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PrimeView™ 5.31 - GE Healthcare Life Sciences

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1. 1 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 Result The Picture dialog box opens 2 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 omp emf jpg and tif can be used Result A preview of the selected picture is displayed 3 Select the desired Settings and click OK Result The picture is inserted onto the page 102 PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 5 How to create and print a customized report How to add a chromatogram or peak table The table below describes how to add a chromatogram to the report The layout can also be defined to include a peak table if desired Step Action 1 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 Settings Fonts Tl Thick lines I Landscape Chromatogram I Start on new page PEs T Full page Header text T Original file name __Headertext _ Layout E Current Dei Cancel Help 2 Select which chromatogram s to insert from the Selected chromatogram s droplist e Ac
2. How to change the curve colors and styles The Curves pane displays graphs for the selected curves in different colors The table below describes how to change the curve colors and styles PrimeView 5 31 User Manual 28 9972 43 AA 65 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane Step Action 1 Select View Properties Result The Properties dialog box is displayed Select the Curve Style and Color tab e Select a curve from the Curve list e Select an appropriate color and style How to change the scale of the 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 Action e Select View Properties Result The Properties dialog box is displayed e Select the Y axis tab e Select the appropriate curve e Select Fixed and type a minimum and maximum range in the fields within the specified limits Repeat step 2 for other curves if needed Click OK Y axis Step fl 2 3 4 66 PrimeView 5 31 User Manual 28 9972 43 AA 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane How to change the scale of the X axis The table below describes how to change the scale of the X axis Step Action 1 e Select V
3. e peak tables The displayed areas for the views can be adjusted by dragging the borders with the mouse cursor between the views The illustration shows the PrimeView module with the Curves and Logbook panes dis played Pe Ven Help BOG UV1_215 Cond pH Pressure Temp Conc mAU 7 z min 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 DOO ren Ran staneg For Help press FL Rn Bek l i iowa Kerticted Dy pra PrimeView 5 31 User Manual 28 9972 43 AA 79 6 How to view results 6 2 Basic presentation of chromatograms 6 2 2 The chromatogram window How to view peak table information The table below describes how to display peak table information if the result has been integrated Step Action 1 Open a result file 2 e Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box opens 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 Run curves default appearance and information 80 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 Section 6 3 5 How to save and apply a layout on page 92 Information for each curve Each curve is automatically assig
4. as File name a full search path must be entered in answer to the question In the part of the source curve limited by the Left limit and Right limit every lt n gt sample is exported EXPORT_CURVE_WKS Exports the source curve to the file defined in Export to File in WKS format If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question In the part of the source curve limited by Left limit and Right limit every lt n gt sample is exported EX Exports an evaluation log in ASCII format to the file de PORT_EVAL_LOG_ASCII fined in Export to file If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question EX Exports an evaluation log in WKS format to the file defined PORT_EVAL_LOG_WKS in Export to file If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question EXPORT_EVAL_LOG_XLS Exports an evaluation log in XLS format to the file defined in Export to file If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as Fil
5. integration The table below describes how to perform a basic peak integration Step Action 1 2 Open a result file in the Evaluation module e Choose Integrate Peak Integrate or e Click the Peak Integrate toolbar icon po Result The Integrate dialog box opens 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 Section 8 3 How to optimize the baseline with a morphological algorithm on page 129 and Section 8 4 How to optimize the baseline with a classic algorithm on page 134 e Click the Baseline settings button to change the calculation algorithm in the Settings dialog box The default algorithm is Morphological e Change the selections or values e Click OK e Click the Peak window button to edit the peak window limits if necessary e Click the Reject peaks button to set the parameters for peak rejection if necessary e Edit the Column height or Column V values if necessary PrimeView 5 31 User Manual 28 9972 43 AA 123 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 in tegrated curve for editing See Section 8 5 How to edit the baseline manually on page 143
