from the default of Selected Peak gt Fixed Peak and choose the name fro
40. eleon MS spectrum against NIST Libraries 3 Right click on the MS spectra and select NIST MS Library Search this action will automatically launch the NIST MS Search program if it is not running 4 Leave the Enable Mass Defect unchecked and click OR to continue The search result will be shown in the NIST MS Search program as shown in Figure 6 the default view here an adipate standard is used for the demonstration The hits are sorted by probability on the bottom right corner Additional information is also available such as the spectra of the unknown and the top hit analyte in the library NOTE For additional information about the features of displaying and manipulating the form and format of the NIST MS Search display refer to the Help section of the program VE NIST MS Search 2 0 ident Presearch Default InLib 137 58 spectra Jee D Ble Search yew Toots indem Help BE SEESE Ode S 1 adipate AV 5 56 5 66 min 7 58 0 V pea eure AR LAU Lo emis s vtm MY te JJ 42 UJ i KX Ara EE 7 C ext Fle oona AV 554 5 ii mn 5 84 293 44 SRD 442 FlotiText of Search Specture A Pit of Seach oec X Fict Text si Spec Let y Figure 6 Search Result in NIST MS Search Program 9 2 Chromeleon MSQ Plus Operator s Guide EDI ONEA MSQ Using the NIST MS Search with Chromeleon Ain a Chromeleon MS spectra to an Existing Library 9 2 Adding a Chr
41. entify the status of the Server a Ifthe server is not running the server monitor appears as a small green Chromeleon caricature with a red cross over the top b Right click on the server monitor icon and start server Open Quit Monitor 2 4 53 PM amp 4 53 PM c When the server is running idle the red cross disappears from the Chromeleon icon and the tune icon for the MSQ Plus mass spectrometer appears in the task bar JI XE SES 3 The Server must be on and idle before proceeding The tune monitor for the MSQ Plus shows the status of the mass spectrometer It automatically appears when the Chromeleon Server is started The color of the icon displays the status it is red when the instrument is vented flashing yellow during pump down The icon must show a solid yellow pumped idle or green active circle before you can access the mass spectrometer EDI N F X Chromeleon MSQ Plus Operator s Guide 2 1 MSQ Chromeleon Software Starting Chromeleon Chromeleon Software 3 1 Starting Chromeleon Enter all commands for the chromatography system through Chromeleon software 1 Locate the Chromeleon icon on the Desktop of the computer 3 The software is configured to reveal either the Browser or the Panel Tabset 2 Double click the icon 3 2 The Browser The Browser is designed to mirror Windows Explorer Use the Browser to navigate to data files hardware programs and quantificati
42. f the Program Wizard the program information is displayed in a basic format Chromeleon New Program File Commands SEE n File Edit View Workspace Qualification Control Window Help X D ck ztg B R Title Pressure LowerLimit 0 psi Fret Pressure UpperLimit 5000 psi Mere A Equate reat E Pump InjectValve State LoadPosition Commands Data Collection Rate 5 0 Hz CellTemperature Nominal 35 0 c Suppressor Type None Suppressor Current O mA Surveyor MSQ ECD Total Step 0 20 s ECD Total Average Off Channel Pressure Step 0 20 s Channel Pressure Average Off JP Range 6 Pump ECD Smoothing None eee Flow 1 00 ml min i 0 000 Autozero ICS 2000 ECD 1 Acqon ECD Total Acqon Channel Pressure AcqOn MS Data Acquisiton On Pump InjectValve InjectPosition Duration 30 00 Relay and State Devices 0 01 MS Start Closed Duration 20 00 vas V p0 000 ECD 1 Acqoff AS ECD Total AcqoOff Post acquisition Channel Pressure AcqOff steps MS Data Acquisiton Off End sjm gt Line 28 SHenday IC MS Mass Spec Scan Parameters Click the icon for the mass spectrometer to define the scan parameters of the program file A In the upper right section of the screen you will see the field for ionization mode ESI or APCI and Probe Temperature 1 The probe temperature is the temperature in degrees Celsius that the nitrogen gas is heated to by the Probe to desolvate your sample 2
43. f the polarity of a sample is unknown Relay and State Devices Options Click Next to enter the Relay and State Devices Options page In order to trigger the mass spectrometer to start collecting data a relay closure is given from the IC or LC device Upon installation of the system the cabling was connected In the program the steps to trigger the device must be added to the program file A Itis recommended to always have the TTL or Relay in the Open position at the start of the program To trigger this 1 Click on the by the TTL Relay name In this example the TTL was named MS Start Click State Leave the Retention Time blank Select Open or Off from the State Options Click Add E A E BDI N F Chromeleon MSQ Plus Operator s Guide 3 9 Chromeleon Software Program Files MSQ B The command to start the mass spectrometer must also be programmed 1 Click on the Closed or On option under the relay name 2 Inthe retention time field enter the time for the mass spectrometer to start acquiring data Piram Wizard Relay and State ET rr MS Start Retention Time 3 Yr State Open sm Pun Bee Tine Deve ST tae 1 pnl Meseososcecscesccesososccecosececeocesceccsocescoosvoceocecsoccosceseocecccecossccsosececececeneo What commands will you need to add Use this space to make a list of the relay commands you will need in order to control your system e g
44. g the internal standard the following steps must be taken 1 Left click Ret Time to select that column 2 Right click the Ret Time column to open the context menu 3 Goto Columns and select Duplicate Column 4 Click Add Channel Then use the pull down menu to select the SIM channel of the internal standard Click OK Click OK to the Duplicate column retention time box p At this point the column for retention time has been duplicated for that specific SIM channel Delete all values from the column except the retention time of the analyte in that SIM channel Io Peak Hame Ret Tim Howto Type Peak Type Group Comment default2 1 EET whats this Auto Autogenera 3 default2 2 BSJ Cut Auto Autogenera E default2 3 EE Copy i Auto Autogenera alarma MEINE Auto Autogenera r 14 43 Thom Auto Autogenera 6 default2 6 17 43 Display Columns pra default2 7 Ti Bra 8 defauk2 6 TIT Edit Amount Columns Es Display User Defined Columns Duplicate Column Skart Integration w Auton Re Integrate Global Settings Unidentified Peaks Load Report Definition a Delete the retention time of the internal standard from the original retention time column b Only the SIM channel for the internal standard should have a retention time entered Chromeleon MSQ Plus Operator s Guide BDI N f X MSQ 1 Cmpd A Starting a Sequence Mass Spectra
