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PrimeView 5.0 - GE Healthcare Life Sciences

1. Curve coordinates can also be used to measure noise levels on the source curve The table below describes how to do this Step Action 1 Use the Zoom function to focus on a part of the curve that is repres entative for the baseline noise 2 Select an appropriate Y axis scale 3 Measure the Y axis coordinates 4 e Calculate the noise range as the difference between the max and min values e Add an extra 20 e Choose Integrate Calculate Baseline and insert this value as the Noise window value e p131 A Evaluation functions and instructions A 2 Peak table column components A 2 Peak table column components Introduction This section contains a list of peak parameters with explanations and calculation formulae when applicable Peak parameters The diagram below illustrates the peak parameters See the parameter list below for illustration explanations Peak parameter The list below contains descriptions of the peak parameters descriptions Parameter Area Asymmetry Baseline height Description Calculated as the area between the curve and baseline between the peak start and peak end time or volume base Gray area in the diagram above Peak asymmetry indicator of column packing See definition below this table Baseline amplitude at peak start peak maximum and peak end A F and G in the diagram above 03 0014 96AD ep 132 Evaluation fu
2. How to view the complete logbook information At some breakpoints there can be more logbook information than what is possible to conveniently display in the chromatogram window The additional information that is not displayed is indicated by an arrow point symbol by the break point e Hold the mouse cursor over the break point to display the complete information in a flyover text box as shown in the illustration below Block System_Volume_Compensation Base Volume ml ip ep55 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 How to optimize the presentation of a chromatogram Introduction This section describes some of the ways you can optimize the presentation of a chromatogram In this section This section contains the following sub sections Topic See How to make changes in the Chromatogram Layout dialog box 6 3 1 The Curve tab and Curve Names tab 6 3 2 The Curve Style and Color tab 6 3 3 How to change and fix the axes 6 3 4 How to save and apply a layout 6 3 5 How to show part of a curve 6 3 6 03 0014 96AD p56 6 3 1 Instruction How to view results 6 How to make changes in the Chromatogram Layout dialog box The Chromatogram Layout dialog box is used to make changes regarding chromatogram presentation The main features of the Chromatogram Layout dialog box regarding chromatograms are described in the subsequent sections in this chapter F
3. Step Action 1 Choose Edit Rename and the relevant option Chromatogram Curve or Peak Table Result The Rename dialog box opens 2 e Select the appropriate object e Type anew name in the Name field e Click OK Note The original raw data curves cannot be renamed They will not be listed as options in the dialog box ep 83 7 How to edit results 7 3 How to export results 7 3 Introduction Data formats Export options How to export curves 03 0014 96AD ep 84 How to export results This section describes how to export curves in different formats and how to copy data and curves to the clipboard You can export data in the following formats AIA cdf ASCII asc Lotus 1 2 3 wks Excel xls XML xml Select File Export in the Evaluation module to export data from an open result file The following export options are available Curves Export curve to AIA Peak table Documentation Evaluation log The table below describes how to export curves in the Evaluation module Step Action Choose File Export Curves Result The Export Curves dialog box opens Saraco chromatog arn Chaves to expert fs 201 125200101 1_UV1_280nm 02 125200101 1_U 2_250nm 1403 125200101 1_U 3_Onm SON 1252001 01 1 UVI 20m TOR 1252001 01 1_UV2_250rm TOR 125200101 1 U2 Ones T04 1252001 01 1_Cond T05 125200101 1 Cond T06 125200101 1_Cone 207 12520
4. The table below describes how to clear the contents of a temporary chromatogram Step Action 1 Open the relevant result file How to view results 6 Step Action e Select Edit Clear Temporary Chromatogram e Click the Yes button to confirm ep51 6 How to view results 6 2 Basic presentation of chromatograms 6 2 2 The chromatogram window 6 2 2 The chromatogram window Main views The chromatogram window is divided into two main views e curves e peak tables The displayed areas for the views can be adjusted by dragging the borders with the mouse cursor between the views How to view peak The table below describes how to display peak table information if the result has table information been integrated 1 Open a result file 2 e Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box opens 3 e Click the Peak Table tab e Select a peak table in the Select peak table to display list e Select what peak table columns to display e Check if global peak table data should be displayed or not e Click OK 03 0014 96AD ep52 Run curves de fault appearance and information Run curves short cut menu Optimizing the workspace How to view results 6 The first time a result file is opened and viewed a default layout is applied to display all the original curves The default layout can be changed by the user see 6 3 5 How to sav
5. from External e Ifthe files were saved using the function Copy to External they will automatically be decompressed How to use Copy The table below describes how to use the function Copy from External from External Step Action 1 e Right click in the Open Results dialog box and select Copy from External Result The Copy from External dialog box opens 2 Select the files you want to copy 3 Click Save Result The result files are copied into the open folder in the Open Results dialog box How to rename The table below describes how to rename files and folders in the Open Results dialog files and folders box Step Action 1 Select the item that you want to rename 2 e Right click and select Rename from the shortcut menu Result The Rename dialog box opens 5 Type a new name 4 Click OK Howto delete files The table below describes how to delete files and folders in the Open Results dialog and folders box Note Home folders cannot be deleted this way Step Action 1 Select the item that you want to delete 03 0014 96AD ep 30 Backup security Files and folders in PrimeView 4 Step Action 2 e Right click and select Delete from the shortcut menu or e Press the Delete key 3 Confirm the delete action in the confirmation dialog box Backup copies should be taken regularly to avoid data loss in the event of hard disk failure or accidental
6. Example View Panes Customize i e the menu command Customize in the sub menu Panes from the View menu Text entries that PrimeView generates or that the user must type is represented by a monotype typeface Example Connection change ep5 2 PrimeView concepts Introduction In this chapter 03 0014 96AD ep6 PrimeView concepts This chapter contains e Definitions and descriptions of some of the specific concepts that are presented in this manual e An overview of the PrimeView user interface Note General concepts and common chromatography terminology are not explained here This chapter contains the following sections Topic See Concept definitions 2 1 The PrimeView user interfaces 2 2 2 1 Introduction Chromatogram Curves Method Result files Template PrimeView concepts 2 Concept definitions This chapter contains explanations and definitions of a number of PrimeView concepts that are used in this manual The concepts are organized in alphabetical order A chromatogram is a collection of data represented by a number of curves that have been created during a separation run including UV conductivity pH fraction marks etc The original raw data curves cannot be deleted or modified They can be used as a basis for evaluation procedures and subsequent creation of new curves A chromatogram can also contain curves that have been created and saved during
7. R Rename files and folders 30 Reports ow to create a blank customized report 69 dit mode toolbar buttons 69 x E How to add or delete pages 70 How to change the page setup 70 How to add objects to a report 72 How to add free text 72 How to add picture objects 73 How to include chromatograms 74 How to include a peak table 74 H ow to add documentation 75 03 0014 96AD epvi How to add the Evaluation log 76 Toolbar icons in Report Edit Mode 77 How to print 78 How to save the report format 78 Result files How to open 26 How to save 88 S Searches General functions 13 Security Backup 31 Snapshots How to view 16 System Control module Description 9 T Templates How to start a run from an application template 33 How to start a run from a method template 34 Temporary chromatogram Description 50 Toolbar icons In the PrimeView module 10 Y Y axis How to choose the Y axis scale 53 Index e pvii Index Z Zero baseline Definition 90 Zoom function How to enlarge parts of a curve 66 03 0014 96AD e p viii E Elanders sterv la 2006 www gehea Ithcare com UNICORN Drop Design and AKTA are trademarks of GE Healthcare companies GE imagination at work and GE monogram are trademarks of General Electric Company GE Healthcare Bio Sciences AB Microsoft and Windows are trademarks or registered trademarks of the Bj rkg atan 30 Microsoft Corp
8. 01 57606 1627 e Belgium Tel 0800 73 888 Fax 03 272 1637 Canada Tel 800 463 5800 Fax 800 567 1008 e Central East amp South East Europe Tel 43 1 982 3826 Fax 43 1 985 8327 e Denmark Tel 45 16 2400 Fax 45 16 2424 e Finland amp Baltics Tel 358 0 9 512 39 40 Fax 358 0 9 512 39 439 e France Tel 01 69 35 67 00 Fax 01 69 41 96 77 Germany Tel 0761 4903 490 Fax 0761 4903 405 e Italy Tel 02 27322 1 Fax 02 27302 212 Japan Tel 81 3 5331 9336 Fax 81 3 5331 9370 e Latin America Tel 55 11 3933 7300 Fax 55 11 3933 7304 Middle East amp Africa Tel 30 210 9600 687 Fax 30 210 9600 693 Netherlands Tel 0165 580 410 Fax 0165 580 401 e Norway Tel 815 65 555 Fax 815 65 666 Portugal Tel 21 417 7035 Fax 21 417 3184 e Russia amp other C I S amp N I S Tel 7 095 232 0250 956 1137 Fax 7 095 230 63 77 e South East Asia Tel 60 3 8024 2080 Fax 60 3 8024 2090 e Spain Tel 93 594 49 50 Fax 93 594 49 55 e Sweden Tel 018 612 1900 Fax 018 612 1910 e Switzerland Tel 0848 8028 12 Fax 0848 8028 13 UK Tel 0800 616928 Fax 0800 616927 e USA Tel 800 526 3593 Fax 877 295 8102 imagination at work 03 0014 96 AD 05 2006
9. 06 id 48Quantitate001 1_Cone 07 08 id148Quantitate001 1_Pressure Peak integration 8 How to display The table below describes how to display peak labels peak labels Step Action e Choose Edit Chromatogram Layout or e Click the Chromatogram Layout icon aii Result The Chromatogram Layout dialog box opens Click the Curve Style and Colour tab 3 Select one or more of the following labelling options in the Peak label field e Number Result The peaks will be numbered sequentially e Peak Name Result Peak names will be displayed See 8 6 How to edit the peaks on page 111 for information about how to name the peaks e Retention Result The retention volume or time will be displayed e Click OK ep95 8 Peak integration 8 3 How to optimize the baseline with a morphological algorithm 8 3 Introduction The Morphologic al algorithm How to set a Mor phological baseline 03 0014 96AD ep 96 How to optimize the baseline with a morphological algorithm The first choice when you want to optimize the peak integration is to change the baseline parameters This section describes how to optimize the baseline with a morphological algorithm The Morphological algorithm can be described as a line that follows the chromatogram parallel to the X axis Data points for the baseline are created whenever the line touches the curve and the points are joined at the end t
10. Delete at Diaw srat to net point E The table below describes how to use the zoom function in the Edit Baseline dialog box Step Action 1 e Click the Zoom icon Result The cursor is changed into a magnifying glass 2 e Press and hold the left mouse button e Drag the cursor over the area you want to zoom in on e Release the mouse button Result The area is enlarged Right click and select Reset zoom to re store the full view Peak integration 8 How to editand The table below describes how to edit and insert baseline data points insert data points Step Action 1 Select Integrate Edit Baseline Result If there are more than one baseline available the Select Baseline to Edit dialog box opens If not proceed to step 2 e Select the baseline you want to edit from the list e Click OK Result The Edit Baseline dialog box opens 2 e Click the Set Curve Points icon te oco Result The cursor is changed into a cross 3 Add a data point e Click the left mouse button to place a new baseline point in the chromatogram Result Anew point is created marked by a green square The baseline curve is redrawn as a spline function based on the old and the new points The baseline is guided by the points but does not necessarily pass through them 4 Delete a data point e Double click the data point or e Click the data point to select it and click the Delete button
11. How to finish the Press the OK button to finish the run at the Method Complete prompt This will cause run all valves to return to the default position 1 The run can be aborted before it is complete at any time by pressing the End button 03 0014 96AD ep 36 How to perform method runs 5 5 2 How to monitor a method run Introduction This section describes how to monitor a method run by using the PrimeView module and how to customize the different panes In this section This section contains the following sub sections Topic See How to customize PrimeView panes 521 The Curves pane 5 2 2 The Logbook pane 5 2 3 ep37 5 Howto perform method runs 5 2 How to monitor a method run 5 2 1 How to customize PrimeView panes 5 2 1 How to open the PrimeView mod ule Illustration 03 0014 96AD p38 How to customize PrimeView panes The PrimeView module displays the status of the KTAprime system run The PrimeView module can be open on the Windows desktop before a run is started in which case it will either display a blank Curves pane or show the curves from the previous run The PrimeView module can also be opened after the run has been started in which case it will display the whole progress of the run from the beginning The list below describes how to open the PrimeView module e Click the PrimeView icon Result The PrimeView module opens The illustration shows the PrimeView module with
12. a 9 41 3 4405 42 176 9 14 0 2736 2 037 8 86 0 1840 1 715 3 46 0 3746 1 311 0 95 2 2954 6 052 mole Result002 Example ResuMO02 res Peak nare Retention min Area mAU min Height mAU Peak A 0 2 Peak B 0 2 Peay coin gt t 5 65 6 53 7 06 77 60 5051 14 6092 20 4377 ELETT 336 628 95 761 125 560 147 422 Fes fom Fes Note You can also use the Reject peaks function in the Integrate dialog box to reduce the number of peaks based on the total number of accepted peaks or the minimum peak height Missing peaks Peak integration 8 Sometimes obvious peaks are not detected in the peak integration The probable cause is that the Noise window is set too high See the illustration below ALAA All peaks are detected if the Noise window is decreased see example below Note Missing peaks can also be caused by improper settings for Reject peaks in the Integrate dialog box or Filter peaks in the Chromatogram layout dialog box ep 105 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm When to change In rare cases the top of a broad flat peak can be incorporated as a baseline segment the Max baseline This is one of the very few situations where it is useful to change the Max baseline level level The illustration below is an example How to set the The table below describes how to set the Max baseline leve
13. CHrOMATOGFAM ccceccssssssssssssssssesssccecccessssssnnssesesseeseesesssssnnneeseeesesee 82 7 2 How to rename chromatograms curves and peak tables ccccccccccsssssssssseesecscceeesssssnnneeeeeeeee 83 PS HOW LO EXPONE FOS UES n a A ataac aes 84 7 4 How to save results and exit the Evaluation MOUIE ssssssssssssssssssssssnnnesseeseceececcsssssnnnmesseeeeeees 88 Be PECK integrati n esera cuee did ases bck theceveua cide susan cepnnsecuceda sas sdaunieveuvscacadensedseisecdecoueseyes 89 8 1 Baseline GOCE OM saaassssssscsostsscessssssssscsscedsentsccenssssasiscsssd tsstsccensssiaagucnagggast cnsnennesssssooopbseeceonncsbesbyssassopoenonnonnen 90 8 2 HOW to perform a peak INteQratiOn csssssesssccscssccccssssssnnnnnnessccseecesessssssssnmeseseececeeeessssssumeeeceseeceessesees 91 8 3 How to optimize the baseline with a Morphological AIGOFItHM ee eeccccssccccccssssssssesseesseeseeeeesees 96 8 4 How to optimize the baseline with a classic GIQOFItH IM eessssssssssccssssssssnnssesseseececessssssnneeeees 100 8 5 IOWA Edit the Baseline Man esses aashdasacbcescecccesssssssssszescccscecocsssssssaasaneseceeeecccennstatas 108 e A NAE SIE o1 A S O AAA 111 8 7 How to integrate part of a curve and how to exclude or SKIM P OKS ececscsccccssssssseeeeeeeee 119 8 8 MECSUPEMEMHS ceeeccssssescesssseseessnsccersnscesssnsecessusscesssusscessnsscessunsccessusecessunsccessusscesssnscsessuessessuuecsessneessssnneesesaneeess 124 A Evaluation
14. Result Chromatogram name Number given automatic 11 ally during a run or a name defined by the New_Chromatogram in struction Curve name Curve type for example UV detection of an eluted component How to choose You can choose to view only part of the curve name The table below describes how curve name ap to do this pearance Step Action 1 Open a result file 2 Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed 3 Click the Curve Names tab 4 e Select the appropriate boxes for Curve name appearance e Select the appropriate Curve legend position e Click OK 03 0014 96AD p58 How to view results 6 Note It is usually sufficient to select the Curve Name option if only one chromatogram is being evaluated However confusion can arise when more than one chromatogram is shown so more complete names might be necessary ep59 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 3 The Curve Style and Color tab 6 3 3 Introduction Peak label set tings Fraction text and Logbook text alignment set tings How to change the color and style of a curve How to display a hatched back ground 03 0014 96AD p60 The Curve Style and Color tab All curves within a chromatogram are represented by a default color and line style Curves imported into the chromatogram or newly created curves are automat