6. 55 B Baseline Calculation options 121 Definition of asegment 168 How to adjust the baseline graphically 148 How to edit manually 144 Parameters 169 Reuse existing 122 The Calculate function 121 BatchID Logbook illustration 71 Blank curve Calculate baseline based on 121 C Chromatogram Layout Curve tab 86 Default curve names 86 How to choose curve name appearance 86 The Curve Style and Color tab description 88 Chromatograms Description 77 How to add annota tions 112 How to add a second Y ax is 90 How to apply a layout 93 How to change and fix the X axis 91 How to change and fix the Y axis 90 How to edit annotation text 112 How to make layout changes general 85 How to print active chro matograms 95 How to rename 114 How to save a layout 92 How to set a reference point 165 Temporary chro matogram 77 Chromatogram window How to display a vertical marker 82 How to display the Logbook overlay 83 How to optimize the workspace 81 Shortcut menu 81 Classic algorithm Definition 134 169 How to measure baseline segments 172 How to measure noise lev el 172 How to set 134 How to set Max baseline level 141 Missing peaks 140 Noise window 139 Parameters 134 Shortest baseline seg ment 136 Slope limits 137 When to change the Max baseline level 141 Curves Default curve names 86 Export options 115 Fraction text alignment op tions 88 How to add a second Y ax
7. 6 2 Basic presentation of chromatograms 6 2 2 The chromatogram window How to display a vertical marker line The table below describes how to display a vertical marker line Step Action 1 2 Right click the Curves pane and select Marker 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 Sec tion 2 2 5 Snapshots on page 23 for more information about the Snapshot function How to set a reference point The table describes how to set a reference point Step Action i 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 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 be tween the reference point and the new position 82 PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 2 Basic presentation of chromatograms 6 2 2 The chromatogram window How to display the logbook overlay The table below describes how to display the logbook entries as an overlay in the chro matogram Step Action 1 e Right
8. Disable network interface card power settings 39 Disable Windows 7 power save settings 37 How to install UNICORN basic instruction 30 Prerequisites for PrimeView installation 30 Prerequisite software appli cations 31 Repair or remove installa tion 36 PrimeView 5 31 User Manual 28 9972 43 AA Index Select destination folder for the installation 33 System Control module Description 13 T Templates How to start a run from a method template 56 How to start a run from an application template 55 Temporary chromatogram Description 77 Toolbar icons n the PrimeView module 14 U User Account Control How to disable on Windows 7 27 How to enable on Windows 7 42 W Windows 7 User Account Con trol How to disable 27 How to enable 42 Y Y axis How to choose the Y axis scale 80 Z Zero baseline Definition 122 Zoom function How to enlarge parts of a curve 94 193 For local office contact information visit www gelifesciences com contact GE Healthcare Bio Sciences AB Bj rkgatan 30 751 84 Uppsala Sweden www gelifesciences com unicorn imagination at work GE imagination at work and GE monogram are trademarks of General Electric Company PrimeView UNICORN companies KTA and AKTAprime are trademarks of GE Healthcare All third party trademarks are the property of their respective owners 2005 2011 Genera First published May 2011 Electric
9. Result The Color and Pattern dialog box opens Color El Ce Bee sie fae ADETE f Imi oe S E E E i EEEE NENNE Ennn E 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 PrimeView 5 31 User Manual 28 9972 43 AA 151 8 Peak integration 8 6 How to edit the peaks Peak start and end points 152 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 PrimeView 5 31 User Manual 28 9972 43 AA How to split a peak 8 Peak integration 8 6 How to edit the peaks It 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 a e Click the peak in the curve or in the peak table to select the peak e Right click and se
10. gt Network and Sharing Center Search Control Ponel View your basic network information and set up connections W ie See full map SQA 003 Network Internet This computer View your active networks Connect or disconnect P e Network Access type Internet Work network Connections J Local Ares Connection Change your networking settings Set up a new connection or network Set up a wireless broadband dial up ad hoc or VPN connection or set up a router or access point Eg Connect to a network Connect or reconnect to a wireless wired dial up or VPN network connection Choose homegroup and sharing options Access files and printers located on other network computers or change sharing settings Troubleshoot problems Diagnose and repair network problems or get troubleshooting information PrimeView 5 31 User Manual 28 9972 43 AA 39 3 Software Installation 3 4 Windows 7 post installation settings Step Action 3 Click the Change adapter settings link Result The Network Connections dialog opens 4 Double click the network interface card you need to change Result The Network Connections dialog opens nmk ated Bytes 117 676 932 906 356 317 40 PrimeView 5 31 User Manual 28 9972 43 AA 3 Software Installation 3 4 Windows 7 post installation settings Step Action 5 Click the Properties button Result The Properties dialog opens E Aow the
11. 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 104 PrimeView 5 31 User Manual 28 9972 43 AA Step 6 How to view results 6 5 How to create and print a customized report Action e f desired change the Fonts e Select if the documentation should start on a new page e If Select All or Logbook was selected make the necessary changes to the Base and Logbook filter settings Click OK Result The selected documentation items are inserted into the report How to add the Evaluation Log The table below describes how to add the Evaluation Log to the report Step Action 1 e Click the Evaluation Log icon 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 e If desired change the Fonts e Select if the Evaluation Log should start on a new page Click OK Result The Evaluation Log is inserted into the report PrimeView 5 31 User Manual 28 9972 43 AA 105 6 How to view results 6 5 How to create and print a customized report How to move and resize objects freely The table below describes how to select move and resize objects freely If you want then toselectasingle object e click the Select icon D e click the object of interest to select several objects e cli