45. he beginning and end of an analytical run 4 14 Chromeleon MSQ Plus Operator s Guide EDI N F MSQ Starting a Sequence Mass Spectra Data Extraction Integration and QNT Editor Views To Enable Background Subtraction via Mouse Clicks Please note Only fixed background can be enabled via mouse clicks 1 View the chromatogram in either Integration or QNT Editor mode 2 Identify an area of the baseline to subtract Press and hold the right mouse button at the beginning of this area Without letting go of the mouse draw a box around the baseline region 4 Release the right button of the mouse but do not click anywhere A context menu appears next to the box Select Set MS Background Subtraction Range 1 6 Ifa second range is desired repeat steps 2 4 In the menu select Set MS Background Subtraction Range 2 1 default2 1 4 907 zoom Set Averaged Baseline Start Set Averaged Baseline End Peakname Mami Set UY Background Subtr Range 1 min default2 1 n a default2 4 Set MS Background Subtr Range 1 default2 6 imis mei ipis 2 ear ackground 5uDtr Ranges default2 7 g ISTD Set Minimum Area Set Minimum Height Set Minimum Width Set Peak Slice amp Sensitivity Set Inhibit Integration Range Set Void Volume Treatment Range Cancel To View the Subtracted Spectra Go to View Select Show mass spectra or press the show mass spectra icon Right click on the mass spectra to ope
46. k starts Related parameters Minimum Width Minimum Height hf asimum Height hf asimum Width hM aximum Area Reject Maximum Height Reject Cancel Help Use the retention time column to specify the time of the integration step The detection parameters are time dependent For example Minimum Area can be set to different values throughout the integration of the chromatogram by having multiple retention times for the Parameter Name Use the Channel column to specify the channel for the parameter Parameters can be custom tailored for each detection channel so the integration for the UV data will not interfere with the integration of the MS data EDI N F X Chromeleon MSQ Plus Operator s Guide 4 7 Starting a Sequence MSQ Mass Spectra Data Extraction Integration and QNT Editor Views Peak Table Tab The Peak Table tab defines the criteria for labeling peaks based on retention time and how to draw the calibration curve fit In order to create a list of peaks with the retention time from the chromatogram 1 Right click on the grey space of the peak table to open the context menu 2 Select Autogenerate Peak Table How Fo What s this Cut Copy Lines gt Columns gt Edit Field Start Integration 4utom Re Integrate Global Settings Unidentified Peaks Load Report Definition Save Report Definition Autogenerate Peak Table Detection Peak Table Amo
47. le B 35ppb Filter Type Moving average Moving average Filter Size Olympic Saviteky Gola teratianis n Smoothed Channel SIM_03_MA_005_001 Apply to all samples of current sequence Cancel Help definitions of the filters 4 Filter Size The amount of points to smooth keep this number as low as possible Iterations How many cycles to smooth the data e g selecting 2 will smooth the smoothed data 6 Smoothed channel The name of the new channel If you do not want to create a new channel then name it the same as the data channel you are smoothing but this will overwrite your data EDI N F X Chromeleon MSQ Plus Operator s Guide 4 17 MSQ Overlaying Data Channels or Multiple Injections Mass Spectra Data Extraction Integration and QNT Editor Views Overlaying Data Channels or Multiple Injections To visually compare data from finished samples follow these steps 1 Open a finished sample file 2 While holding down the Ctrl key on the keyboard click the icon for the previous next channel or previous next sample For ease in sorting the channels are arranged alphabetically 3 The data defaults to overlay with a signal offset of 10 per chromatogram To adjust the display right click on the chromatogram and open the context menu 4 Select Decoration from the list D c B s Oy Mk de o4 SN SO S zu S la kK a 7 id e aa do e x1 1 LINDA AND CARY 6 DA stds
48. leon MS spectrum against NIST Libraries 1 To search an acquired MS spectrum double click the sample from the sequence to open the data 2 Click on Show MS Spectra button from the toolbar as shown in Figure 5 to view the MS spectra on screen Select Automatic Tool to click the desired peak or use Spectra Plots Tool to select the time range to display the MS spectra i Chromeleon MSQ20194_local LEO ICMS MS Library for Anions Anion Library 22 adipate ECD 1 MSQ20194_local LEO ICMS MS Library for Anions Anion Library Jeg la File Edit View Workspace Qualification Window Help mx urs Baim t DcuW sm evum SIN S E ER D X9 oes e I Oo Click on Show MS Spectra to display E E np A Q Spectra l t Plots Tool MS Spectra on the bottom of the screen TA Anion Library 22 adipate ECD 1 ae Automatic Tool 0 500 0375 s 0 250 a 0 125 0 100 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 0 10 0 Retention Time min 104 Peak 33 RT 5 61 min SB1 1 86 2 93 66 SB2 6 63 8 02 85 NL 1 25E6 T 0 1 c ESI corons sid 50 00 det 1612 00 Full ms 15 00 300 00 amp Right click on the area of the spectra eo select NIST Library Search Rel Intensity X 4 22 min 0 70 f Zoom LWang Figure 5 Viewing an MS Spectrum in Chromeleon EDI N M LLL Chromeleon MSQ Plus Operator s Guide 1 9 1 Using the NIST MS Search with Chromeleon MSQ Search Chrom