15. The PrimeView panes The Curves pane The Logbook pane The Status bar PrimeView concepts 2 The PrimeView module The PrimeView module is used to monitor separation runs The PrimeView module contains two different display panes that can be opened both at once or one at a time e The Curves pane e The Logbook pane The Curves pane displays monitor signal values graphically See the illustration below 00 Of O62 03 O04 OF 06 OF 06 O8 10 13 42 43 14 15 16 t 88 8 20 The Logbook pane displays all actions during a separation run e g method start and end base instruction method instructions and manual instructions such as Pause or Hold See the illustration below 0 00 min Method Run 2003 12 01 14 4403 W Europe Standard Time Methed Resut pime AT2003dec0Ino01 RES Logbook 0 00 min Borch ID BEADES95 767E 4005 4154 BOFFSOFI BEES 0 00 rnin Base Time O00minPeuse 0 0 2003 12 01 14 4403 W Europe Standerd Time Manuel 0 00 min Error 62 Chack thet tube position is OK 0 00 rnin Concertration 0 B 0 00 min injection Valve Wasto 0 00 min Cornus 2003 12 01 14 44 09 W Europe Standord Tine Manual 0 00 min Flow 40 0 miirin 087 min Broek poirt 08 min Flow 5 0 rnlinin 0 89 min injection Valve Load 04 min End 2003 12 01 14 4312 W Europe Standard Tima 5 04 min Flow 0 0 ml min The Status bar in the bottom of the PrimeView module displays the current status of the separation run See
16. Welcome dialog box is displayed e Click the Next button to continue 2 e The PrimeView Software License Agreement dialog box is dis played You must accept the license agreement to install PrimeView e Click the Yes button to continue 3 e The User Information dialog box is displayed Type your name company and the product serial number of the software The serial number can be found on the License Agreement that is shipped with the CD e Click the Next button to continue Step 3 Selectthe You must define the COM port which the AKTAprime system is connected to COM port e Select the appropriate COM port e Click the Next button to proceed Select COM Port xj Choose the COM port listed below which the instrument is connected to Once you have selected a COM port press the next button to continue the installation COMI C COM2 C COM3 C COM4 lt Back Cancel 03 0014 96AD p20 Software Installation 3 Step 4 Select In the Select Drive dialog box you choose the installation folder for the PrimeView Drive software Select Drive Follow the instructions in the table to select a disk drive Step Action Select the disk drive where the program is to be installed This should be a physical disk drive usually C on the computer where you install PrimeView not a network disk drive e Click the Next button to continue e Click the Yes button if asked wh
17. a baseline segment where The length of the box corresponds to the Shortest baseline segment The height of the box corresponds to the maximum level of noise on the baseline segments This is referred to as the Noise window The box is allowed to be tilted with a maximum slope corresponding to the Slope limit The box is not allowed to move up above the Max baseline level The illustrations below shows the baseline parameters graphically Shortest baseline segment C Noise Window ep129 A Evaluation functions and instructions A 1 Baseline calculation theory Baseline segment identification Baseline points Classic algorithm Baseline drawing 03 0014 96AD p 130 Max baseline level t Slope limit The table below describes the baseline segment identification process Description The box is virtually moved along the source curve in steps of one third of the Shortest baseline segment length to look for baseline segments A baseline segment is found whenever the currently examined part of the source curve fits completely within the box 3 The found baseline segments are joined by connecting adjacent seg ments provided that the slope of the joining lines does not exceed the Slope limit When the baseline segments have been defined and joined they are replaced by baseline points at the start and end of each segment The line between these is also filled with
18. and instructions A 2 Peak table column components Sigma formula Peak resolution algorithms 03 0014 96AD ep 134 Parameter Type of peak limits Width Width at half height Description Identifies the criteria for peak start and peak end as either the baseline intersec tion or dropline to the baseline or skim line Difference in retention between the peak end and peak start time or volume base G A in the diagram above Calculated by taking the maximum height of the peak above the baseline then determining the peak width at half this value above the baseline Time or volume base B D in the diagram above where BD bisects CF The formula below is used to calculate Sigma n Sigma gt v Xi Xmax r i l peak Where e nis the number of data points e xis the volume or time value e Xymax is the volume or time value at the maximum amplitude value e Apeak is the area of the peak Note The peak width for a Gaussian peak is 4 x Sigma The peak resolution is calculated with one of the following three algorithms 1 Veo Vra Who Wp 2 2 Veo Vay Sigma Sigma x 2 3 Vpo Vra 2 x Who Why 2 354 Evaluation functions and instructions A Where Vri Wp1 Sigma and Wj are the retention width Sigma and width at half height of the previous peak VR2 Wb2 Sigma and Wh2 are the retention width Sigma and width at half h
19. deletion You can use the function Copy to External to save your files on the network server Note GE Healthcare cannot accept responsibility for the replacement of results that were lost as a result of computer failure or other incidents ep3l 5 How to perform method runs 5 How to perform method runs Introduction This chapter describes how to perform and monitor different kinds of runs from the PrimeView module It also describes how to control the system with manual commands and instructions In this chapter This chapter contains the following sections Topic See How to start a method run 5 1 How to monitor a method run 5 2 03 0014 96AD ep 32 5 1 Before you start Four ways to start an AKTAprime run How to start an application tem plate run How to perform method runs 5 How to start a method run Before you start a method make sure that e the AKTAprime system is prepared according to the instructions in the AKTAprime system documentation The method runs are all operated from the AKTAprime unit There are four different types of AKTAprime runs e Application template runs e Method template runs e Operator created method runs e Manual runs Application templates are available for the most frequent purifications All process parameters except the sample volume are preset The table below describes how to start an Application template run on the AKTAprime unit All param
20. dialog box opens ob gJ wo 160 Wo Oo wo Ln PS O Bime paw O coat tee j 2 e Type new X axis values for the Left limit and the Right limit or e Drag the vertical cursor lines to define the limits ep119 8 Peak integration 8 7 How to integrate part of a curve and how to exclude or skim peaks How to exclude peaks How to include negative peaks 03 0014 96AD ep120 Step Action 3 Click OK Result The baseline will be calculated from the whole curve but the calculation of the peak areas is only performed on the selected section You can define criteria to exclude peaks from integration The table below describes how to define peaks to be excluded in the Integrate dialog box Step Action 1 Click the Reject peaks button Result The Reject Peaks dialog box opens 2 e Select the appropriate checkboxes and type values for height width and area e Define how many of the largest peaks you want to include e Click OK Select the Accept negative peaks checkbox of the Integrate dialog box to include negative peaks in the integration Result The negative peaks will be reported as negative areas in the peak table By default negative peaks are not included in the integration Peak skimming vs drop lines How to skim peaks Peak integration 8 The area under a peak can be calculated either using separating drop lines or peak s
21. e Click OK Note Peak tables are exported as text strings in ASCII format and numerical values in the Lotus 1 2 3 formats All possible columns in the peak table are exported How to export The table below shows how to export documentation and evaluation logs documentation and evaluation Step Action logs 1 Select the data you want to export 2 e Select options in the dialog box e Click the Export button 3 e Select a destination folder and type a file name e Click OK Copy to the clip You can also use the Windows clipboard to copy the contents of the active window board and paste it into other programs e g Microsoft Word Curves and documentation are copied as Windows enhanced metafiles emf and peak tables are copied as text Only the peak table columns that are selected in the spreadsheet will be copied e p87 7 How to edit results 7 4 How to save results and exit the Evaluation module 7 4 How to save results and exit the Evaluation module Introduction After you have finished the evaluation process you can save all the changes you have made to the chromatograms including newly created curves and chromatograms that you have imported and created How to delete un All the curves that you created during your manipulations will be saved in the wanted curves chromatogram If some of these curves are not be needed anymore select Edit Delete Curves in the Evaluation module to remove
22. functions and instructions si L27 A 1 Baseline calculation tHEOY eesssssssssccccsssssssnnssssssscceccesssssnnummssesssescecessssssnnuuesseeeeeceesssssnnumesssseeeeeeeeee 128 AZ Peak tObIScolUmMmM COMPONENTS ssns Ea 132 03 0014 96AD e pii Introduction In this chapter Introducing PrimeView 1 Introducing PrimeView This chapter contains e A general overview of the PrimeView system e Information about the user documentation for PrimeView and how to use it This chapter contains the following sections Topic See About PrimeView t 1 About this manual 1 2 ep3 1 Introducing PrimeView 1 1 About PrimeView 1 1 Introduction What is PrimeView Operating environ ment Windows func tions Help functions 03 0014 96AD ep4 About PrimeView This section is a general overview of the PrimeView system PrimeView is a complete control software package for supervision of AKTAprime automated liquid chromatography systems PrimeView runs on a PC under Microsoft Windows 2000 or Microsoft Windows XP It is designed to run under English keyboard settings Most Windows functions are also available in PrimeView including e cut and paste e right click short cut menus Note Drag and drop is not available File and folder handling in PrimeView also differs from the general Windows file manager standard An online help utility is included in the PrimeView sof
23. name Layout I Current Dei coc e Select which chromatogram s to insert from the Selected chromato gram s droplist e Active chromatogram inserts the chromatogram that currently is active in the Evaluation module e All chromatograms inserts all chromatograms that are open in the Evaluation module e 1 2 etc inserts the corresponding chromatogram 3 e Select the desired Settings e If desired change the Fonts Note Separate fonts can be selected for the Chromatogram the Peak table and the Header text 03 0014 96AD ep 74 How to view results 6 Step Action e Click the Define button in the Layout field if you want to re define the layout of the chromatogram Result The Report Chromatogram Layout dialog box opens e Make the appropriate changes and click OK to return to the Setup Chromatogram dialog box Note The changes that you make will only affect the report and not the view of the chromatograms in the Evaluation module 5 Click OK Result The chromatogram is inserted onto the page Note All curves can be de selected in the Report Chromatogram Layout dialog box leaving only the selected peak table s in the report How to add docu The table below describes how to add documentation to the report mentation Step Action 1 e Click the Documentation icon e Press and hold the left mouse button on the report page and drag out a bo
24. peak limits too high up on the peak slopes Note You can also use the Reject peaks function in the Integrate dialog box to reduce the number of peaks based on the total number of accepted peaks or the minimum peak height Peak integration 8 Minimum distance The Minimum distance between points is a measure of the distance between the between points data points used to generate a baseline The largest number of data points is produced at the slopes of the curves If you increase the Minimum distance between points value fewer points will be collected on the slopes The illustration below is an example of a baseline A that is created with the Minimum distance between points parameter set at a low value The number of data points is reduced when the Minimum distance between points parameter is set to a higher value B A Zoomed Curves epg99 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm 8 4 How to optimize the baseline with a classic algorithm Introduction The first choice when you want to optimize the peak integration is to change the baseline parameters This section describes how to optimize the baseline with a classical algorithm What is the Clas The Classic algorithm searches for all parts of the source curve that are longer than sic algorithm a defined minimum baseline segment and fall within limiting parameters Together the parameter values def
25. renumbered e p113 8 Peak integration 8 6 How to edit the peaks How to add color The table below describes how to add a fill color and a pattern to a peak in the Edit to a peak Peak Table dialog box Step Action e Click the Edit peaks icon m e Move the cursor over the peak you want to edit Result The cursor is changed into a larger arrow e Click to select the peak 2 e Right click and select Fill Peak from the shortcut menu or e Select Edit Fill Peak Result The Color and Pattern dialog box opens Color and Pattern e Select a color and a pattern e Click OK Result The peak is filled according to the selections Note The color and pattern selections will override the general Fill settings that can be selected for all peaks on the Peak Table tab in the Chromatogram Layout dialog box 03 0014 96AD ep114 Peak start and end points How to split a peak Peak integration 8 The beginning of each peak is marked with a drop line above the curve and the end of each peak is marked with a drop line below the curve The illustration below shows an example of start and end point drop lines Peak start Peak end Where there are two peaks beside one another the end of the first peak will be at the same point as the beginning of the next peak Thus there will be a drop line below and above the curve at the same point See the illustration below It
26. the Curves and Logbook panes displayed UV1_215 Cond pH Pressure Temp Cone r min 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 1 7 18 19 2 0 D0 ren Ron sianed or Hep press PE Ona Bea i jot eroabed by prime How to select what panes to display How to customize PrimeView panes How to perform method runs 5 The PrimeView module displays one or two panes for monitoring different aspects of the run To select what panes to display either e click the Customize Panes icon or e choose View Panes Change the size Select a split bar and drag up and down to change the size of a specific pane Maximize restore or hide Right click a pane and select the appropriate option to e maximize e restore or e hide the pane ep39 5 Howto perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane 5 2 2 The Curves pane Introduction The Curves pane of the PrimeView module displays monitor signal values graphically The figure below shows an example of the Curves pane SWI A e ee ere Orrea 145 min bed 183 10 mau How to select The table describes how to select the curves to be displayed on the screen curves to be dis played Step Action 1 In the PrimeView module select View Properties Result The Properties dialog box is displayed 2 Select the Curves tab 3 In the Display curves list select the curves you want t
27. value is set at the widest peak in the chromatogram multiplied by 1 5 The illustration below is an example of how a morphological baseline follows the peaks at the different levels in the curve ep97 8 Peak integration 8 3 How to optimize the baseline with a morphological algorithm Thecorrect struc Too low settings ture width set tings Noise window 03 0014 96AD e p98 Too low Structure width settings can result in a baseline that reaches too high up in the peaks of the curve Sometime a wider peak is not recognized because it contains a cluster of smaller peaks The Structure width is then set to a value according to the largest width of the identified narrower peaks and must be increased Too high settings Too high Structure width settings mean that narrower peaks especially in fluctuating curves are not properly followed This happens when an artifact in a curve is identified as the widest peak by the morphological algorithm and then is used to set the default Structure width value The illustration below is an example of baselines using the default morphological algorithm settings A and a morphological algorithm with an increased Structure width value B Sometimes you get too many peaks after the peak integration usually because noise on the baseline is erroneously detected as peaks The solution to this is to increase the Noise window parameter However this can result in
28. window Shortcut menu 53 How to optimize the workspace 53 How to display a vertical marker 54 How to display the Logbook overlay 54 Chromatograms Description 50 Temporary chromatogram 50 How to make layout changes general 57 Index epi Index How to change and fix the Y axis 62 How to add a second Y axis 62 How to change and fix the X axis 63 How to save a layout 64 How to apply a layout 64 How to print active chromatograms 67 How to add annotations 82 How to edit annotation text 82 How to rename 83 How to set a reference point 125 Classic algorithm Definition 100 Parameters 100 How to set 100 Shortest baseline segment 101 Slope limits 102 Noise window 104 Missing peaks 105 When to change the Max baseline level 106 How to set Max baseline level 106 Definition 129 How to measure baseline segments 131 How to measure noise level 131 Curves How to copy into the Temporary chromatogram 50 Run curves default appearance 53 How to choose the Y axis scale 53 Default curve names 58 Peak labels 60 Fraction text alignment options 60 Logbook text alignment options 60 How to change the color and style 60 How to set a hatched background 60 How to change and fix the Y axis 62 How to add a second Y axis 62 How to change and fix the X axis 63 How to save a layout 64 03 0014 96AD pii How to apply a layout 64 How to use the zoom function 66 How to rename 83 Export opt
29. windows side by side Window Cascade to stack the open windows like a deck of cards The table below describes how to display a vertical marker line Step Action Right click the Curves pane and select Marker 2 Drag the marker line with the mouse Result Where the line bisects the curve the X axis and Y axis values are displayed at the top right corner of the pane Note Right click and select Snapshot to record the marker position values See 2 2 5 Snapshots on page 16 for more information about the Snapshot function The table describes how to set a reference point Step Action 1 e Display a Marker in the Curves pane e Right click and select Set Marker Ref Point to define a reference point for the marker position 2 When the marker is moved from the reference point the X axis and Y axis values for the new position are displayed together with e the new position in relation to the reference point e the minimum maximum and average values for the curve interval between the reference point and the new position The table below describes how to display the logbook entries as an overlay in the chromatogram Step Action T e Right click in the chromatogram window and choose Properties on the shortcut menu Result The Chromatogram Layout dialog box opens How to view results 6 Step Action 2 e Choose the Curve tab e Select the Logbook curve
30. 0101 1_sH 208 125200101 1_ Pressure TOS 1252001 01 1 Fow D10 126200101 1_ Temp toe Ot ouves Reduce number of sampler I Nomakse retenc Eom fi m Reduce by tactor 12 5 eem Io fsa Maxno sampler 306 CE ee e How to limit the exported curves How to edit results 7 Step Action e Select the curve s you want to export e Enter parameters to limit the curvels if necessary e Click the Select button e Repeat Step 2 to select more curves Click the Export button Result The Export Curves to File dialog box opens Select the export file format from the Save as type droplist e ASCII files asc e Lotus 1 2 3 files wks e Excel files xls e AIA files cdf 5 e Select a destination folder e Type a file name and click OK Note Curves are exported as series of numerical coordinates that refers to the time volume and signal respectively You can optimize the exported curves to only the parts that you want to focus on in the Export Curves dialog box The table below describes how to use these editing options Dialog box option Instruction Enter retention values in the text boxes to limit the curve to only a portion of the original curve Cut curves Cut graphically This button opens the Export Cut dialog box Move the vertical markers to the correct cutoff points Reduce number of samples Adjust the factor value or the maximum num
31. GE Healthcare PrimeView 5 0 User Manual UNICORN Table of Contents Table of Contents 1 IEFODUCING PRIMO VIEW esis ccesesscsasees sasssenesciessdecsaesiesnscandcacuesslosastitedscuttensavuedeststevapeeviaaseueu aE CETE shs koas 3 LL ADOUt PiIMO VICW Q ccccsscssssssesssccsssssssesscssssssssssssssssssssssssssssssessessssssusssessssssssssessssssusssecsssssuusssessssssussessssssuuessessssssueesees 4 25M ECS MANUA ssaa aan arana NN aranana NANa E ANEA N A S ENTANA TENAN 5 2 PrimeView concepts eeeeseeeseseseseesossseesossessescssssrecsessorseessseneseserroreessesceeseesoreeesrsesesrseeseseerorsesssreeess 6 Z Lz CONC DE defiMitiONS sssri sraNyata Neasa NN NERN NONNA RANON ATANIR ERANO ANANIRA IEPER A NANITA NDERE 7 2 2 The PrimeView user interfaces wi av 8 2 2 1 The PrimeView MOCUIC cccsseeesssssssssssessccsssssssssesssssssessecssssssssssessssssusssessssssssssescssssuussssesssssisssssessssisesseensssssees 9 2 2 2 The PrimeView Evaluation MOU cecccccsssssessssccssssseessccssssssessscssssssssssssssssssessesssssssuesssssssssssssssesssseesee 11 22S SCACCO S A 13 22 A E TUG EI A E eE EEEE 15 22 57 SNAPS NOS ssscssvcssscscosssesseessccssossscscosssossnssoosssesssescescsesussssce sees ssescesesesssssccc sees ssescoccsesssssce sees sccccesessssssceseoususesse 16 3 Software INStAllAtion cssscscsssssssscscssscssescssscscessssscscsesceesscseseacscscsesscsescaessescaescaesesesasscseseaesseess 18 3 1 How to ins
32. Open icon Lay Result The Open Result dialog box opens Open Result f o x CA prime Name Size Type Modified c ini Example Result001 Result File 2002 04 24 08 46 Example Resultot Result File 2002 04 24 08 51 Li Example Resultdt Result File 2002 04 24 08 52 i Example Result004 Result File 2002 04 24 08 51 u ExampleResult GF001 Result File 2002 04 24 08 41 laij ExampleResult GF002 Result File 2002 04 24 08 35 Cancel Help 2 e Double click the result file or e Select the result file and click the OK button Result The file is opened in the Evaluation module Quick View Quick View is a preview function for result files to make it easier to select the correct result file You can preview the first curve in the first chromatogram 03 0014 96AD ep 26 Files and folders in PrimeView 4 How to use Quick The table below describes how to preview result files in Quick View View Step Action 1 Select a result file in the Open Result dialog box 2 e Right click and choose Quick View from the short cut menu Result The Quick View dialog box opens Quick iew C prime Example ResultO01 res Example Resut001 1_UV1_215nm 3 e Click the Open button Result The result file that is displayed in the dialog box opens in the Evaluation module ep27 4 Files and folders in PrimeView 4 3 How to arrange and locate your files 4 3 How to arrange and locate your files Introduction This s
33. Result The Chromatogram Layout dialog box opens 2 Click the Peak Table tab 3 e Click the check boxes in the Filter Peaks field to select the filter criteria e Specify filter values e Click OK To filter peaks vs The table below describes the major differences in the effect of filtering peaks to reject peaks compared to excluding the peaks by rejection Filter peaks Reject peaks excludes the peaks from display permanently excludes peaks from the integration does not exclude the peaks from the excludes the peaks from the calculation calculation of the total peak area of the total peak area ep93 8 Peak integration 8 2 How to perform a peak integration Peak labels 03 0014 96AD ep94 Filter peaks Reject peaks can be reversed cannot be reversed Peaks can be labelled with their retention sequentially numbered or be marked with specific identification names See table below for an instruction on how to display peak labels The label type can be selected on the Curve Style and Colour tab in the Chromatogram Layout dialog box De select all label options to hide the labels e g for presentations The illustration below shows the Chromatogram Layout dialog box with the Curve Style and Colour tab opened Chromatogram Layout 1 02 id 48Quantitate001 1_ 03 id1 48Quantitate001 1_UV3_Onm 04 id 48Quantitate001 1_Cond 05 id 48Quantitate001 1_Cond
34. This chapter contains the following sections Topic See How to create folders 41 How to open and preview files 4 2 How to arrange and locate your files 43 How to copy delete rename and backup files and folders 44 03 0014 96AD ep 24 4 1 Introduction How to create a new folder Files and folders in PrimeView 4 How to create folders This section describes how folders are organized in PrimeView and how to create a new user specific folder for the user s methods and results The table below describes how to create a new folder in the Evaluation module Step Action e Select File Open or e Click the Open icon Result The Open Result dialog box opens e Right click on an empty area of the dialog box e Select New Folder from the shortcut menu Result The Create New Folder dialog box opens e Type a name for the new folder e Click OK Result The new folder is displayed in the Open Result dialog box ep2s 4 Files and folders in PrimeView 4 2 How to open and preview files 4 2 How to open and preview files Introduction This section describes how to open your saved result files You can also preview your result files to identify the correct file before you open it How to open a The table below describes how to open result files in the Evaluation module result file Step Action 1 e Choose File Open Result or e Click the
35. an evaluation session The monitor signals from the chromatography run are displayed graphically as curves The program instructions for a run are defined in a Method The Method is programmed in the KTAprime system The KTAprime system creates Result files when a method is run The Result files contain e Run data from the monitors in the chromatography system Example UV absorbance flow rate conductivity etc e Documentation from the run Example Logbook entries settings text method etc e Saved results from evaluations of the run data Example Peak integrations etc Templates are basic methods that can be used as a starting point for developing customized methods The method variables in a suitable Template is adjusted to create a method for another application Method Templates are supplied with the AKTAprime system ep7 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 The PrimeView user interfaces Introduction This section is an overview of the two PrimeView modules with descriptions of some of the elements of the user interfaces The section also contains a description of the search functions in PrimeView In this section This section contains the following sub sections Topic See The PrimeView module 2 2 1 The PrimeView Evaluation module 2 2 2 Search functions 2 2 3 Help functions 2 2 4 Snapshots 2 2 5 03 0014 96AD ep8 2 2 1 Introduction
36. arch from top of Select the check box to start the search from the top document of the document otherwise the search will start from the cursor position Direction Choose whether to search upwards or downwards in the document Commands Use the commands below to find more occurrences of a text string after you have found the first one e Press F3 to search for the next occurrence of the string or right click and choose Find next e Right click and choose Find previous to search for a previous occurrence General informa e The default setting is to search in all result files or chromatograms tion about e User entered search filters to a maximum of 10 will be saved in the drop down searches menus for both Result and Chromatogram selections More than one string can be used as a search delimiter insert between strings and search filters are automatically saved and stored within user profiles e Click All to return to the default setting to search in all result files or chromatograms 03 0014 96AD ep14 PrimeView concepts 2 2 2 4 Help functions Introduction There are different ways to get help and instructions in PrimeView e From the Help menu in each module e From the context sensitive help in each dialog box e By pressing the lt F1 gt key The Help menu e From the Help menu in each module you can access the Help file The illustration below shows the Help menu of the Evaluation m
37. aseline Peak integration 8 Too high slope A too high Slope limit value can cause peak limits too high up on the peaks This can limit be the case when the chromatogram includes a very large flow through or solvent peak The large peak affects the calculation of the default parameters and leads to too high values for the Slope limit Note A too high value for the Noise window can have the same effect and be caused by the same situation often also in combination with a high Slope limit Peak limits are defined on peaks in the example below due to the high Slope limit The example below has a much lower Slope limit and a lower Noise window e p 103 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm Noise window 03 0014 96AD ep 104 Sometimes you get too many peaks after the peak integration usually because noise on the baseline is erroneously detected as peaks The solution to this is to increase the Noise window parameter However this can result in peak limits too high up on the peak slopes The illustration below is an example of noise detected as peaks A and the result of a second peak integration with an increased Noise window B esult lExampte Result002 Example ResuROO2 res xample Result002 t v UNECORN Local fit N das n A Enamgle Pen A0021 UVI _21Sr 0 PEAKI No Pesk nane Retention min Area mAU min Height mAU
38. ation icon on the Windows desktop Primeview Evaluation Result The PrimeView Evaluation module opens The table below describes how to open a result file in the PrimeView Evaluation module Step Action 1 e Select File Open or e Click the Open icon lay Result The Open Result dialog box opens 2 e Select the result file and click OK Result All contents of the opened result file are transferred to the Evaluation module Note By default the chromatograms in a run are shown as opened windows The chromatogram window on top is the active window There is also a minimized Temporary chromatogram window See 6 2 Basic presentation of chromatograms on page 49 for further information about chromatograms How to view results 6 6 2 Basic presentation of chromatograms Introduction This section describes how to access result files and optimize the presentation of a chromatogram and its curves via the Chromatogram Layout dialog box In this section This section contains the following sub sections Topic See Introduction and temporary chromatograms 6 2 1 The chromatogram window 6 2 2 ep49 6 How to view results 6 2 Basic presentation of chromatograms 6 2 1 Introduction and temporary chromatograms 6 2 1 Contents of a chromatogram Temporary chro matograms How to copy curves into Tem porary How to clear a temporary chro matogram 03 0014 96AD p50 Introduct
39. ber of samples To reduce the number of samples by a factor of five means that only every fifth point will be sampled for export ep8s 7 How to edit results 7 3 How to export results How to export curves in AIA format How to export peak tables 03 0014 96AD ep 86 Dialog box option Instruction Normalise retention Select the Normalise retention check box to have all exported curves normal ized to a common X axis The table below describes how to export curves in AIA format Step Action 1 Select File Export Export curve to AIA Result The Export curve in AIA format dialog box opens 2 e Select the source chromatogram and the curve you want to export e Click the Export button Result The Export Curves to File dialog box opens 3 e Select a destination folder e Type a file name e Click OK The table below describes how to export peak tables Step Action Choose File Export Peak Table Result The Export Peak Table dialog box opens e Select the source chromatogram and the peak table you want to export e Click the Export button Result The Export Peak Table to File dialog box opens 3 Select the export file format from the Save as type drop list e ASCII files asc e Lotus 1 2 3 files wks e Excel files xls e XML files xml How to edit results 7 Step Action 4 e Select a destination folder e Type a file name
40. d select Snapshot in the menu Result The Snapshot is displayed in the Snap Shot dialog box e Click the Save to File button if you want to save the information as an Excel file xls or a tabbed text file txt e You can also copy the information to the clipboard Click and drag the mouse in the table to select the information you want to copy Press CTRL C The information can now be pasted in a text editor e Click the Print button if you want to print the information e Click the Close button Repeat steps 2 to 4 if you want to view more Snapshots epl7 3 Software Installation 3 Software Installation Introduction The PrimeView software is normally pre installed by a GE Healthcare representative Follow the instructions in this chapter to install the program yourself if your system is not pre installed In this chapter This chapter contains the following section Topic See How to install PrimeView for the first time 3 1 03 0014 96AD ep18 3 1 Installation pre requisites Installation notes Upgrading a PrimeView install ation Do not copy the CD ROM or decom press the files Step 1 Insert the Setup CD Software Installation 3 How to install PrimeView for the first time Before you start the installation procedure the following prerequisites have to be met e The operating system Windows 2000 XP must be correctly installed on your computer See the
41. dit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed 3 Click the X Axis tab 4 Select the appropriate option in the Base field e Time of retention e Volume Note Some calculated curves for example baselines exist in only one base and might seem to disappear when the base is changed Curves are collected in time and recalculated for display in volume Thus switching the base between Time and Volume can slightly alter the resolution 5 e Click the Fixed option in the Axis scale field to set the axis limits manually e Type the desired minimum and maximum values e Click OK ep63 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 5 How to save and apply a layout 6 3 5 How to save and apply a layout Introduction All configurations that you make in the Chromatogram Layout dialog box can be saved as a layout It is possible to apply saved layouts to other chromatograms All saved layouts are user specific How to save a The table below describes how to save a layout layout Open a result file Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed Make the appropriate layout configuration within the various tabs View your changes Click OK if you want to return to the chromatogram window to see the applied affects of a given configuration Return to the Chromato gram Layout dialog box to perform further chang