49. m the pull down arrow The name comes from the associated qnt file b The Channel box from the default Selected Channel to Fixed Channel Choose the SIM channel that associates with the name of the peak for Fixed Peak a Repeat the above steps for all other parameters of the table height area amount concentration Chromeleon MSQ Plus Operator s Guide EDI N f X MSQ Report Definitions a Removing the Retention Spectra 11 Go up to the Workspace menu Select Save Report Definition You can overwrite the existing file you may want to save after each step you are happy with since there is no undo function 12 Copy the table that was just created and paste an identical one right below it 13 Modify each column as above for the so the specific SIM channel and Peak Name are aligned 14 Minimize the rows with the additional headers so it looks like it is in one big table 7 2 Removing the Retention Spectra Retention spectra appear the first time you click on the peak to find the mass spectra They are seen as a split screen on the right side of the page Their purpose is to show the spectra of the chromatography peak at the beginning middle and end of the peak At times these may act as more of a hindrance than a help EM File Edit View Table Workspace Qualification Window Help mix D kb He R ko 4o SN PD PAA Fw uz E M JS ld ics A A AS 11 16 07 26 35 ppb CD 1 Total
50. min SB1 0 21 1 96 100 SB2 23 18 26 91 302 NL 2 32bE5 Tee eee ee Pee ee er er ee 169 9 mz As previously noted the raw data can be smoothed as the data is collected If you prefer the data can be smoothed post data acquisition Smoothing data can help produce a uniform peak shape 1 Open a data file to the SIM channel or desired data channel to smooth 4 16 Chromeleon MSQ Plus Operator s Guide el N F MSQ Starting a Sequence Mass Spectra Data Extraction Integration and QNT Editor Views 2 Right click on the chromatogram to open a context menu select Smoothing 3 A menu will appear Select the Filter Type from the pull down menu Hit F1 for 9 000 126 75 127 25m z pte 5 275 5 000 e 4 000 Ri 9 S D Lid a N How to y z What s this E 2 000 ij 2 L Tools m xd Q o Bromate External UV Background Subtraction gt MS Background Subtraction gt Full Size 800 Autoscale Decoration Detection Parameters gt gt 400 Export Load Report Definition Save Report Definition 48 7 Copy Channel 18 3 39 9 en lie ull 0 Arithmetic Combination hime 40 0 0 10 0 20 0 30 0 40 0 50 0 60 0 10 60 6 74 1 93 2 112 6 120 1 141 4 175 8 58 2 85 3 101 0 or 11 Lil ll eli ll li Hla ullu tha A 0 100 120 140 160 180 Loa 60 8 151 0 la Smoothing Current Channel SIM 3 Current 5 amp
51. n the context menu Select Decoration from the menu m dc om Locate the Peak Spectra tab EDI N EX Chromeleon MSQ Plus Operators Guide 1 4 15 Starting a Sequence MSQ Mass Spectra Data Extraction Integration and QNT Editor Views 5 Check the boxes for Background spectrum and Original spectra Mass Spectra Decoration Isotopes Bunching Mass Defect Noise Reduction Labels Scale Frame amp Axes Colors Peak Spectra MS Filter Spectra sampling points A M Front 1 10 Ix v Iall 10 1 M Fong 5 Hx M taz o 4x Reference overlay None C Retention time spectrum of recent standard Retention time spectrum of a fixed sample Background subtraction overlay Background spectrum Original spectra Cancel Help lA File Edit view Table Workspace Qualification Window Help 5 fe D Skt Wik d Eod SR P PAG Fi Keo 7180 g ke du B ss HB At 11 19 07 curve 5 9 00 uS CD 1 Total B SB1 0 21 1 86 100 SB2 23 18 26 81 302 NL 1 34E4 T 0 0 c ESI corona sid 70 00 det 1400 00 Full ms 10 00 180 00 79 9 175 4 18 3 256 342 548 610 76 2 95 0 107 8 1330 4426 1559 o AME EM a EL Lb EL ELLLLLELE M bL EELE LL LLL LU LLL au ds E Lue cud LOL LLL Jinsha talis 0 lodide RT 17 05 min NL 2 34E5 T 0 0 c ESI corona sid 70 00 det 1400 00 Full ms 10 00 180 00 39 5 UI MI lodide RT 17 05
52. n the right side of the screen 2 In SIM mode it is on the left side of the screen 3 Click on this bar As the bar wipes across the screen it changes the view from full to SIM scan events MSQ Method Editor nied v Show Method Options Show Method Options Commands Preview Per Method Parameters ynToTG 5233 3 Tir Description Setpoint lonization Mode ESI bd All Scans Full Scans 100 Probe Temperature C 450 00 SIM Scans 90 vA Parameters a z Scans gt 70 5 Surveyor MSO Add Full B t Add SIM 50 g A 40 E DP 30 i a Pump ECD E 3 T ICS 2000 10 0 0 00 5 00 10 00 15 00 20 00 25 00 30 00 35 00 40 00 45 00 50 00 55 00 60 00 Time minutes er ELECTRON CORPORATION Pump_ECD 2000 SIM Scan Events Name Mass Span Time Range min Dwell Time Polarity Cone V SIM 1 Pb 103 60 0 50 0 00 60 00 0 50 Ve 60 00 SIM 2 PbOH 224 20 0 50 0 00 60 00 0 50 ve 60 00 E Programming SIM scan events is similar to programming full scan events 1 The probe temperature and ionization mode are global parameters they do not need to be changed for SIM scans 2 Name SIM 1 In this field you can also add the name or chemical formula of your analyte 3 Mass Enter the single mass you are interested in scanning 4 Span The mass window around the desired mass a Value is total window value e g Setting the m z 195 span 0 30 gt scans m z 194 85 195
53. nished 11 29 2007 5 19 23 1 00 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 5 54 02 1 00 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 6 28 42 1 00 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 7 03 22 1 00 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 7 38 02 1 00 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 8 12 42 1 00 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 amp 47 22 1 000 Finished 11 29 2007 9 14 29 1 00 Finished 11 29 2007 9 51 15 1 00 Finished 11 29 2007 10 18 2 1 00 Finished 11 29 2007 10 55 0 1 000 Zuma BL 07 Finished 11 28 2007 11 29 4 1 00 Zuma 17 1 7 5 Unknown 15 100 0 Id qrad4 TEMP default2 Finished 11 30 2007 12 04 2 1 00 Zuma 18 1 7 5 Unknown 16 100 0 grad4 TEMP default2 Finished 11 30 2007 12 383 0 1 00 IC MS Other Templates J THERMO E7508E 1 u3000 oO ON qi SF UOUN 21 E shutdown Blank 18 100 0 shutdown MS and IC default2 Finished 11 30 2007 1 40 54 1 00 i b rs o a Sy CO OO oO as mi nn el ojja o m w r2 lt T C Chromel data 14 GB free SHenday BDI N F Chromeleon MSQ Plus Operator s Guide 3 19 Chromeleon Software Sequences MSQ 3 Sequences Once the program file is created a sequence is built The sequence has two functions 1 Sequences organize the samples in the order to be analyzed by the instrument 2 The sequence stores the data collec