42. e and apply a layout on page 64 Information for each curve Each curve is automatically assigned a default color and style with default information about each curve displayed in the key above the curves This information includes e result file name e chromatogram name e curve name Choose the Y axis scale Each curve has a correspondingly colored Y axis To choose the appropriate Y axis scale e click on the Y axis until the desired scale is displayed or e click on the name of the curve When viewing curves in the Evaluation module you can access a menu that provides a quick alternative to menu commands Right click the run curves view to display the menu shown in the picture below Add Text Edit Text Mode iL Peak Integrate Hatch Marker Copy to Clipboard Copy to Metafile Base Type gt E Properties The chromatogram window can be minimized and maximized using ordinary Windows commands The table below describes extra features to optimize the workspace Use the command if you want Window Arrangeicons to arrange icons of minimized windows ep 53 6 How to view results 6 2 Basic presentation of chromatograms 6 2 2 The chromatogram window How to display a vertical marker line How to set a refer ence point How to display the logbook over lay 03 0014 96AD ep 54 Use the command if you want Window Tile to view several chromatogram
43. e marker is moved from the reference point the X axis and Y axis values for the new position are displayed together with e the new position in relation to the position of the reference point e the minimum maximum and average values for the curve interval between the reference point and the new position The table below describes how to record a Snapshot of the current curve values Step Action e Right click in the chromatogram and select Snapshot from the shortcut menu Result The Snapshot dialog box opens 2 The dialog box displays all the curve data that was current at the moment the snapshot was taken e Click the Save to file button to save the snapshot as an Excel file e Click the Print button to print the snapshot The retention time and amplitude of any peak can be viewed directly in a peak table after an integration This data and more is selected in the Chromatogram Layout dialog box The table below describes how to select peak table data Step Action Click the Chromatogram Layout icon Result The Chromatogram Layout dialog box opens 2 Click the Peak Table tab epi25 8 Peak integration 8 8 Measurements 03 0014 96AD ep126 Step Action e Select the checkboxes on the Select peak table columns list for all items that you want to display in the table e Click OK A Introduction In this chapter Evaluation functions and i
44. e selected folder as denoted by the asterisk To select specific result file s click the Browse button and select the result file s e You can use wildcard characters to search for chromatograms within result files with a specific name profile represents any number of characters represents any single character Wildcard character examples iex will search files named iex iex will search all files with names that begin with iex iex will search all files with names that end with iex iex will search only 4 character names that end with iex The asterisk indicates that all chromatograms within a result file will be selected Click Browse to select one or several specific chromatograms The UV curves are identified by number To search for all UV curves select UV in the Curve name text field The Find command is used to search for text strings Find x Find what l j I Match whole word only Diracin Cancel I Match case wil C Down Tl Search from top of document epl3 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 3 Search functions Field Description Find what Type the text string you want to find Match whole word only Select the check box if you only want complete string matches not partial matches Match case Select the check box if you only want matches which correspond according to upper case and lower case letters Se
45. e the Templates menu e Press the OK button Result The Templates menu is displayed e Choose the Method template menu e Press the OK button Result The first method template is displayed e Step through the list of method templates with the up or down buttons until the desired template is displayed e Press the OK button Result The Sample inject by menu is displayed e Select sample injection through the injection valve or through the system pump e Press the OK button e Continue to set method parameters with the up and down buttons in the subsequent menus and press the OK button to proceed e After all parameters are set navigate to the Method ready menu with the arrow button e Press the OK button Result The Save Method menu is displayed If you want to save the method continue with step 5 below If not select no in the next menu and proceed to step 6 How to perform method runs 5 Step Action 5 e Choose yes and press the OK button e Use the up and down keys to select a free method number and press the OK button Note Up to 40 methods can be stored If the method number already is used you can press OK and then clear the number in the Clear Method menu 6 e Press the OK button at the Press OK to start run prompt Result The method runs starts How to run a The table below describes how to run a saved method on the AKTAprime unit All saved method parameters are selected with the a
46. eaceeeeseees 49 6 2 1 Introduction and temporary chromatogrAMS ssssesssssssonsnsnsssnsanssii 50 6 2 2 PAS CHO MMATOGF GI WIM OW scssccccccseccesssssscesesssccccesescosssssssasssssceosesosocssssssscsssssscssanssssssnssassaansssssnnssssnnsstis 52 6 3 How to optimize the presentation of a ChHromatOgrai ssscecececececesecteeceeeeeeeeeseers 56 6 3 1 How to make changes in the Chromatogram Layout dialog DOM essssssscccssssssssneneees 57 6 3 2 The Curve tab and Curve Names tab 6 3 3 The Curve Style and Color tabu cessessssssssssscsccssssssnnssessscceceesssssnnnmmsssessseeeeeeessssnnnnmsseseseceeeesesssnnnnneess 65 4 AON tO CHANJE ONA TIX LACS MCS cceceeccceeccccccecccscosscssssssssssccceesssscsscsssssvssssceeccsssssssssssxscsssscceccssssescssssstee 03 0014 96AD epi Table of Contents 6 3 5 HOW to SAVE AN APPLY a IGYOULL ee eecccccsccsssccssssssnmnsessscceceecsssssnunmmsssseeseeeeeeessssnnnnmssseesseeeeeesssssnnnueeess 64 6 36 HOW TO SHOW DON OF OGUN Orminn EEEE 66 6 4 How to print active CHFOMALOGFIMS sssssssssssssssssscccessssssssnnessssssesececesssssnssnusssceeeeeeeessssssunuseseseeeeeessanes 67 6 5 How to create and print a customized report s ss sssisssissirsssisssirssrisssrrssnirssrrnsnirsstrnnntrnsnnrntrnnnnrnnnna 69 6 6 Run documentation TaHoWw to edit ES UNES 25 ae esccze dues ceceus ara iiion see Seea ced aorar aoaaa osca odiare aeea aioi p Eaa NEE EAE EEEa 7 1 How to enter and edit text in the
47. eatures regarding peak tables are described in 8 2 How to perform a peak integration on page 91 The table below describes how to make changes in the Chromatogram Layout dialog box Step Action Open a result file e Right click the chromatogram window and select Properties or e Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed The view from which you activate the Properties command determines the tab that is displayed in the Chromatogram Layout dialog box 3 Carry out the changes on the different tabs to get the desired layout for header curves and peak table Select Apply to all chromatograms if you want to apply changes made in the Chromatogram Layout dialog box to all open chromato grams Click OK ep57 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 2 The Curve tab and Curve Names tab 6 3 2 The Curve tab and Curve Names tab The Curve tab The Curve tab of the Chromatogram Layout dialog box contains a list of all the curves included in the chromatogram Select the curves you want to display in the chromatogram and click OK Curve name ap You select options for the curve name appearance on the Curve Names tab This is pearance an example of a default curve name Result 11_UV The table below describes the three components that make up the default curve name Component Description Example Result name Name of the result
48. ected object s click on the objects hold down the left mouse button and drag the object s to the new position to resize the selected click one of the object border anchors either in the object s corners or in the middle of a border and drag the box to the new size Note Some Text objects cannot be resized 03 0014 96AD ep 76 How to view results 6 Alignmenttoolbar Objects can be placed in exact positions and sized in relation to other objects The icon functions table below describes the function of the Alignment toolbar icons in the Report Editor Toolbar Function icon ae Align left Matches the left alignment of all selected objects to that of the high lighted object Align right Matches the right alignment of all selected objects to that of the highlighted object Align top Ba g Matches the top alignment of all selected objects to that of the high lighted object Align bottom Matches the bottom alignment of all selected objects to that of the highlighted object Adjust to margins Stretches the selected object s to the left and right margins Adjust to left margin Adjusts the selected object s to the left margin Adjust to right margin 64 00 Ibe Adjusts the selected object s to the right margin Adjust to centre oO Adjusts the selected objectls to the center of the page Make same size BI Adjusts the selected objects t
49. ection describes how to arrange the way the files are displayed in the Open Results dialog box and how to locate files through a search Different view You can choose how the files and folders are displayed in the Open Results dialog modes box The options are the standard Windows alternatives e Details e List e Large icons e Small icons How to change If you want to change the view you the view mode e Right click and select View and the option that you want from the shortcut menu Sort order The files can be sorted in different orders The table below shows the options Sorted by Order Name Alphabetical order or reverse alphabet ical order Size Smallest or largest files first Type Alphabetical order of file extension type Modified Most recently modified files first Created Most recent creation dates first How to change Select one of the methods below to change the sorting order the sorting order Right click and select Sort and the option that you want from the short cut menu or e Click the column header for the option that you want to sort by a second click on the same header will reverse the order 03 0014 96AD ep 28 4 4 Introduction How to copy or move files and folders The function Copy to External How to Copy to External Files and folders in PrimeView 4 How to copy delete rename and backup files and folders PrimeView has some file and fold
50. egative peaks must be selected before the peak integ ration if you want to be able to drag a data point to move the baseline above the curve Howtocalculate The baseline can be recalculated in the Edit Peak Table dialog box The table below a new baseline describes how to do this Step Action a e Select Baseline New Calculate or e Right click and select New Calculate from the shortcut menu Result The Settings dialog box opens 2 e Select an algorithm Morphological is default 3 e Adjust the Baseline parameters as desired or e Click the Default Values button for the default values 4 e Click OK Result The baseline is recalculated Note Select Baseline New Zero Baseline to replace the calculated baseline with a zero baseline 03 0014 96AD ep1l12 Peak integration 8 The Edit Peak The illustration below shows the Edit Peak Table dialog box Table dialog box raer rae Fie Edt Bareine Integrate RES Example tesult003 1_Uy Example teult 003 1_UV 01 BASEM ey 1947 9552 How to delete a The table below describes how to delete a peak in the Edit Peak Table dialog box peak Step Action 1 e Click the Edit peaks icon K e Click the peak in the curve or in the peak table to select the peak 2 e Right click and select Delete Peaks from the shortcut menu or e Select Edit Delete Peaks Result The peak is deleted and the remaining peaks are
51. eight of the current peak Capacity factor The formula below is used to calculate the Capacity factor formula ae V Vi Where e Vp retention volume e V total liquid volume Asymmetry for The formula below is used to calculate the Asymmetry mula Asymmetry B A Where e Aisa partial peak width measured at a percentage of the peak height for the leading part of the peak e Bisa partial peak width measured at a percentage of the peak height for the tailing part of the peak 10 peak height e p135 A Evaluation functions and instructions A 2 Peak table column components HETP formula 03 0014 96AD ep136 The formula below is used to calculate the HETP value HETP L N N 5 54x p p assuming a Gaussian peak Where e N no of theoretical plates e L bed height in cm e Vp peak retention elution volume or time e Wh peak width at half height expressed in the same units as Vp A Application templates How to start a run 33 B Baseline Calculation options 90 The Calculate function 90 Reuse existing 90 How to edit manually 109 How to adjust the baseline graphically 111 Definition of a segment 128 Parameters 129 BatchiD Logbook illustration 45 Blank curve Calculate baseline based on 90 C Chromatogram Layout Curve tab 58 Default curve names 58 How to choose curve name appearance 58 The Curve Style and Color tab description 60 Chromatogram
52. elow describes how to do this Step Action 1 e Choose Integrate Edit Peak Table Result The Select Peak Table to Edit dialog box opens e Select the peak table to edit and click OK Result The Edit Peak Table dialog box opens Peak integration 8 Step Action e Click the Peak Window icon Result Two vertical cursor lines are displayed e Drag the cursor lines to the beginning and the end of the selected part of the curve No Peax pase Retention win Peak start min Peak end min Area mAUrminj 3 Internal st 5 83 5 53 6 28 61 1651 2 Peak A 0 5 52 6 26 6 94 44 0967 3 Peak B 0 8 i 6 84 2 36 60 5619 Teak c 0 5 7 78 2 36 8 68 115 9696 Note All operations described below will only affect the selected part of the curve If desired change the integration parameters Reject peaks e Choose Integrate Settings Result The Reject Peaks dialog box opens e Change the settings as desired and click OK Skim peaks e Choose Integrate Peak Skim Result The Peak Skim dialog box opens e Select the Skim Peaks checkbox and type a ratio e Click OK 4 e Choose Integrate Peak Integrate Result The selected part of the curve is peak integrated based on the changed parameters ep123 8 Peak integration 8 8 Measurements 8 8 Introduction Measurement op tions How to make dir ect measure ments 03 0014 96AD ep124 Measurem
53. ents It is possible to determine the coordinates of any point on a curve and to obtain values for retention and peak height This is a useful tool for many other functions such as for measuring the parameters used in baseline calculations Coordinates can be obtained in two ways e Through direct measurement e From peak table data The table below describes how to make direct measurements in a chromatogram Step Action Right click in the chromatogram and select Marker Result A vertical line is set in the chromatogram A text box in the top left corner of the chromatogram displays the X axis and Y axis values of the curve at the point where the vertical Marker line crosses the curve See the illustration below 11 01 min 399 987 MAY Note The color of the Marker is the same as the selected curve Move the Marker with your mouse to display the peak data Click the curve name legend above the chromatogram to change to another curve Result The Y axis is changed to the one corresponding to the new curve Right click and select Marker again to de select the function How to set a refer ence point How to record a Snapshot How to select peak table data Peak integration 8 The table describes how to set a reference point Step Action 1 Right click in the chromatogram and select Set Marker Ref Point to define a reference point for the marker position 2 When th
54. er handling functions that are slightly different from the general Windows functions This section focuses on the differences If you copy a folder you will also at the same time copy all files and folders that it contains The table below describes how to copy files and folders Note Follow the same steps but select Move to move files and folders Step Action 1 Select a file or folder in the Open Results dialog box 2 e Right click and select Copy from the short cut menu Result The Copy dialog box is opened 3 Select a target folder or floppy disk drive 4 Click OK Use the function Copy to External when you need to copy files and folders outside of your own user folders Copy to External should be used specifically when you need e tocopy toa floppy disk drive The files are automatically compressed into a zip file The file will also automatically be spanned across several disks if necessary The table below describes how to use the function Copy to External Step Action 1 Select the file you want to copy 2 e Right click and select Copy to External from the shortcut menu Result the Copy to External dialog box opens 3 Select the destination drive and folder 4 Click the Save button ep29 4 Files and folders in PrimeView 4 4 How to copy delete rename and backup files and folders The function Copy The function Copy from External can be used to import files and folders
55. es e Select the Layout Library tab e Click the Save current layout as button Result The Save Layout dialog box is displayed 5 e Type aname for the layout e If you want the current layout to be the new default layout select the Save as default option e Click OK Result The new name is added to the Saved layouts list e Click OK How to apply a The table below describes how to apply a layout layout Step Action 1 Select the Layout Library tab on the Chromatogram Layout dialog box 03 0014 96AD ep 64 How to view results 6 2 e Select a layout from the Saved layouts list e Click the Apply selected layout button Result The layout is automatically applied to the active chromato gram window e Ifthe same layout is to be applied to all chromatograms on the Evaluation workspace select the Apply to all chromatograms checkbox e Click OK ep65 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 6 How to show part of a curve 6 3 6 How to show part of a curve Introduction You can select a part of a curve in order to examine details more closely It is also possible fix the axes see 6 3 4 How to change and fix the axes on page 62 How to use the In the active chromatogram window you can zoom in on a designated area of the zoom function chromatogram This is the easiest and quickest way to enlarge different parts of a cu
56. es pane you can set the displayed units The table below describes how to do this Step Action 1 Right click in the Curves pane and select Properties in the displayed menu Result The Properties dialog box is displayed 2 Select the Y Axis tab 3 Select the Pressure curve and select the appropriate Pressure unit button Click OK How to edittextin You can select the way that text is aligned for the Logbook and Fraction curves You the Curves pane can also select to show only part of the Logbook information The table below describes how to do this Step Action 1 Right click in the Curves pane and select Properties in the displayed menu Result The Properties dialog box is displayed ep 43 5 Howto perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane Step Action Select the Curve Style and Color tab 3 Select the following e Logbook or Fraction curve in the Curve list as appropriate e Select the appropriate Logbook text alignment or Fraction text alignment option Horizontal Vertical Fly over displays the text if you place the mouse pointer over the generated mark Click OK Howtoviewthe At some breakpoints there can be more logbook information than what is possible complete logbook to conveniently display in the Curves pane The additional information that is not information displayed is indicated by an arrow point symbo
57. escribes how to take Snapshots in the Evaluation module shots in the Evalu ation module Step Action e Open a result file in the Evaluation module e Right click and select Marker in the menu Result A vertical line indicating a certain point is displayed Click the marker line and drag it to the desired point where you want to take a Snapshot Right click and select Snapshot in the menu Result The Snapshot is displayed in the Snap Shot dialog box e Click the Save to File button if you want to save the information as an Excel file xls or a tabbed text file txt e You can also copy the information to the clipboard Click and drag the mouse in the table to select the information you want to copy Press CTRL C The information can now be pasted in a text editor e Click the Print button if you want to print the information Click the Close button 5 Repeat steps 2 to 4 if you want to view more Snapshots 03 0014 96AD ep16 How to view a method run PrimeView concepts 2 The table below describes how to view Snapshots in the PrimeView module during Snapshots during a method run Step Action A method is running and the PrimeView module is running e Right click in the Curves pane and select Marker in the menu Result A vertical line is displayed Click the marker line and drag it to the desired point where you want to take a Snapshot Right click in the Curves pane an
58. esults 6 3 How to optimize the presentation of a chromatogram 6 3 4 How to change and fix the axes 6 3 4 How to change and fix the Y axis How to add a second Y axis 03 0014 96AD ep62 How to change and fix the axes The table below describes how to change and fix the Y axis Open a result file Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed Click the Y Axis tab e Select the appropriate curve from the list e Click the Fixed option e Type the desired minimum and maximum values e Click the All with this unit button if you want other curves with the same Y axis units as the current scaled curve to be similarly scaled Note The values will only be applied to existing curves They will not be applied to new curves created after this function was last used e Click the appropriate Pressure unit MPa psi bar option to change Y axis units for pressure curves e Click OK The table below describes how to add a second Y axis to the chromatogram Action Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed Click the Y Axis tab e Select the appropriate curve from the Right Axis droplist e Click the OK button How to view results 6 How to change The table below describes how to change and fix the X axis and fix the X axis Step Action 1 Open a result file 2 Choose E
59. eters are selected with the arrow buttons on the unit The selections are confirmed with the OK button Step Action e Choose the Templates menu e Press the OK button Result The Templates menu is displayed e Choose the Application template menu e Press the OK button Result The first application template is displayed e Step through the list of application templates with the up or down buttons until the desired template is displayed e Press the OK button Result The Sample appl volume menu is displayed 4 e Set the sample volume with the up or down buttons e Press the OK button Result The Press OK to start run prompt is displayed e Press the OK button Result The purification run starts ep 33 5 How to perform method runs 5 1 How to start a method run AKTAprime meth od templates How to start a method template run 03 0014 96AD ep 34 Note If needed the sample volume should include the sample wash out volume The four most common purification techniques are available as method templates Some parameters must be set by the operator when a run is prepared from a method template The settings can be saved for later use before the run is started The table below describes how to start a method template run on the AKTAprime unit All parameters are selected with the arrow buttons on the unit The selections are confirmed with the OK button Step Action e Choos
60. ether Setup should create the UNICORN program folder Note The UNICORN folder will contain all PrimeView files and folders ep21 3 Software Installation 3 1 How to install PrimeView for the first time Step 5 Select In the Select Program Folder dialog box you choose where to store the program Program Folder icon Select Program Folder i x Setup will add program icons to the Program Folder listed below You may type a new folder name or select one from the existing Folders list Click Next to continue Program Folders PrimeView Existing Folders Accessories Administrative Tools Gadwin Systems Hewlett Packard Logitech Lotus Applications Novell Common zi lt Back Next gt Cancel The table below describes how to select a program folder for the PrimeView icon PrintMe Internet Printing Step Action 1 In the Select Program Folder dialog box you select the Start menu folder where you want the PrimeView icon to be placed You can either e accept the suggested folder named UNICORN recommended or e create a new folder Type the name of the new folder in the text field Program Folders or e select a folder that already exists by clicking its name on the list 2 Click the Next button to continue 03 0014 96AD ep 22 Step 6 Start Copying Files Step 7 Setup Complete Software Installation 3 The Start Copying Files dialog box disp
61. grams on the default Windows printer Step Action al Open all chromatograms that you want to print in the Evaluation module 2 e Select File Print or e Click the Print toolbar icon Result The Print Chromatograms dialog box opens 3 Select print format and layout options e p67 6 How to view results 6 4 How to print active chromatograms 03 0014 96AD p 68 Step Action or Click OK to print Proceed with step 5 to preview and edit the layout Click the Preview button Result The Customise Report window opens or Click the Edit Mode button to make changes e g change the order of the chromatograms see 6 5 How to create and print a custom ized report on page 69 for more information about how to edit Click the Preview button to return to preview mode Select File Print Click the Print toolbar icon Result The Print dialog box opens Select the print range and number of copies Click OK 6 5 Introduction How to open the Report Editor in edit mode The Edit mode window Toolbar button functions in the Report Editor How to view results 6 How to create and print a customized report You can choose from a variety of objects to include in a report including chromatograms methods documentation free text and more in the customized report interface You can also place align and size the objects as you please This section describes how to create a cus
62. ically assigned a color and line style Peaks can be labeled on the Curve Style and Color tab of the Chromatogram Layout dialog box Use a combination of the following labels e Retention the default label e sequential Number e user defined Peak name Both Fraction text and Logbook text can be set to the following alignment options e Vertical e Horizontal e Fly Over which sets text labels as hidden text that appears only when the cursor is carefully positioned over a fraction mark The table below describes how to change the color and style of a curve Step Action 1 Open a result file 2 Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed 3 Click the Curve Style and Color tab 4 e Select the curve you want to change from the list e Select the desired color and style e Click OK The table below describes how to display a hatched background in the chromatogram window Step Action 1 Open a result file How to view results 6 Step Action e Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed 3 e Click the Curve Style and Color tab e Select the Hatch box e If desired select the Apply to all chromatograms box and click OK Result Hatch marks are displayed as a background Note You can also right click in the Chromatogram window and select Hatch ep l 6 How to view r
63. igh value How much the values should be changed depends on the cause of the peak integration problem The table below is a general guideline Baseline parameter Recommended initial change Shortest baseline segment 20 50 Noise window 10 30 Max baseline level Usually not necessary to adjust Slope limit 25 50 Note If necessary click the Default button to restore the default values Shortest baseline If a too high Shortest baseline segment value is set short curve segments between segment peaks in the middle of the chromatogram are not identified as baseline segments The calculated baseline does not follow the source curve see below r e p101 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm Slope limit 03 0014 96AD ep 102 The Shortest baseline segment value is decreased by 50 in this example A changed Slope limit will often improve the baseline calculation The Slope limit sets the maximum slope of the curve to define when a peak is recognized A too high Slope limit will cause the up slopes of the peaks to be recognized as baseline segments The example above was improved by the shorter baseline segments but the high slope of the short segments in the region between the second and the fourth peak still makes the baseline unacceptable In the example below the Slope limit is increased by a factor of 2 5 which produces a correct b
64. ine the limits for a rectangular box A part of the source curve must fit entirely inside this rectangular box to be identified as a baseline segment The Classic algorithm is particularly useful when you need to integrate curves with negative peaks and when quantitative data from negative peaks are important Classic algorithm The parameters for the Classic algorithm are parameters e Shortest baseline segment e Noise window e Max baseline level e Slope limit See more information about the parameters below Howto seta Clas The table below describes how to set a Classic algorithm and define a baseline sic baseline Step Action 1 Click the Baseline settings button in the Integrate dialog box Result The Settings dialog box opens 2 e Select the Classic algorithm e Change the Baseline parameters See more information about the parameters below this table e Click OK Note The same settings can be edited in the Calculate Baseline dialog box when a new baseline is created Choose Integrate Calculate Baseline to open the dialog box 03 0014 96AD ep 100 Peak integration 8 Test your para The best way to optimize the baseline is to change the baseline parameters step by meter changes step and then check the resulting baseline after each change When the desired effect is accomplished it is best to go back and try a parameter value in between the two last settings to avoid an unnecessarily low or h
65. ion and temporary chromatograms Chromatograms can be viewed in the Evaluation module A chromatogram includes a number of curves that have been created during a method run such as UV conductivity pH fraction marks etc A chromatogram also contains the curves created and saved during an evaluation session The original raw data curves cannot be deleted or modified A Temporary chromatogram is essentially an empty chromatogram that is specific to the Evaluation module Information contained within a Temporary chromatogram is automatically saved from one evaluation session to the next but is not saved within the result files Curves can be copied into Temporary and comparisons or evaluations can be performed This is particularly useful if you do not want to clutter up your original chromatograms with a large number of curves It can also be used to keep blank run curves or curves to compare when you open different result files The table below describes how to copy curves into Temporary Step Action 1 Open a result file 2 Select Edit Copy Curves Result The Copy Curve dialog box is displayed 3 Select a source chromatogram and a curve to be copied in the Source Chromatogram fields 4 Select Temporary as the target chromatogram and a position for the new curve in the Target Chromatogram fields 5 Click the Copy button Result The curve is copied into the Temporary chromatogram Click the Close button
66. ions 84 How to export 84 How to export in AIA format 86 How to delete unwanted curves 88 Curves pane in PrimeView Description 40 How to display a vertical marker 40 How to set a reference point 41 How to change curve colors and styles 41 How to change scale of the Y axis 41 How to change scale of the X axis 42 How to zoom in regions of the pane 43 Reduce scale of zoom 43 How to select curve pressure units 43 How to select text alignment 43 How to display complete Logbook information 44 D Delete files and folders 30 Documentation How to view 80 How to export 87 E Evaluation How to start the Evaluation module 48 Chromatogram window views 52 How to display peak table information 52 Chromatogram window shortcut menu 53 How to optimize the chromatogram workspace 53 How to display a vertical marker 54 How to set a reference point 54 Index e iii Index How to make chromatogram layout changes general 57 How to exit the module 88 Evaluation logs How to export 87 F Files and folders Copy to external 29 How to copy from external 30 Folders How to create 25 Installation Software 19 Prerequisites 19 Software license agreement 20 L Logbook How to display an overlay in the Curves pane in PrimeView 44 How to display an overlay in the chromatogram window 54 Logbook pane Description 45 Autoscroll function 45 How to filter the contents 45 Sea
67. is possible to split the peak into two new peaks by inserting a drop line The table below describes how to split a peak in the Edit Peak Table dialog box Step Action 1 e Click the Edit peaks icon K e Click the peak in the curve or in the peak table to select the peak 2 e Right click and select Split Peak from the shortcut menu or e Select Edit Split Peaks Result Anew drop line is inserted at the middle point between the two existing drop lines and the peak is split Note The area under each new peak will not be the same if the symmetry of the original peak was not perfect e p115 8 Peak integration 8 6 How to edit the peaks How to join peaks Itis possible to join the areas of adjacent peaks if they are separated by a drop line The table below describes how to join adjacent peaks in the Edit Peak Table dialog box Step Action 1 e Click the Edit peaks icon Ie e Click the peak in the curve or in the peak table to select the peak 2 e Right click and select Join Left or Join Right from the shortcut menu or e Select Edit Join Left or Edit Join Right Result The original intervening drop line is removed and all peaks are renumbered How to add peak The table below describes how to add names in the Edit Peak Table dialog box to names identify the peaks Step Action 1 e Click the Edit peaks icon iv e Click the peak in the curve or in the peak table to select the
68. kimming Drop lines are vertical marks that split two peaks at the valley Drop lines are used mostly for peaks of relatively similar size When a peak has a shoulder splitting with drop lines will cause the first peak to lose too much of its area to the peak that forms its shoulder The Peak skim option can be used to skim off the smaller peak with a straight line that starts in the valley between the peaks and ends at the other side of the smaller peak at the point where the skim line and the curve slope are equal The illustration below is an example of how a drop line A and a skimmed peak B affects the area under the main peak and the peak shoulder The peak shoulder area is marked in gray Drop line The table below describes how to select a ratio to skim peaks in the Integrate dialog box Step Action 1 Select the Peak skim checkbox e p121 8 Peak integration 8 7 How to integrate part of a curve and how to exclude or skim peaks How to integrate part of a curve 03 0014 96AD epi122 Step Action 2 Determine the ratio when peak skimming should be applied based on the relationship in the illustration below h pL hy _ gt aki l hyo hy skim ratio Note The default ratio value is 10 3 Type the ratio value in the text box Part of a curve can be selected in the Edit Peak Table dialog box and integrated with settings that differ from the rest of the curve The table b
69. l Max baseline level Step Action 1 Right click in the chromatogram and select Marker Result A vertical line is set in the chromatogram A text box in the top left corner of the chromatogram displays the X axis and Y axis values of the curve at the point where the vertical Marker line crosses the curve 2 e Move the Marker with your mouse e Measure the height of the peak you want to exclude from the baseline 3 Choose Integrate Calculate baseline 4 e Select the Classic checkbox as the Chosen algorithm e Type anew value for Max baseline level Set the level slightly lower than the value that you measured in step 2 e Click OK 03 0014 96AD ep 106 Peak integration 8 Example ofa cor The illustration below is an example of a correct baseline after the Max baseline level rect baseline has been changed e p 107 8 Peak integration 8 5 How to edit the baseline manually 8 5 The Edit Baseline dialog box How to use the zoom function 03 0014 96AD ep 108 How to edit the baseline manually You can edit the baseline manually in the Edit Baseline dialog box in the Evaluation module e Select Integrate Edit Baseline to display the dialog box The Edit Baseline dialog box displays the baseline and the curve it was calculated from The baseline points are marked with green squares Hold the cursor above the baseline point to display its coordinates See the illustration below 200 un prae