54. oesecseocceocccocococococococococococosocosocococococosososesececesesecececeseseo 3 1 gl Sarung Chron leo ess E TENS 3 1 Da TEBO i e NC o 3 1 3 3 The Panel Tabset cccccccccccccccccccccccccccccccccccccccccucccucccsccsccescccccsecescesceusceasceusccauceasscauscaeceaces 3 2 3 4 Creating Modifying the Panel Tabset sse eene n nnne 3 3 SX VIDRIO 3 6 36 Shutdown Propias asientos etenim itta esp E eii ee ee eee ee eee 3 15 S AME DEJU IE EU Tm 3 20 3 8 Famliliarization with the Sequence Format eese nnne 3 23 A AP ENN hs E T E E T IL TTL T 4 1 Al Tein Daa FE eer 4 2 4 2 Tod ar O 4 4 4 3 Mass Spectra Data Extraction Integration and QNT Editor Views cccccssssccceceeeeeeeeeees 4 4 CTC Ta E o EEEE E E AA EEEE ATS 4 6 DCC Oi TaD eaen A AEA 4 7 Peak Fable TaD RERO 4 8 SJ N F X Chromeleon MSQ Plus Operator s Guide Chromeleon MSQ Plus Operator s Guide MSQ Defining Internal Standards in the Peak Table Tab eeeeeeeeeeeeessss 4 10 Amon Table 1 AD cT 4 13 Back CrOUNG SUDMACION jer co nscosaediadedceatetdnncnstecucedessssianttadadideteenacmasecndede E sui adultus bt TiS 4 14 SPO OCH Dati FG ecse E S 4 16 5 Overlaying Data Channels or Multiple Injections sseeeeoocsssssseecocccssssscccoocosssssceeocsossssssee 5 1 6 Backing Up Exporting Data Files avssccccecesesaiicevesccesevescteveussacecssesstavevasccesssaste
55. of the screen updates showing the spectra for the peak generated by the left mouse click of step 4 Identify the most intense peak of the spectra Single left click on the most intense ion of the mass spectra to extract that single ion as a chromatogram ion intensity vs time out on the left side of the screen If the scale is offset too much by overlaying mass spectra data with CD UV data a Right click on the UV CD data overlay with mass spectrometer data b Select Decoration from the context menu c Locate the Comparison tab e On the Comparison tab find the box for Overlay Select Overlay with right signal axis and click OK e UV CD data is displayed on the left scale MSQ data on the right scale Chromeleon MSQ Plus Operator s Guide 4 5 Starting a Sequence MSQ Mass Spectra Data Extraction Integration and QNT Editor Views General Tab Title Unidentified peaks Retention time settings Amount interpretation Global calibration settings Use recently detected retention times Dimension of amounts mg mL Mode Total of last Reference inject volume Iw Auto Recalibrate Peak retention time determination f Use inject volume af first standard f Use absolute greatest signal value C Fined Curve Fitting Normal Use relative greatest signal value over men the baseline Dual Calumn Separate Calibration Dead Delay time s Blank Run amp Matris Blank Subtraction f
56. ogenerated 7 default 7 4 700 min 0 050 amp G External Area Lin Auto Autogenerated 8 default 8 5 033 min 0 117 AG External Area Lin Auto Autogenerated 9 default 8 5 900 min 0 100 amp G External Area Lin Auto Autogenerated 10 defautt 10 8 500 min 0 133 4G External Area Lin Auto Autogenerated a Window is the span of time around the total retention time that the software will examine to label your peak e g If the Ret Time is set to 4 00 minutes with a Window of 0 500 min the software will look at all data between 3 75 4 25 minutes to label your peak b Additional parameters for Window can be found by double clicking the listed window EDI N k X SC Chromeleon MSQ Plus Operator s Guide 4 9 Starting a Sequence MSQ Mass Spectra Data Extraction Integration and QNT Editor Views Defining Internal Standards in the Peak Table Tab Using internal standards is crucial when quantifying peaks by mass spectrometry An internal standard is a substance that is added in known identical quantities to your standard and unknown samples The addition of internal standards corrects for sample variation due to matrix effects fouled entrance source etc In mass spectrometry the ideal internal standard is an isotopically labeled substance so it will have a similar retention time and chemical behavior as the analyte of interest Internal standards are set up as a SIM scan in the mass spectrometer In order to quantify the data usin
57. ogram metroa Status Ini Daten ui 11062007 SI E DI Vater Standard 20 0 ASG1SmMKOH10min ASIG Finished 11 13 2007 3 LALILLZ 2l 11132007 BE 2 a et Standard 1 a 11142007 B D Noride Standard 2 fia FINAL DATA 4 m 1 Chloride Standard 2 fa STACY amp u 22 05 28 Dionex Template HPLC amp S1B Finizhed AS16 Finished AS16 Finished NOTE NEVER CHANGE THE STATUS OF A SAMPLE FROM FINISHED TO SINGLE WHEN OPERATING A MASS SPECTROMETER ALWAYS ADD A NEW SAMPLE TO THE LIST To add more samples to the list there are two options 1 Right click the sample list and select Append Sample 2 With the last sample highlighted press the down arrow on the keyboard Click Yes to append a sample EDI N F X Chromeleon MSQ Plus Operator s Guide 3 23 MSQ Starting a Sequence Familiarization with the Sequence Format Starting a Sequence From the Browser Screen 1 Locate the Batch Menu 2 Click Start Chromeleon Sequence1 te File Edit View Workspace Qualification Batch Tools Window Help ye Lie X h Edit Ctrl B Starts the sample batch 3 The Batch List screen opens 4 The name of your sequence appears in the list 5 Click the Ready Check button Among many other checks this ensures e There are no errors in the program e All modules are connected to the software e Alllamps are on for the UV e You are not running a manual ba
58. ography and mass spectrometry systems ESI is a very soft ionization technique and usually produces a single main ion If you want to create fragments from an API spectrum using collision induced dissociation CID with the Cone Voltage there is the problem that fragmentation is method and instrument dependent and in most cases substantially different from the spectra produced by EI Due to the different ionization mechanisms of interfaces coupling GC and LC to MS the GC EI MS library is not applicable for LC MS spectra search Users wishing to library search API spectra should make their own libraries 8 6 Install NIST MS Search Program The NIST MS Search program can be installed from the Xcalibur software CD shipped with the MSQ Plus instrument Contact your Dionex service representative to obtain the recommended versions of software if you don t have them available Possible additional charges may apply for Chromeleon and Xcalibur upgrades To install the MS Search program EDI N F X Chromeleon MSQ Plus Operator s Guide 8 3 Establishing NIST 2 0 Anion Library MSQ Download and Install NIST MS Search Program Upgrade 1 Insert the Xcalibur software CD to start the installation 2 From the pop up window shown in Figure 1 select the NIST 2 0 and follow the on screen instructions to finish installing the NIST MS Search X MSO 2 0 SP1 Setup Xcalibur Control software for MSQ 2 0 SP1 Surveyor PDA Plus 1 0 Read me