70. l by the break point e Hold the mouse cursor over the break point to display the complete information in a flyover text box as shown in the illustration below 500 400 End Block lock Start_Conc_B ase SameAsMain fadient 0 00 B 0 000 CV nd Block lock Column_Valve ase SameAsMain olumnPasition Position Bypass nd Block lock System_Volume_Compensation ase Volume ml 300 mDOMODOMgaoOD 200 100 0 0 0 2 04 0 6 0 8 For Help press F1 Run 03 0014 96AD ep 44 5 2 3 Introduction Illustration Autoscroll How to filter the logbook contents How to perform method runs 5 The Logbook pane All actions including method start and end base instruction method instructions and manual interventions such as Pause or Hold and unexpected conditions such as warnings and alarms are logged for every run with date time and current user name where appropriate The logbook thus provides a complete history of any given run The log is saved in the result file The illustration below shows an example of the Logbook pane 0 00 min Botch ID BEADES95 767E 4005 415 BOFFSOFI BEES 0 00 min Bose Time G00minPeuse 0 0 2003 12 01 14 4403 W Europe Standerd Time Manuel 0 00 min Eror 62 Chack thet tube positionis OK 0 00 min Concertration 0 B 0 00 min Injection Valve Wasto 0 00 min Corinue 2003 12 01 14 44 09 W Europe Standord Time Manual 0 00 min Flow 40 0 miji
71. lays the installation choices made Start Copying Files x Setup has enough information to start copying the program files If you want to review or change any settings click Back If you are satisfied with the settings click Next to begin copying files Current Settings PrimeView 5 00 Software Setup User Information User name RUM Company Amersham Biosciences Target Destination C UNICORN Selected COM port 1 Folder Selection PrimeView The table describes how to start copying the program files from the CD Step Action 1 The setup program is ready to copy the files The Start Copying Files dialog box displays all the selections that have been made and the components to be installed Note If you want to make any changes you can click the Back button one or more times 2 If the settings are correct click the Next button to copy the files The installation is complete and the computer must be restarted e Click the Finish button to exit the setup program and automatically restart the computer ep23 4 Files and folders in PrimeView 4 Files and folders in PrimeView Introduction All PrimeView data is organized in files and folders Files and folders are handled like in any other Windows application with some exceptions This chapter describes how to work with PrimeView files and folders with the focus on the topics that are specific for PrimeView In this chapter
72. lbar or e Choose an object from the Insert menu e Press and hold the left mouse button on the report page and drag out a box to the size of the item you want to insert Note The mouse pointer shows a symbol for the type of item you have selected e Release the mouse button Result A Setup dialog box opens The dialog is specific to the type of item that you want to insert 3 e Select the desired options and click OK Result The object is inserted onto the page Note If you want to edit an object later double click the object box How to add free The table below describes how to add free text to the report text Step Action e Click the Free Text icon T e Press and hold the left mouse button on the report page and drag out a box to the size of the text Release the button Result The Setup Free Text dialog box opens 2 e Type text in the edit field e Select if the text is to start on a new page e Select if the text box should be automatically sized e Select if the text should appear in the same position on all pages for example as header and footer text 03 0014 96AD ep 72 How to view results 6 Step Action 3 e Click the Font button to change the default font Result The Font dialog box opens e Make the necessary changes and click OK to return e Click OK Result The text object is inserted onto the page How to adda pic The Pictu
73. lt files and result folders in the Open Result dialog box The Save icon saves the edited result file The Print icon opens the Print Chromatograms dialog box The Report icon opens the Generate Report dialog box which is used to select a report format ep11 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 2 The PrimeView Evaluation module Function The View Documentation icon opens the Documentation dialog box which is used to view and edit the result documentation The Peak Integrate icon opens the Integrate dialog box which is used to select peaks to integrate in a modified peak table The Chromatogram Layout icon opens the Chromatogram Layout a dialog box which is used to select and format curves and display items in the chromatogram 03 0014 96AD epi2 2 2 3 Introduction Search the Folder list Search the Result list Search the Chro matogram list Search the Curve name list Find a text string PrimeView concepts 2 Search functions This section describes the general search functions that can be used to locate for example chromatograms curves and text strings in PrimeView These functions can be used in several program modules dialog boxes and wizards The search will take place in the displayed folder only To select another folder click the Browse button and open the desired folder The search will take place in all result files within th
74. moved along the curve up the peak until it reaches the contact points The curve parts below the horizontal line and the line will now form a curve with a plateau The center point in the plateau formed by the horizontal line will be the data point for the baseline e The data points fulfil the Minimum distance between data points This parameter reduces the total number of data points that are created from a curve 03 0014 96AD ep128 Classic algorithm Baseline paramet ers Baseline paramet ers illustration Evaluation functions and instructions A The Classic algorithm searches for all parts of the source curve where e The curve parts are longer than the Shortest baseline segment This parameter determines the minimum length for a part of the source curve to be considered a possible baseline segment The curve has no point outside the Noise window The noise window is defined as a rectangular corridor parallel to the slope of the curve and centered on the first and last points within the currently inspected segment e The slope is less than the Slope limit This limits the maximum slope of the baseline to differentiate baseline segments from peaks The curve parts are lower than the Max baseline level This parameter determines the highest acceptable signal level for the baseline The baseline parameters can be illustrated as a rectangular box that the source curve has to fit into in order to be identified as
75. n Area mAU min Height AU 5 83 0 75 63 1651 337 439 6 52 0 57 44 0967 275 224 7 04 0 51 60 5619 351 079 7 74 1 33 115 9646 472 670 Total number of detected peaks 369 SEEPEPe Total area mAUtmin 208 9306 _8 Area in evaluated peaks wAU min 201 7093 9 Ratio peak area total area 0 912241 Ki Thal Note Peak tables can be copied from one chromatogram to another with the Edit Copy command However to display the table you must right click in the chromatogram choose Properties and then select the new peak table on the Peak Table tab of the Chromatogram Layout dialog box 03 0014 96AD ep92 Peak integration 8 How to display The peak retention times and several other peak characteristics are calculated peak characterist automatically The table below describes how to display other peak characteristics ics Step Action 1 e Right click in the active chromatogram e Select Properties from the shortcut menu Result The Chromatogram Layout dialog box opens 2 Click the Peak Table tab 3 e Select options from the Select peak table columns list e Click OK Result The selected items will be displayed in the peak table How to filter Peaks can be removed from display in a peak table The table below describes how peaks from view to filter the peaks Step Action 1 e Right click in the active chromatogram or peak table e Select Properties from the shortcut menu
76. nctions and instructions A Parameter Fraction tube id Height Plate height HETP Peak endpoint heights Peak endpoint retention Peak name Percent of total area Percent of total peak area Resolution Retention Sigma Description Fraction number at peak start peak maximum and peak end Maximum amplitude above the baseline C F in the diagram above Height equivalent to theoretical plate and plates meter The column height must be entered in the Integrate dialog box for this parameter to be calculated See definition below this table Amplitude above the baseline at left A in the diagram above and right peak limits E G in the diagram above Retention value at peak start and peak end time or volume base A and G in the diagram above Name of the peak Peak area as a percent of the total area under the curve above the baseline Time or volume base Note This value can differ in time and volume base if the flow rate is not con stant throughout the method Peak area as a percent of the sum of all integrated peaks Note This value can differ in time and volume base if the flow rate is not con stant throughout the method Peak resolution See definition below this table Retention at the peak maximum time or volume base C in the diagram above Standard deviation for a Gaussian shaped peak See definition below this table ep 133 A Evaluation functions
77. nstructions A Evaluation functions and instructions This appendix describes the functions that are implemented in the Evaluation module This chapter contains the following sections Topic See Baseline calculation theory Al Peak table column components A2 e p127 A Evaluation functions and instructions A 1 Baseline calculation theory A 1 Baseline calculation theory Overall process The table below describes the overall process of a baseline calculation Stage Description 1 The baseline segments are defined 2 The baseline points are selected 3 The baseline is drawn Baseline segment Baseline parameters are used to find the baseline segments The default values for definition the parameters are determined from the source curve The baseline segments are found by different parameters that are based on the type of algorithm that is selected Note The parameters can be displayed in the Evaluation module if you choose Integrate Calculate baseline function You can also click the Baseline settings button in the Integrate Peak integrate dialog box Morphological al The Morphological algorithm searches for all parts of the source curve where gorithm e The curve parts come into contact at both ends of a horizontal line of the length defined in the Structure width parameter The default value of this parameter is based on the widest detected peak in the curve The horizontal line is
78. o create a baseline The Morphological algorithm gives the best result in curves with drifting baseline and peak clusters The morphological baseline follows the curve faithfully and a curve with a baseline at a more even level can be created by subtracting the morphological baseline The Morphological algorithm does not work well if there are negative peaks or if quantitative data from negative peaks are important in the run Note The Morphological algorithm is the default baseline setting The table below describes how to choose a Morphological algorithm and define baseline settings Step Action 1 Select Integrate Peak Integrate Result The Integrate dialog box opens 2 Click the Baseline settings button in the Integrate dialog box Result The Settings dialog box opens 3 e Select the Morphological algorithm e Change the Baseline parameters if necessary See more information about the parameters below this table e Click OK Note The same settings can be edited in the Calculate Baseline dialog box when a new baseline is created Choose Integrate Calculate Baseline to open the dialog box Peak integration 8 Morphological al The parameters for the Morphological algorithm are gorithm paramet structure width ers i e Noise window e Minimum distance between points Structure width Structure width determines the length of the straight line that follows the chromatogram The default
79. o display If you want all curves to be displayed click the Select All button If you do not want any curves to be displayed click the Clear All button Click OK How to displaya The table below describes how to display a vertical marker line vertical marker line Step Action al Right click the Curves pane and select Marker 2 Drag the marker line with the mouse Result Where the line bisects the curve the X axis and Y axis values are displayed at the top right corner of the pane Note Right click and select Snapshot to record the marker position values See 2 2 5 Snapshots on page 16 for more information about the Snapshot function 03 0014 96AD ep 40 How to set a refer ence point How to change the curve colors and styles How to change the scale of the Y axis How to perform method runs 5 When the vertical marker is displayed you can set a reference point to display curve data The table describes how to set a reference point Step Action 1 e Display a Marker in the Curves pane e Right click and select Set Marker Ref Point to define a reference point for the marker position 2 When the marker is moved from the reference point the X axis and Y axis values for the new position are displayed together with e the new position in relation to the position of the reference point e the minimum maximum and average values for the curve interval between the reference p
80. o the same size as the highlighted refer ence object Make same width p Adjusts the selected objects to the same width as the highlighted ref erence object ep77 6 How to view results 6 5 How to create and print a customized report Toolbar Function icon i Make same height Adjusts the selected objects to the same height as the highlighted reference object Note The Make same size and Make same width functions can only be used to resize the width of chromatograms free text and picture objects Howto printthe The table below describes how to print the report report Step Action e Choose File Print or e Click the Print icon Result The Print dialog box opens Note The report will be printed on the default Windows printer 2 e Select the printing range e Select the number of copies e Click OK Note You can also print the report from the Generate Report dialog box How to save the The table below describes how to save the finished report format report format Step Action 1 e Choose File Save or e Click the Save icon ji Result The Save Report Format dialog box opens 03 0014 96AD p78 How to view results 6 Step Action e Type a name for the format Note The name for the default format will automatically be changed to DEFAULT e Click OK ep79 6 How to view results 6 6 Run d
81. ocumentation 6 6 Introduction How to view and print the run docu mentation 03 0014 96AD p80 Run documentation The full documentation for a method run is stored in the result file This section describes e how to view and print the run documentation The table below describes how to view and print the run documentation Action Open a result file e Choose View Documentation in the Evaluation module or e Click the view Documentation icon g Result The Documentation dialog box opens e Click the Print button Result The Print dialog box opens e Select the documentation items you want to print and click OK Result The documentation is printed on the default Windows printer How to edit results 7 7 How to edit results Introduction This chapter describes e how to edit the results that are presented in the Evaluation module e how to export results For more information about how to view results see chapter 6 How to view results on page 47 In this chapter This chapter contains the following sections Topic See How to enter and edit text in the chromatogram 7A How to rename chromatograms curves and peak tables 7 2 How to export results 7 3 How to save results and exit the Evaluation module 7 4 e p81 7 How to edit results 7 1 How to enter and edit text in the chromatogram 7 1 How to enter and edit text in the chromatogram H
82. odule Help i Help for Evaluation About The Help file The table below describes how to open and use the Help file Step Action Choose Help Index Result The Help file is displayed e Type a word you want help on in the text box in the left pane Result The closest matches are displayed in the list e Select a match and click the Display button Result The associated help text is displayed in the right pane 3 e You can also click the Contents tab to view the contents of the Help file divided into sections e Click the plus signs to expand the tree structure e Click a topic to read the associated help text Context sensitive In each dialog box there is a Help button If you press that button either of the help following will be displayed e A message box with relevant information for example the dialog box options e The Help file with relevant information displayed in the right pane epi5 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 5 Snapshots 2 2 5 Snapshots Introduction A Snapshot provides information about a method run at a certain point in time It contains monitor values at the selected point Snapshot functionality is available in e the Evaluation module where you can take Snapshots from a result file using the Marker e the PrimeView module where you can take Snapshots during a run using the Marker Howto take Snap The table below d
83. oint and the new position The Curves pane displays graphs for the selected curves in different colors The table below describes how to change the curve colors and styles Step Action 1 Select View Properties Result The Properties dialog box is displayed 2 Select the Curve Style and Color tab 3 e Select a curve from the Curve list e Select an appropriate color and style In most cases the Y axis is automatically scaled for each of the curves Values on the Y axis apply to the curve with the same color as the axis markings To get the correct Y axis click the legend The table below describes how to fix the scale of individual curves Step Action 1 e Select View Properties Result The Properties dialog box is displayed e Select the Y axis tab ep4i 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane Step Action 2 e Select the appropriate curve e Select Fixed and type a minimum and maximum range in the fields within the specified limits 3 Repeat step 2 for other curves if needed 4 Click OK How to change The table below describes how to change the scale of the X axis the scale of the X axis Step Action 1 e Select View Properties Result The Properties dialog box is displayed e Select the X axis tab 2 Select the appropriate base Time or Volume Note Curves are collected in time and recalc
84. on of the view Add Page This button adds a blank page to the report Delete Page This button deletes the current page from the report Exit This button closes the Customize Report window Howtoaddand The table below describes how to add or delete report pages in the Report Editor delete report pages If you want then to add new pages e click the Add Page toolbar button Result A new page is added after the last page to delete a page while in One Page mode e select the page with Next Page or Prev Page e click the Delete Page toolbar button and confirm the deletion to delete a page in Two e select the page with Next Page or Prev Page Page mode e click an object on the page e click the Delete Page toolbar button and confirm the deletion How to change The page layout is changed in the Page Setup dialog box The table below describes the page layout how to set up the page layout Step Action 1 Double click anywhere on the report page in the Report Editor not on an object Result The Page Setup dialog box opens 03 0014 96AD ep 70 How to view results 6 Step Action e Type new values for the Margins if necessary e Select the appropriate Settings and Unit Note An extra Header tab will appear if you de select the option to have the same header on all pages The First Header tab is used for the first page header only and the Header tab i
85. operating system documentation for details Also notice the following e You can exit the installation at any point by clicking on either the Cancel button or the Exit button If you do this however the installation will be incomplete and the software cannot be used Installing a new version of the PrimeView software over an existing PrimeView installation is no problem You do not have to uninstall the previous version before installing the new version PrimeView is supplied on a CD ROM Files on the CD ROM are compressed and cannot simply be copied onto the hard disk During the installation procedure the required folder structure is created on the hard disk and the files are decompressed Do not attempt to decompress the files using any other file decompression utility Follow the instructions in the table below to begin the installation Step Action e Insert the CD ROM disk into the CD ROM drive The PrimeView Setup Program should start automatically If not e click the Windows Start button and select Run e type the command d setup where d is the unit for your CD ROM drive e click OK 2 The PrimeView Setup Program is launched Continue the setup below ep19 3 Software Installation 3 1 How to install PrimeView for the first time Step 2 License This table describes how to complete step 2 of the PrimeView Setup Program agreement and user information Step Action 1 e The
86. or e Right click the data point and select Delete Point from the shortcut menu Result The data point is deleted and the curve is redrawn 5 Move a data point e Select the data point and drag it to a new position Result The baseline curve is redrawn 6 Click OK Result The Save Edited Baseline dialog box opens ep 109 8 Peak integration 8 5 How to edit the baseline manually Step Action e Confirm the location and type a new name if necessary e Click OK Result The new baseline is saved Edited baseline The illustration below is an example of a baseline before and after editing How to draw a straight line Action Select the first of the two points in the point list Click the Draw straight to next point button Result The baseline is drawn through the points as a straight line 03 0014 96AD ep110 Peak integration 8 8 6 How to edit the peaks Introduction Once a peak table has been generated based on an appropriate baseline it is possible to split or join peaks and to manually adjust the peak start and end points The peaks will then be renumbered and the peak values will all be recalculated How to open the The table below describes how open the peak table for editing The editing options peak table for are described below this table editing Step Action e Select Integrate Edit Peak Table Result If there are more
87. oration in the United States and or other countries 75184U ppsa aq Adobe Acrobat and Distiller are trademarks or registered trademarks of Sweden Adobe Systems Inc All goods and services are sold subject to the terms and conditions of sale of the company within GE Healthcare which supplies them GE Healthcare reserves the right subject to any regulatory and contractual approval if required to make changes in specifications and features shown herein or discontinue the product described at any time without notice or obligation Contact your local GE Healthcare representative for the most current information UNICORN Any use of this software is subject to GE Healthcare Standard Software End User License Agreement for Bio Sciences Software Products 2006 General Electric Company All rights reserved GE Healthcare Bio Sciences AB a General Electric Company GE Healthcare Bio Sciences AB Bj rkgatan 30 SE 751 84 Uppsala Sweden GE Healthcare Europe GmbH Munzinger Strasse 5 D 79111 Freiburg Germany GE Healthcare UK Ltd Amersham Place Little Chalfont Buckinghamshire HP7 9NA UK GE Healthcare Bio Sciences Corp 800 Centennial Avenue P O Box 1327 Piscataway NJ 08855 1327 USA GE Healthcare Bio Sciences KK Sanken Bldg 3 25 1 Hyakunincho Shinjuku ku Tokyo 169 0073 Japan Asia Pacific Tel 852 2811 8693 Fax 852 2811 5251 e Australasia Tel 61 2 9899 0999 Fax 61 2 9899 7511 e Austria Tel 01 57606 1619 Fax
88. ow to enter text Text can be added to the chromatogram The table below describes how to do this Step Action 1 e Right click the curves view of the chromatogram window and select Add text from the menu or e Choose Edit Text Add 2 e Click where you want to insert text in the chromatogram Result A text box opens e Type the text e Click outside the text box to set the text How to edit the The table below describes how to edit inserted text text Step Action Choose Edit Text Edit Result The Edit Texts tab of the Chromatogram Layout dialog box is displayed 2 e Select the text that you want to edit and make the appropriate changes in the Selected text field e Click the Change text button or the Delete text button e Use the Font and Set Orientation buttons if needed and make the desired changes in the resulting dialog boxes e Click OK to apply the changes Shortcut option You can also right click outside the text box and select Edit Text Mode from the shortcut menu This activates all the text boxes in the chromatogram The list below describes how to edit the text e Click the text and type the new text e Click outside the text box to set the text 03 0014 96AD p82 How to edit results 7 7 2 How to rename chromatograms curves and peak tables Instruction The table below describes how to rename chromatograms curves or peak tables in the Evaluation module
89. peak 2 e Right click and select Peak Name from the shortcut menu or e Choose Edit Peak name or e Double click the peak in the peak table or the curve Result The Edit Peak Name dialog box opens The number and reten tion of the selected peak is displayed 3 Type a name in the Peak name textbox and click OK 03 0014 96AD ep116 How to adjust peak areas with drop lines How to use the zoom function The Integrate menu Peak integration 8 The table below describes how to move the drop lines to adjust the peak area in the Edit Peak Table dialog box Step Action e Click the Edit peaks icon m e Click the peak in the curve or in the peak table to select the peak Result Two vertical bars become superimposed over the drop lines that delimit the selected peak The area between the bars is filled with a yellow fill pattern Drag the bars to define the new limits for the selected peak Result The drop lines are moved and the peak areas are automatically recalculated Note A drop line can never be moved beyond another drop line or beyond a point where the peak meets the baseline The table below describes how to use the zoom function in the Edit Peak Table dialog box Step Action 1 e Click the Zoom icon P Result The cursor is changed into a magnifying glass 2 e Press and hold the left mouse button e Drag the cursor over the area you want to zoom in on e Relea
90. points Note The baseline points are shown as green squares in the Integrate Edit baseline function of the Evaluation module The baseline points are used to create the baseline curve using a spline interpolation The spline function ensures that the baseline curve is guided by the baseline points However the curve does not necessarily pass through the baseline points The baseline will be a smoothly curved function passing close to or through the points How to measure the baseline seg ment Classic al gorithm How to measure noise level Clas sic algorithm Evaluation functions and instructions A To reduce the effect of noise at the peak integration the created baseline is forced equal to the source curve in every position where the difference between the baseline and the source curve is small enough Choose Integrate Calculate Baseline If the Accept negative peaks option is off the baseline will be forced down to the level of the source curve whenever the created baseline goes above the source curve You can try to measure the Shortest baseline segment length directly on your chromatogram The table below describes how to do this Step Action 1 Locate the shortest segment of the curve that you consider a part of the baseline 2 Use the marker box on the chromatogram to measure the length of the segment 3 Choose Integrate Calculate Baseline and insert this value as the Shortest baseline segment value
91. rch function 46 M Manual runs How to run the system manually 36 03 0014 96AD epiv Measurements How to make direct 124 Method runs Logbook pane description 45 Method templates How to start a run 34 Methods How to run a saved method 35 Morphological algorithm Description 96 How to set 96 Structure width 97 Incorrect structure width 98 Noise window 98 Minimum distance between points 99 Definition 128 P Peak integration How to perform 91 Differences between to filter peaks and to reject peaks 93 How to display peak labels 95 How to select part of a curve for peak integration 119 Peak skim Compared to drop lines 121 How to select a ratio 121 Peak table How to display information 52 How to rename 83 How to export 86 How to select contents 125 Peaks How to filter from view 93 Labels 94 Index epv Index How to display peak labels 95 How to open the peak table 111 How to delete a peak 113 How to add a fill color and pattern 114 Drop lines description 115 How to split a peak 115 How to join peaks 116 How to add peak names 116 How to exclude before integration 120 Include negative peaks in integration 120 How to select a skim ratio 121 Edit integration for part of a curve 122 Peak parameters 132 PrimeView module How to open 38 How to select the displayed panes 39 How to customize the panes 39 Q Quick View How to preview result files 27
92. re dialog box is useful to insert logos pictures or other figures in the report ture The table below describes how to add a picture object to the report Step Action e Press and hold the left mouse button on the report page and drag out a box to the size of the picture item Release the mouse button e Click the Picture icon aj Result The Picture dialog box opens e Click the Browse button to locate the desired picture file e Select the picture file and click the Open button Note The file formats bmp emf jpg and tif can be used Result A preview of the selected picture is displayed 3 e Select the desired Settings and click OK Result The picture is inserted onto the page ep73 6 How to view results 6 5 How to create and print a customized report How to add a The table below describes how to add a chromatogram to the report The layout can chromatogramor also be defined to include a peak table if desired peak table Step Action e Click the Chromatogram icon e Press and hold the left mouse button on the report page and drag out a box to the size of the chromatogram Release the mouse button Result The Setup Chromatogram dialog box opens Setup Chromatogram x Selected chromatogram s hromatogram Settings Fonts T Thick lines T Landscape Chromatogram I Start on new page Peak table I Full page een Header text T Original file
93. rin 0 87 min Broek point 2 0 87 min Flow 5 0 mymin 0 89 min Injectan Valve Load 04 min End 2003 12 01 144312 W Europe Standard Time 5 04 min Flow 0 0 mymin Note The second logbook line is the BatchID that is automatically generated The Logbook pane can autoscroll to display the latest entries Right click in the pane and select Autoscroll You can also select the Autoscroll option in the Properties dialog box View Properties and select the Logbook tab You can choose to display only selected items in the logbook The table below describes how to activate the filter Step Action 1 e Right click in the Logbook pane and choose Properties Result The Properties dialog box opens 2 e Choose the Logbook tab e Select the items you want to display in the logbook all items are selected by default e Click the OK button Result Only the selected items will be displayed in the logbook The Logbook title in the upper right corner will show the text Filter on to indicate that not all items are visible All items will still be logged in the result file e p45 5 How to perform method runs 5 2 How to monitor a method run 5 2 3 The Logbook pane How to find log The logbook can be searched for specific text entries The table below describes the book text entries function Step Action 1 Right click in the Logbook pane and choose Find Result The Find dialog box opens 2 e T
94. rrow buttons on the unit The selections are confirmed with the OK button Step Action e Choose the Run Stored Method menu e Press the OK button Result The Run Stored Method menu is displayed e Select System or PC e Press the OK button e Choose the method number e Press the OK button Result The Press OK to start run menu is displayed 3 e Press the OK button Result The method runs starts Note Important parameter values are displayed on the AKTAprime unit during the run Refer to the AKTAprime User Manual for instructions on how to change some of these parameters if needed ep35 5 How to perform method runs 5 1 How to start a method run How to run the The table below describes how to run the AKTAprime unit manually All parameters system manually are selected with the arrow buttons on the unit The selections are confirmed with the OK button Step Action 1 e Choose the Manual Run menu e Press the OK button Result The Set Method Base menu is displayed 2 e To edit the method base press OK and select the base with the arrow buttons e Proceed to select parameters with the arrow buttons in the sub sequent menus and press OK to continue 3 e After the last parameter selection navigate to the Start run menu e Press the OK button Result The method runs starts Note Refer to the AKTAprime User Manual for instructions on how to select the parameters if needed
95. rve The table below describes how to do this Step Action 1 Open a result file 2 e Place the mouse pointer in any corner of the area you want to magnify e Press and hold the left mouse button A magnifying glass icon will be added to the mouse pointer arrow on the screen e Drag a box to cover the area to be magnified and release the mouse button Result The selected region is now displayed in the entire chromato gram window together with appropriate scales for the Y and X axes 3 Use the arrow keys on the keyboard to move around in the chromato gram at the current zoom scale 4 Undo zoom Right click in the window and select Undo zoom to undo the last zoom step Reset zoom Right click in the window and select Reset zoom to reset all zoom steps at once 03 0014 96AD p66 How to view results 6 6 4 How to print active chromatograms Introduction This section describes how to print the chromatograms that are open in the Evaluation module The Print Chroma This is an illustration of the Print Chromatograms dialog box tograms dialog ote The selected print format is outlined in red box Print Chromatograms x Printer Acrobat Distiller m Print Format H 9 L J Chromatograms in each column fi Chromatograms in each row fi I Use thick lines icv T Landscape Cancel Help owes e Instruction The table below describes how to print active chromato
96. s used for all sub sequent pages e Click the First Header tab e Select all the items you want to include in the header from the Se lect Items list e Click the Font button to change the font for all items if necessary e Type header text in the Free text box and click the Font button to alter the default font if necessary e Type the report title in the Report title box and click the Font button to alter the default font if necessary e Select the Logo check box and click the Browse button if you want to locate and select a logo image file e Select the Alignment for the logo if necessary Note The logo file must be in bitmap format omp and smaller than 64 kB Larger logo files or files in other formats must be inserted as Picture objects If you want to have a line under or over the header select the appro priate option in the Layout field e Repeat steps 3 to 6 on the Footer tab and the subsequent pages Header tab Note All Header and Footer tabs contain the same options You can have all information in either the header or footer or split information between the header and footer as required e Click OK ep71 6 How to view results 6 5 How to create and print a customized report How to add ob The table below describes how to add objects to the report The various objects are jectstothereport described below this table Step Action e Click the appropriate icon in the Report items too