59. omeleon MS spectra to an Existing Library A spectrum can be added to an existing library e g the Dionex Anion Library as a new entry or a replacement of an existing entry 1 Perform the library search as described in Search MS spectra from Chromeleon against NIST Library section 2 Click on the Librarian tab on the bottom tab bar and navigate to the library entry window Select the analyte by clicking on the analyte listed in the left panel and click on the Edit Spectra button from the toolbar as shown in Figure 7 4 Enter all known related information of the analyte spectrum such as name formula molecular weight and CAS number To replace an existing entry type in the same Name as the entry you want to replace 5 Select Add to Library after entering related spectrum information and select the desired library when a pop up window shows up asking which library to add into and click OK to finish spectrum entry NOTE To add a structure to a library entry special software is required to draw the chemical structure e g ChemDraw or use an existing chemical structure file with the file extension MOL or SDF The structure display is an option and is not required to make an entry in the library e A y fea y Hen x Lhe silts T adege Ww SSeS dmm 7 T4 Bk2v3154 La 1 Click Edit Spectrum to add additional information and add the spectrum to NIST MS library 2 Click Add
60. on methods Chromeleon SHENDAYLAP_local ionex Templates Browser UE File Edit View Workspace Qualification Batch Tools Window Help ED c bel PE k s Sf sonet oes SHEMDANLAP local IC Applications 252008 11 13 17 J Analyst Panels 1 21 2008 3 50 39 P Customer Data yj Reports 2H 5 2008 11 13 17 vC Applications 25 2008 11 13 25 AUDIT 12 4 07 Diagnostics 0001 manual eg IC IC M5 J Other Templates J THERMO E7508676_local J u3na BDI N M LLL Chromeleon MSQ Plus Operators Guide 1 3 1 Chromeleon Software The Panel Tabset MSQ 3 3 The Panel Tabset The Panel Tabset is designed to give the user access to direct control over the chromatography system Each panel tabset is unique for the hardware configuration The Panel Tabsets shown in the following figures may not represent the actual screens on your computer however all statements are fully transferable Chromeleon Pi File Edit View Dad te ICS 2000 System with Column Heater and Eluent Generator IC_MS SHENDAYLAP Sequence Control Status MSOPlus 4ICS 2000 Pump Sample System Log Audit Trail on IC MS l H Pump On Datasource SHENDAYLAP local 4 31 16 PM Pump ECD Please verify the solvent and waste level values 4 31 17 PM Manually acquired samples will be ample stored temporarily in sequence
61. rds have been defined in the sequence the Edit Amount Columns menu appears 2 Use the pull down menu to assign standards on the basis of Name Once they are assigned on the basis of name the list of the standards appears on the right side of the dialog box Click Auto Generate to open another option on the screen 4 Click Apply to Generate a separate amount column for EACH standard Click OK Edit Amount Columns Assign Standards on the basis of Marnie Add remove or double click to rename Amount Columns below Select an Amount Column Standards drag amp drop between comm ls Peak Hame Ret Time Amount Comment Amt Default 1 Total Cmpa A 1 533 min 1 000000 rrr Autogenera 5j mpd B 1 933 min 1 000000 PRG Autogenera 3 isTDA 2 367 min 1 000000 Autagenera T V General Detection A Peak Table Amount Table Peak Tracking fh Mew Delete Auto Generate Cancel Edit Amount Columns Name Add remove or double click to rename Amount Columnea below Assign Standards on the basis of Select an Amount Column Standards drag amp drop between columns Amt Default 6 Columns with the standard names appear on the Amount Table Tab Enter the amount information into the appropriate columns and rows If using an internal standard be sure to specify the same concentration for the internal standard for each concentration EDI N F
62. red and asks if you would like to create the file 6 Click Yes Chromeleon Method file default qnt doesn t exist Create it Yes to all No No to all 4 2 Chromeleon MSQ Plus Operator s Guide EDI N F MSQ EDIONEX Starting a Sequence Examining Data Files Examining Data Files continued With the method defined in the sequence simply double click on the sample in the sequence to open the chromatogram This view is known as the Integration View This screen is purely for viewing the data and the results Chromeleon SHENDAYLAP_localCustomer Fatal 1137007 BACKGROUND TESTS 463 10 ppm Chiaride CD 13 n Die pdt yem Table Workspace Qual ksion Window Hein D c d sp Wat kol ob kih D BR E HiT BAC GAN TEATA FF A0 ppm Chie a n L H ament T Height HeL res Hesclutinn mit a hi In order to integrate the data name the peaks and define the points of the calibration curve enter the quantification QNT view To enter the QNT view 1 Locate View in the menu bar 2 Select QNT Editor S hromeleon SHENDAYLAP_local Customer Data 1 1132007 BACKGROUND TESTS 3 10 ppm Chloride CD_1 SHEN J Table Workspace Qualification Window Help Toolbars kde S S OREA 111320 Ful Size 10 ppm Chloride Autoscale ys Decoration 0 Split Zoom v Show Report D Show Trend Show Mass Spectra Show Calibration Curve Show Inject Tray Show Fraction Tray Refre
63. removed To maintain the integrity of the data it is recommended to set the points to a low number e g 7 Points If more smoothing is required filters can be added later during the data quantification 1 None No smoothing will be applied 2 Boxcar Synonymous with Moving Average filter data points are equally weighted As such its ability to discriminate between noise and signal is limited 3 Gaussian Applies the Gaussian distribution for chromatogram smoothing EDI N F X Chromeleon MSQ Plus Operator s Guide 3 Chromeleon Software Program Files 3 8 Program Wizard MS Options Range E 1 10 Scaling Factor used for online plot during data acquisition Enter lag1l af the expected maximum count value Smoothing Mane Mane Boxcar Gaussian Back Cancel Help 9 Click Next to define the scan conditions for the MSQ Plus 10 The wizard creates a scan template based upon the selection in this page Probes MSQ A APCI Atmospheric Pressure Chemical Ionization Typically used on nonpolar compounds lt 1000 Da B ESI Electrospray Ionization Typically used on polar compounds always used in ion chromatography IC applications Program Wizard Surveyor MSQ Template Options Please select an existing template to create a new Surveyor MSG method Template Using amp PCI FullScan Negativelon APC Full5can Positi