97. se the mouse button Result The area is enlarged Right click and select Reset zoom to re store the full view If needed you can use the selections on the Integrate menu to perform a peak integration in the Edit Peak Table dialog box This is useful for example if you want to re integrate the curve using different settings or integrate only part of a curve with different settings e p117 8 Peak integration 8 6 How to edit the peaks See 8 7 How to integrate part of a curve and how to exclude or skim peaks on page 119 for more information 03 0014 96AD ep118 8 7 Introduction How to select part of a curve Peak integration 8 How to integrate part of a curve and how to exclude or skim peaks There are several possibilities to improve the results if the peak integration is unsatisfactory This section describes e How to select only part of a curve for integration e How to exclude peaks e How to skim peaks These operations can be performed both in the Integrate dialog box in preparation for the peak integration or in the Edit Peak Table dialog box to adjust an unsatisfactory peak integration This section describes both alternatives The table below describes how to select only a part of a curve for peak integration in the Integrate dialog box Step Action e Choose Integrate Peak Integrate Result The Integrate dialog box opens e Click the Peak Window button Result The Peak window
98. source curve and then perform peak integration on the resulting curve with the Calculate baseline instruction Note In addition to blank run curves it is also possible to select any curve from the current chromatogram as the baseline e g an edited baseline To use a Zero baseline means that there is no baseline subtraction at all To reuse an existing baseline for the selected curve is the default alternative whenever there is an existing baseline available The option Correlated baseline is selected if this is the case Peak integration 8 8 2 How to perform a peak integration How to performa The table below describes how to perform a basic peak integration peak integration Step Action 1 Open a result file in the Evaluation module 2 e Choose Integrate Peak Integrate or e Click the Peak Integrate toolbar icon yi Result The Integrate dialog box opens 3 e Select a source curve e Select a baseline or a calculation method from the Baseline list e Click OK to integrate with the default selections or e Proceed with steps 4 to 6 to change the default selections Note See also 8 3 How to optimize the baseline with a morphological algorithm on page 96 and 8 4 How to optimize the baseline with a classic algorithm on page 100 4 e Click the Baseline settings button to change the calculation al gorithm in the Settings dialog box The default algorithm is Morpho logical e Change the selections or
99. tall PrimeView for the first tiM eccccccssssseessccssssssesssssssssseessescsssssesssessssssussessssssseeseceesssseeseess 19 4 Files and folders in PrIMOVIOW sis cisiscecssiaccccscessescseccnesascecdesnstcsoncoasesocasesedsaecsopesscocoedeesensdcoedasceaseeseade 24 AD HOw to create TOI SNS ieeisssccdeccessssccccscessssssccscessssssscsscesssssssssst5sssssssssessssassscsse5sssscssssssssssssecscsasssassssesesssssscssessssicd 25 A 2 HOw LOO PEN and PFE VIGW TIES ssissssessaczctescessscssssssssssesssesssesssasssessovssssssasssessscsssesssessssssssssasssasssasssesssasssnssoestetie 26 4 3 How to arrange dnd locate YOur fil eSis 28 4 4 How to copy delete rename and backup files and folders eecccccsssssssssssssssnsseeesecceccessssnsnneess 29 5 How to perform method runs csessssssecscecscesscecesescecscsceeseeeseeesssssecesssesececsceescseaeseaeseacseeeeeseenes S HOWTO St CAMEO O Mereaina 5 2 How to monitor a method run 5 2 1 How to customize PrimeView panes 5 22o MAS CUVES CIN iiti ASL ELE EEE EL EEE EEE 525s MG GOGO OI CAC OO 6 HOW t View PESUIES iccccesscesesd ceccste cece coveceatelslevcccdevsase stress telecscedl oueasdesibecdistsevencicunecdeseuedtesees cuted 6 1 HOW to open q result FIC eccccccsseeesssccsssssessesssssssessecccsssssessecssssssessecssssssssssessssssssseecsssssuuscessessssseceeseessssessess 6 2 Basic presentation Of CHrOMAtTOGFAMG scscececececececsseescessceesceescsecesectsecesencecsce
100. than one peak table available the Select Peak Table to Edit dialog box opens The name of the baseline on which the peak table was based is displayed at the bottom of the panel e Select the peak table from the list and click OK e Select one or more Help Curves to be displayed for reference if necessary Result The Edit Peak Table dialog box opens Note The Edit Peak Table dialog box will be opened immediately if you select Save and Edit Peak Table as the last step of the peak integ ration Perform the changes described in the instructions below Click OK Result The Save Edited Peak Table dialog box opens The dialog box displays a suggested name and location for the peak table 5 Confirm the name and location and click OK How to adjust the The baseline can be adjusted graphically see also 8 5 How to edit the baseline baseline manually on page 108 in the Edit Peak Table dialog box The table below describes this Step Action 1 e Click the Set Curve Points icon Result The cursor is changed into a cross e p111 8 Peak integration 8 6 How to edit the peaks Step Action 2 Perform the operations below as desired e Click to insert a new data point e Double click on a data point or right click the point and select De lete Point from the short cut menu to delete the point e Click a data point and drag the point to a new position to move the baseline Note Accept n
101. the curves Note The original curves that were created during the run can never be deleted How to save the You can either save your edited results in the original file or in a new result file The results table below describes how to save the results in the Evaluation module If you want to save the then edited results in the original result file e select File Save e click the Save toolbar icon in a new result file e select File Save as Note The previous version of the result file will be overwritten if you save the changes This cannot be reversed However the raw data curves remain unchanged How to exit the The table below describes how to exit the Evaluation module Evaluation mod ule Step Action 1 Choose File Exit Result lf there are unsaved changes a dialog box opens with an option to save the changes before exit 2 Select Yes if you want to save the changes Result The result file is closed 03 0014 96AD p88 Peak integration 8 8 Peak integration Introduction Peak integration is used to identify and measure a number of curve characteristics including peak areas retention time and peak widths This chapter describes e How to perform peak integrations e How to optimize peak integrations In this chapter This chapter contains the following sections Topic See Baseline calculation 8 1 How to perform a peak integration 8 2 How to optimi
102. the illustration below For Help press Ft Ofan Bick 5 4l The current system status is represented by the colored dot e A green dot represents a running system e Ared dot represents a system in Pause state e A yellow dot represents a system in a Hold state e A white dot represents a system in an End state ep9 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 1 The PrimeView module Toolbar iconsin The table below describes the toolbar icons in the module the PrimeView module Icon Function The Customise Panes icon opens the Customise Panes dialog box which is used to select the display panes that are open The View Documentation icon opens the documentation pages Run notes can be entered in the Notes page and settings can be changed The View Properties icon opens the Properties dialog box which is a used to control the data display in the PrimeView panes 03 0014 96AD ep 10 The PrimeView Evaluation module PrimeView concepts 2 2 2 2 Introduction The module win dow evaluate curve data The PrimeView Evaluation module provides extensive facilities to present and to below Opened result files are displayed in the Evaluation module window See the illustration Toolbar icons in the Evaluation module The table below describes the toolbar icons in the module Icon Function The Open icon displays all available resu
103. tomized report format Should you need to store store your reports in an electronic format you can save them as PDF files Select an Adobe Acrobat printer as default Windows printer and print the reports The table below describes how to open the Report Editor in Edit mode to create a customized report format Step Action 1 Open a result file in the Evaluation module 2 e Select File Report or e Click the Report icon Result The Generate Report dialog box opens 3 e Click the New button Result The Report Editor opens in Edit mode The illustration below shows the Report Editor window in Edit mode with a blank report open The table below describes the different functions of the Edit mode toolbar buttons in the Report Editor Toolbar button Function Preview Edit This button toggles between a print preview of the re port and the Edit mode Next Page This button displays the next page or pair of pages where there are more than one page ep69 6 How to view results 6 5 How to create and print a customized report Toolbar button Function Prev Page This button displays the previous page or pair of pages where there are more than one page One Page Two Pages This button toggles between single page view and pairs of pages view when there is more than one page Zoom In This button increases the magnification of the view Zoom Out This button decreases the magnificati
104. tware The table below describes how to access the help utility If you want to access Then the general help utility open the Help menu in any of the software modules context specific help e click the Help button in the dialog box topics p or e press the F1 key on your keyboard Note An online version of the PrimeView User Manual is available on the installation CD 1 2 Introduction Document struc ture Typographical representations Introducing PrimeView 1 About this manual This section is a general description of the manual the contents and the pre requisites for the examples and instructions that are presented in the PrimeView User Manual The manual is divided into chapters Each chapter starts with a brief overview that presents the contents and the headings for the sections that the chapter contains Most sections begin with an introduction that summarizes the content Some sections are divided into sub sections A section is divided into blocks of information with separating lines The blocks are identified by a label in the margin This makes it easier for you to quickly scan a page to find the exact topic you are looking for Menu commands field names and other text items from the software are quoted exactly as they appear on the screen in a bold typeface Example Run Setup Search paths are shown in a bold typeface with a separating colon between each level
105. ulated for display in volume Thus the resolution of the two bases may appear slightly different 3 Select the appropriate Axis scale e Total will show the curves as far as they have come in the run e Window allows you to set the portion of the total pane to be dis played either in minutes or ml depending on the selected base e Click OK How to switch e Click the legend of the X axis between time and or volume units e right click and select Base Type to switch the display between time and volume units The run is controlled according to the time volume base defined in the current block regardless of the base in the curves display 03 0014 96AD ep 42 How to zoom in the Curves pane How to select curve pressure units How to perform method runs 5 The table below describes how to zoom in on a selected region of the curve pane Step Action 1 e Press and hold the left mouse button and drag a rectangle out on the screen to encompass the area to be viewed e Release the mouse button Result The display is now zoomed in on the selected area 2 Repeat the process for further magnification of selected areas How to zoom out To reduce the scale of the zoom right click in the Curves pane and select one of the following options e Undo Zoom reverses each zoom in action a step at a time e Reset Zoom reverses all zoom in actions to the default scale If the Pressure curve is displayed in the Curv
106. values e Click OK 5 e Click the Peak window button to edit the peak window limits if ne cessary e Click the Reject peaks button to set the parameters for peak rejec tion if necessary e Edit the Column height or Column V values if necessary ep91 8 Peak integration 8 2 How to perform a peak integration Step Action 6 e Click OK to integrate and close the dialog box or e Click Save and Edit Peak Table to save the integration and open the integrated curve for editing See 8 5 How to edit the baseline manually on page 108 See 8 6 How to edit the peaks on page 111 See 8 7 How to integrate part of a curve and how to exclude or skim peaks on page 119 Peak integration The peak table is displayed underneath the active chromatogram The start point results and end point of each peak are marked by vertical marks drop lines in the chromatogram The peaks are automatically labelled according to what is selected in the Curve Style and Color tab of the Chromatogram Layout dialog box This is an illustration of the results after a peak integration Q Primeview Evaluation Example Result 00I 1 v UNICORN Local fil klas result ifxample Result002 Example ResultO0 Les lee Edt yew Integrate window Help EHH SA aa olu Em a e a Ge 3 D TIRET EZD z fzo hoo peo poo psa po 180 hzo kad do Sb ob z5 A Engle Ron2001 1_UV1_21Sr 01 PEAKI No Retention min Width mi
107. x to the size of the item Release the button Result The Setup Documentation dialog box opens 2 Select the items to be included in the report e Select All includes all items in the report e Clear All removes all selections 3 e If desired change the Fonts e Select if the documentation should start on a new page e Ifwas selected make the necessary changes to the Base and Log book filter settings e Click OK Result The selected documentation items are inserted into the report ep75 6 How to view results 6 5 How to create and print a customized report How to add the The table below describes how to add the Evaluation Log to the report Evaluation Log Step Action e Click the Evaluation Log icon 4 E e Press and hold the left mouse button on the report page and drag out a box to the size of the item Release the mouse button Result The Setup Evaluation Log dialog box opens 2 e If desired change the Fonts e Select if the Evaluation Log should start on a new page e Click OK Result The Evaluation Log is inserted into the report How to move and The table below describes how to select move and resize objects freely resize objects freely If you want then to select a single object e click the object of interest to select several ob jects e click the Select icon e press and hold the lt Ctrl gt key while you click the objects to move the sel
108. ype the text you want to locate e Select search criteria if necessary e Click OK Result The located logbook entry is highlighted 03 0014 96AD ep 46 Introduction In this chapter How to view results How to view results 6 A result file is automatically generated at the end of a method run and contains a complete record of the method run including method system settings curve data and method run log The Evaluation module offers extensive facilities for presentation and evaluation of curve data This chapter describes how to present the chromatograms and curves of your result file and how to create and print reports This chapter contains the following sections Topic How to open a result file Basic presentation of chromatograms How to optimize the presentation of a chromatogram How to print active chromatograms How to create and print a customized report Run documentation See 6 1 6 2 6 3 6 4 6 5 6 6 ep47 6 How to view results 6 1 How to open a result file 6 1 How to start the Evaluation mod ule How to open a AK TAprime result file 03 0014 96AD ep 48 How to open a result file The PrimeView Evaluation module provides facilities for the presentation and evaluation of separation results The module is independent from the PrimeView module and can be started even if the PrimeView module is not operating e Click the PrimeView Evalu
109. ze the baseline with a morphological algorithm 8 3 How to optimize the baseline with a classic algorithm 8 4 How to edit the baseline manually 8 5 How to edit the peaks 8 6 How to integrate part of a curve and how to exclude or skim peaks 8 7 Measurements 8 8 e p89 8 Peak integration 8 1 Baseline calculation 8 1 Introduction Baseline options The Calculate baseline function Baselines based ona blank curve Zero baseline Reuse an existing baseline 03 0014 96AD p90 Baseline calculation The first step when you integrate peaks is to calculate a baseline A correct baseline is crucial for accurate calculation of the peak areas This section describes the options for how to calculate baselines in the Integrate dialog box The Evaluation module offers several options for how to create an accurate baseline e To use the automatic Calculate baseline function e To create a baseline based on a blank curve e To use a Zero baseline e To reuse an existing baseline The Calculate baseline instruction provides automatic calculation of the baseline In most cases the measurement is very accurate The calculation can be performed using the Morphological algorithm or the Classical algorithm A blank curve can be used as the baseline for peak integration e You can use a blank curve with the same chromatographic conditions as the corresponding sample or e You can subtract the blank run from the

PrimeView 5.0 - GE Healthcare Life Sciences

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