64. rence from impurities at the specified MS conditions THE RELATIVE INTENSITIES OF MS PEAKS STRONGLY DEPEND ON THE CONE VOLTAGE SETTINGS and also may vary slightly due to the different operating environments Thus for the best result it is highly recommended to acquire MS spectra at the above specified conditions especially the cone voltage for the best search accuracy or establish a customized user library using your daily operating conditions NOTE The Dionex Anion Library only contains MS Spectra using an ESI interface which is the primary interface for IC MS applications Users may build their own APCI library following the steps described in Section 9 3 Instrument control data acquisition and processing were achieved through Chromeleon chromatography data system software version 6 8 SR6 MSQ Plus was calibrated and tuned through Xcalibur version 2 0 7 and MSQ 2 0 SPI tune program 8 3 System Requirements PCs preinstalled with Chromeleon and Xcalibur are ready for NIST MS Search program installation NOTE Chromeleon 6 8 SR6 and Xcalibur 2 0 7 with MSQ 2 0 SP1 programs are fully tested with the NIST MS Search and thus are recommended versions Chromeleon 7 0 is not currently compatible with MS functionality and can not be used for MS instrument control and MS spectra search 8 2 Chromeleon MSQ Plus Operator s Guide EDI ONEX MSQ Establishing NIST 2 0 Anion Library Lo stallation of NIST MS Search and Updates 8 4 In
65. rl Recommended Current Buppreasorl Othec lusent 0 0 DP 3000 Wait Sampl eRet i Suppressorl Recaommended Current ZI Wait SampleReady 0 000 CDetl Autozero 0 000 CDati Autozaro N Concentration 2 00 mM Concentration 2 00 mM Load Pump 1 Load DP 3000 Wait CycleTime EDI N F X Chromeleon MSQ Plus Operator s Guide 3 17 Chromeleon Software Shutdown Programs MSQ 6 Replace the commands for smoothing with the command line Operation StandbyNoWarning To add this command a Manually type in Operation StandbyNoWarning b Via the commands menu i Press the F8 button on the keyboard to open the commands menu lt Chromeleon Program File IC MS new grad4 TEMP 2 Commands i bl Se Loa NEA Title 27 min run 5mM 0 10 10 20 5 47mM 2 V O lz m 7 76 n ater TUUS T m CellHeater Temper eSet 35 00 c Commande Column_TC Mode On Column TC Tempera Set 35 00 c k Compartment TC a j Compartment TC Te mands Pump 2 Suppressorl Type ee 7 DP 3nfn CurrentSet E39 MS Betention Time mi ne EluentGenerator Pump 1 Flow ki 6B Pu or MS M G9 System is Q Branch Pump 1 94 Log DP 3000 m Message Pump l Curve 4 Protocol Pump Z Flow Q3 wait Pump Z Curve 4 Delay j Wait Column TC T Q4 Trigger EluentGenerator Wait Compartment 3 EndTrigger EG 3000 Suppressorl Car 2 It ORO Sunnrassorl Bi
66. rogram File Select the shutdown standby program file you just created Chromeleon SHENDAYLAP_local Customer Data FINAL DATA Browser tg File Edit View Workspace Qualification Batch Tools Window Help Dc st R e Q amp S MSQ20190 local Title SHENDAYLAP_local shutdown MS and linear ramp 7 60 TEMP AT 35C IcCs3000 MSQ 11 6 2007 2 03 36 SHenday T Analyst C P Ste sass ax Za C EE Customer Data Vd IC MS new grad6 p 27 min run 5mM 0 10 10 27 Qq jcsS3000 MSG 11 27 2007 6 08 33 SHenday 18 KB sd AUDIT R IC MS new grad5 P 27 min run 5mM 0 10 fo z0 POT S000 MSG 11 27 2007 10 24 3 SHenday 18 KB fij 11022007 B MR IC MS new grad4 T 27 min run 5mM 0 10 10 20 RO ICS3000_MSQ 11 28 2007 2 25 20 SHenday 17 KB aj 11062007 5I v IC MS new grad4 T 27 min run 5mM 0 10 10 20 20 ICS3000_MSQ 11 29 2007 3 26 42 SHenday 19 KB fij 11062007 SI ME IC MS new grad3 p linear ramp 7 60 ICS3000 MSQ 11 15 2007 3 03 11 SHenday 15 KB raj 11132007 B v IC MS ne b SHenday 17 KB 11142007 B7 Mi defaut2 18 KB 9 FINAL DATA Wi default q b SHenday 558 KB fg STACY Method Status Inj Date Time Weigt ia 22 05 28 a Dionex Template default2 Finished 11 29 2007 3 00 44 1 00 J HPLC 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 3 35 25 1 00 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 4 10 03 1 00 100 0 IC MS new grad4 TEMP default2 Finished 11 28 2007 4 44 43 1 00 100 0 IC MS new grad4 TEMP default2 Fi
67. romeleon MSQ Plus Operator s Guide 8 5 Establishing NIST 2 0 Anion Library MSQ Importing the IC MS Anion Library 8 8 Importing the IC MS Anion Library MS Spectra and structure information for selected anions are packaged in the Dionex IC MS Anion zip file This package is available from your local Dionex representative and will be available from the Dionex website www dionex com in the near future 1 Click the circled button Create Library in Figure 3 to create a new library with the name IC MS Anions 2 Create a temporary folder on the PC desktop with name Temporary Library Files and extract the files a total of 23 files from Dionex IC MS Anions to this temporary folder Locate the library folder named IC MS Anions in C Program FilesNNISTMSNMSSEARCH 4 Close the NIST MS Search program Copy all 23 files in the Temporary Library Files folder to the NIST library folder created by the MS Search program which will be located in C Program Files NISTMS MSSEARCH IC MS Anions When a Confirm file replace window pops up click Yes to All to replace all old files with the new library files containing anion spectra 8 9 Specify Library Search Options 1 Start the MS Search program again from the desktop shortcut or x from the Windows Start menu Search Ubretes Automation Limits Constraints Available Libs x 2 Select Library Search Options
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69. s 1 100 Copy Ctrl C Bromat T 0 3 c ESI corona sid det 1400 00 SIM ms 126 75 127 25 70 00 didal pe Full Size XE 1 000 i Autoscale 0 900 Extract Mass Trace Extract Temporary Mass Trace Bromat Export Mass Spectrum textFormat 0 800 T 0 3 c ESI corona sid det 1400 00 SIM ms 126 75 127 25 amp 70 00 0 700 127 0 Remove Mass Spectrum 0 600 50 Concentration 7 00 mM Load Report Definition min Save Report Definition c 0 481 el eel 4 48 00 6 00 7 00 8 00 9 00 9 71 125 750 126 800 126 900 127 000 127 100 127 200 127 250 7 To save this layout go to Workspace and save the report definition Mass Spectra Decoration Ed Isotopes Bunching Mase Defect Noise Pre duction Labels Scale Frame amp Axes Colors Peak Spectra MS Filter Spectra sampling points i Retention spectra ho E beim Ww Fonti pU 1 Tall 1 Front 2 7 Tail 2 Heference overlay f Mane t Retention time spectrum of recent standard Retention time spectrum of a teed sample Background subtraction overlay Background spectrum Original spectra Cancel Apply Help Chromeleon MSQ Plus Operator s Guide EDI N f X MSQ 8 1 Establishing NIST 2 0 Anion Library Introduction Establishing NIST 2 0 Anion Library Introduction This section describes the installation procedure for the Chromeleon Anion MS Spectral Library Anion
70. sh F5 3 0 4 0 6 0 7 0 En F I E Printer Layout Area Amount Height Rel Area Resolution pS min na Thy jd H 0 0000 na 0 000 0 00 1 30 2 na 0 277 0 0000 n a 0 001 0 00 0 92 3 na 0 380 0 0000 na BMB 0 000 0 00 1 32 4 na 0 473 X 0 0000 na BMB 0 000 0 00 n a Chromeleon MSQ Plus Operator s Guide 4 3 Starting a Sequence MSQ Toolbar As with the Integration view the QNT Editor view shows the chromatogram on the top of the screen and a series of tabs appears at the bottom of the screen Unlike the Integration view there are no data values in the tabs rather the settings to define the peaks Before we summarize the function of each tab let s examine the icon toolbar 4 2 Toolbar a File Edit View Workspace Qualification winde 4 3 4 4 LAT p axale x i E A L a The labels of the icons that are used frequently with the mass spectrometer are shaded with dots Familiarize yourself with the various icons in the toolbar If you are unsure about the function of an icon hover the mouse over the icon and an informational dialog box names the icon also referred to as the tool tip The remainder of this section and the following on the QNT Editor emphasize the use of these shortcut icons so it will be useful to have knowledge of them before you continue Mass Spectra Data Extraction Integration and QNT Editor Views In many cases such as identification of unknown peaks
71. stallation of NIST MS Search and Updates NIST MS Search program current version 2 0 is required to be preinstalled to enable the MS library search in Chromeleon The NIST MS Search program upgrade is also required to enable building or installing a new customized user library NOTE The NIST MS Search program may already be installed on your system To check for the program from the Windows desktop select My Computer and select the Add or Remove Programs option A list will be populated with the programs installed on your PC If the NIST MS Search is loaded it will be listed as NIST MS SEARCH and AMDIS 8 5 Introduction to NIST Search Program and Libraries The NIST MS Search program is a freeware application package developed by the National Institute of Standards and Technology NIST It can take MS spectra acquired by different instruments compare with the NIST EPA NIH standard spectra database or user customized database for identification and confirmation purposes The search program comes with a preloaded GC EI MS spectra database upon installation The reason EI spectra were chosen for these libraries is that it was the method of choice for GC and there was only the one main parameter the EI setting Changing EI can skew the spectrum enormously so it was forced to one value for all 70eV For liquid chromatographic applications Atmospheric Pressure Ionization API interfaces are often used to couple chromat
72. t asini cet fav Serene Cent Sane Tyee qna Sample Ho x r min T OS op RS a pe ep Rp pp OA kp ae ere po c ey Eanan TIBET Sample Ln 00b 05D 1 00 125 2100 150 100 150 400 450 500 MS S coon Peay fo Dork Range Onda h E Opes tica a Te Hone on amp inaathing L I x SimaathingPeintes zl Aust ai l l FRIES AM Barnially acpi eil narmg c i wil br niborcd Inte a iy ii regem c NEG SHEARS TAP talh B4 ararnial Va AM Cefn hern ALM 19889 Serial Demao iar Version 23599 AA Chop 11 Chip eani deiecied FETTE S4 AM Ciu oil eret wer sen 658 58 Buikl 7368 6 silar Ded serial moet 2714 a Pe eS AM CIS VIE olan chamge FRITA3 AM CITS EE ausim MS daba aceqaiiiien inimi FRITA38 AM CIS ie WE dala ace eque Florae AM CMS VO aalo change Fro AM OTS Sabe change 11 82 43 AM V rs Sherer Irem SHEBRISA LAP uan connected d nel H IS TERAJ AM Gee S Hermalarg Tr erm SHEBISA Y LP uan Hieron ciel hom Eignebase H Is 11 37 43 AM Gee Sheila Tr eam SHEET LP uan connected do tone H I TERAJ AM Gee S Hermalarg Tr orm SHEBISA Y 20UP uan diene ciel hom Egnebase H Bs 11 37 43 AM Gees Sherry Tr eu SHEBISAL LAP uan connected d tone H II Pe AM Gees Shenoy Tren SHEBESAC TL UP foe cep iud fon el ower Timelrase H FI 1 Li 1000 1200 1400 Lx E sud 0 BDI N M LLL Chromeleon MSQ Plus Operators Guide 1 3 5 Chromeleon Software Program Files MSQ 3 9 Program Files Program files define th
73. t2 Finished 11 29 2007 5 54 02 1 0000 m 15ppb Standard F 100 0 IC MS new grad4 TEMP default2 Finished 11 29 2007 6 28 42 1 0000 9 ff 20onb Standard 8 100 0 IC MS new arad4 TEMP default2 Finished 11 29 2007 7 03 22 1 0000 2 File gt Save As the program to a new name such as Shutdown Method Chromeleon Program File IC MS new grad4 TEMP 2 Commands v I3 Edit View Workspace Qualification Control Window Help New Ctrl Open Ctrl 0 Close Save Ctrl S MW Savers Browser r A cqui xclusiveAccess iy ve Position_1 Preferences usiveAccess Print Ctrl P uireExclusiveAccess Print Preview Closed Print Setup 200 psi 3000 psi 1 FINAL DATA IC MS new grad2 6 00 ml min c 2 IC MS new grad4 TEMP 2 ga T 3 FINAL DATA default2 0 psi 4 FINAL DATA default 4000 psi S defaut 6 00 ml min 6 CS12AMS 20mM MSA Lead SIM ga 7 CS512AMS 20mM MSA 30 min p sc Exit Mn n cp Flush Volume 300 Save in E FINAL DATA Pump 1 NeedleHeight O rmm u n DP 3000 CutSegmentVolume 10 n1 t IC MS new grad Vni shutdown MS and IC SyringeSpeed 3 CycleTime 0 min aa IC MS new grada B C MS new gradd TEMP t IC MS new gradd TEMP 2 v IC M5 new grad5 Pos Scan v IC MS new grad6 v IC MS new grad Mame shutdown MS and IL alic xl Cancel Object of type Progam Help 3 16 Chromeleon MSQ Plus Operator s Guide Chromeleon SHENDAYLAP_local Customer Data
74. ted from the analysis There are two avenues to create a sequence 1 Sequence wizard 2 Modification of an existing sequence Chromeleon Sequence Wizard A From the File Menu select New From the New Menu select Sequence using Wizard Chromeleon SHENDAYLAP_local HPLC 1 2 4 07 Browser View Workspace Qualification Batch Tools Window Help Ctrl M Create a new document a d B m ok Control Panel Panel T abset Cancel Sequence using Wizard Sequence from LIMS Worklist Query using wizard Help Program File Method File Spectra Library B Alternatively access the sequence wizard by pressing the Create Sequence button on the Panel Tabset Sequence Control page Both modes lead to the wizard Sequence Control Status stem Log Audit Trail 10 38 35 AM User SHenday from SHENDAYLAP has disconnected from A timebase IC MS 3 10 38 35 AM User SHenday from SHENDAYLAP has connected to timebase IC MS 10 39 35 AM User SHenday from SHENDAYLAP has acquired control over timebase IC MS 100 000 ul from Pos RA1 uS Channel Pressure 0 034 ECD Total ECD 1 min 20 Run Time Elapsed 0 00 0 50 1 00 3 Execute Application Hold Continue Start Batch 1 Create Application Create Program Create Sequence Edit Program o eee 2 Prepare Sys
75. tem System Maintenance Daily Audit Trail Consumable Change Eluent Change Abort Batch 3 20 Chromeleon MSQ Plus Operator s Guide BDI ONEA MSQ Chromeleon Software Sequences C Follow the five steps of the sequence wizard to create the sequence shell Use the technique you learned from the Program Wizard Identify the timebase a b Define unknown sample parameters p Define parameters for the standards p Define method and reporting options for the sequence e Identify where to store the sequence and data collected Chromeleon Sequence Wizard Step 2 of 5 Unknown Samples Unknown Samples Generate samples from a template or import them via clipboard or from another sequence Use template gt Sequence Preview Rack Preview Template for Sample Name Number of Vials 5 1 4 Injections per Vial 1 1 99 Start Position RA1 H RA1 B5 Injection Volume 20 000 0 001 100 000 M Apply gt gt CEREREM lt Back Cancel Help Chromeleon Sequence Wizard Step 4 of 5 Methods amp Reporting E Methods amp Reporting Specify a method or select a pre defined template and indicate reporting preferences Applications includes method Method Files Prograrn Browse Quantification Method
76. to Library after entering necessary information Figure 7 Add MS Spectra to NIST MS Library BDI N F Chromeleon MSQ Plus Operator s Guide 9 3 Using the NIST MS Search with Chromeleon MSQ Create Your Own Library and Add Entries 9 3 Create Your Own Library and Add Entries Users can create their own libraries in the NIST MS Search program This function is useful when the analyte of interest is not included in the existing library or spectra at specific conditions are not available in the existing library e g spectra at high cone voltage for structural information To add a new library click the circled button Create Library in Figure 3 to create a new library and specify the name of library Follow section 3 2 to add new spectra to this library For more information of the NIST functions described in this manual and additional functions refer to the NIST MS Search Program user s manual 9 4 Chromeleon MSQ Plus Operator s Guide EDI ONEA MSQ EDIONEX Using the NIST MS Search with Chromeleon Create Your Own Library and Add Entries Chromeleon MSQ Plus Operator s Guide 9 5
77. unt Table Peak Tracking A MS Tracking Calibration Spectrl 3 Inthe dialog box that appears select the default of Enumerate peaks of current chromatogram Press OK Autogenerate Peak Table t Use Spectra Library Screening results Options Apply only to peaks with greater than Im Signal min Apply only to peaks in current time interval Copy reference spectrum from IP gt rese x Cancel Help 4 8 Chromeleon MSQ Plus Operator s Guide BDI ONEA MSQ Starting a Sequence Mass Spectra Data Extraction Integration and QNT Editor Views 4 Click OK to the warning message Chromeleon Caution Autogenerate will overwrite the entire peak table You cannot unda this command 5 The peak table will generate rows based on how many peaks are defined in the chromatogram 6 Rename the peaks from default 1 2 3 etc to the name of the analyte 7 Adjust the peak window if required 120 um 5 defau 3 default 12 100 x a m a o l Comment 1 1 533 min 0 050 AG External Area Lin Auto Autogenerated 2 default 2 1 933 min D 067 AG External Area Lin Auto Autogenerated 3 default 3 2 357 min 0 083 AG External Area Lin Auto Autogenerated 4 default 4 2 967 min 0 100 amp G External Area Lin Auto Autogenerated 5 default 5 3 300 min D 067 AG External Area Lin Auto Autogenerated B default 5 4 100 min 0 100 AG External Area Lin Auto Aut
78. ve Negative Switching APC FullScan Positivelon APC SIM Megatreelon APCI SIM Positive Negative Switching APC SIM Positivelan ESI Full5can Negativelon ESI Full amp can Positive Negative Switching ESI FullScan Positrvelor ESI SIM Negativelon ESI SIM Positive Negative Switching ESI SIM Positivelon Back Cancel Help Chromeleon MSQ Plus Operator s Guide EDIONEX Chromeleon Software MSQ Program Files Scan Type A FullScan Scans across a definable mass to charge m z range 1 This option is selected to provide the most information about the sample i e A mass spectrum can be generated from a full scan Can be used as a screening tool if m z is unknown 2 The least sensitive mode for quantification B SIM Selected Ion Monitoring The data collected by the mass spectrometer is focused on a single mass with a narrow window 1 This option is selected to provide the most sensitivity high signal noise ratio for the analytes 2 The m z must be known prior to selecting SIM as a scan type Polarity A Positive Data is only collected for cationic species positively charged analytes w Negative Data is only collected for anionic species negatively charged analytes C Positive Negative Switching The MSQ will alternate scans between positive and negative ions allowing for both cationic and anionic species to be detected in a single run 1 Can be used as a tool for screening 1

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