12. 7 1 How to enter and edit text in the chromatogram e Click the text and type the new text e Click outside the text box to set the text PrimeView 5 31 User Manual 28 9972 43 AA 113 7 How to edit results 7 2 How to rename chromatograms and curves 7 2 How to rename chromatograms and curves Instruction The table below describes how to rename chromatograms or curves Step Action 1 Choose Edit Rename and the relevant option Chromatogram or Curve Result The Rename dialog box opens 2 Select the appropriate object 3 Type a new name in the Name field 4 Click OK Note The original raw data curves cannot be renamed They will not be listed as options in the dialog box 114 PrimeView 5 31 User Manual 28 9972 43 AA 7 How to edit results 7 3 How to export results 7 3 Howto export results Introduction This section describes how to export curves in different formats and how to copy data and curves to the clipboard Data formats You can export data in the following formats e ASCII asc e Excel xls Export options Select File Export in the Evaluation module to export data from an open result file The following export options are available e Curves e Documentation e Evaluation log PrimeView 5 31 User Manual 28 9972 43 AA 115 7 How to edit results 7 3 How to export results How to export curves The table below describes how to export curves in the Evaluation module Ste
13. Company All rights reserved All goods and services are sold subject to the terms and conditions of sale of the company within GE Healthcare which supplies them A copy of these terms and conditions is avail able on request Contact your local GE Healthcare repre sentative for the most current information PrimeView Any use o ware End User Licens this software is subject to GE Healthcare Standard Soft e Agreement for Life Sciences Software Products GE Healthcare Europe GmbH Munzinger Strasse 5 D 79111 Freiburg Germany GE Healthcare UK Limited Amersham Place Litt GE Healthcare Bio Sci e Chalfont Buckinghamshire HP7 9NA UK ences Corp 800 Centennial Avenue P O Box 1327 Piscataway NJ 08855 1327 USA GE Healthcare Japan Corporation Sanken Bldg 3 25 1 Hyakunincho Shinjuku ku Tokyo 169 0073 Japan 28 9972 43 AA 05 2011
14. Format dialog box opens Note The to DI 3 Click OK e Type a name for the format name for the default format will automatically be changed EFAULT PrimeView 5 31 User Manual 28 9972 43 AA 109 6 How to view results 6 6 Run documentation 6 6 Run documentation Introduction The full documentation for a run is stored in the result file This section describes e how to view and print the run documentation How to view and print the run documentation The table below describes how to view and print the run documentation Step Action 1 Open a result file 2 e Choose View Documentation in the Evaluation module or e Click the view Documentation icon Result The Documentation dialog box opens 3 Click the Print button Result The Print dialog box opens 4 Select the documentation items you want to print and click OK Result The documentation is printed on the default Windows printer 110 PrimeView 5 31 User Manual 28 9972 43 AA 7 How to edit results 7 Howto edit results Introduction This chapter describes e how to edit the results that are presented in the Evaluation module For more information about how to view results see chapter Chapter 6 How to view re sults on page 73 In this chapter This chapter contains these sections Section See page 7 1 How to enter and edit text in the chromatogram 112 7 2 How to rename chromatograms and curves 114 7 3 How to expor
15. LOOP statements matches the number of ENDLOOP statements MOLSIZE Calculates the molecular sizes from a molecular size curve A Mol size column will be added to the Peak table QC_TEST Performs a QC test QUANTITATE Calculates the concentration and amounts in the sample from a quantitation table Amount and Concentration columns will be added to the Peak table REPORT Prints a report with the specified named report layout and title If Title is then the title in the report layout is used If Report Layout is then a default layout is used RUN_PROGRAM Starts a program as a separate process The Program name string contains the program name and parameters to start it with UPDATE Updates a Quantitation table with new data from one standard concentration level The default Limit value of 12 5 will be used PrimeView 5 31 User Manual 28 9972 43 AA 187 A Evaluation functions and instructions A 3 Procedure instructions Test instructions 188 The Instruction field also contains a group of test instructions These instructions are only available for the UNICORN software development team Instruction Description AUTOSAM PLER_PEAK_INTER VALS Sets the area intervals for the AUTOSAMPLER_PEAK_TEST AUTOSAM PLER_PEAK_TEST Locates the first peak in the peak table Compares the area of the peak in the peak table with the specified maximum and minimum
16. The PrimeView module 13 2 2 2 The PrimeView Evaluation module 16 2 2 3 Search functions 18 2 2 4 Help functions 21 2 2 5 Snapshots 23 12 PrimeView 5 31 User Manual 28 9972 43 AA 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 1 The PrimeView module 2 2 1 The PrimeView module Introduction The PrimeView module is used to monitor separation runs The PrimeView panes 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 The Curves pane displays monitor signal values graphically See the illustration below 00 Of 02 03 Os OF 06 OF 06 OF 1 0 85 42 13 14 15 168 t 10 49 20 PrimeView 5 31 User Manual 28 9972 43 AA 15 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 1 The PrimeView module The Logbook pane 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 Mead Run 2003 12 01 14 4403 W Europe Standard Time Methed Retut pimelAT200idecO no001 RES Logbook 0 00 min Borch ID BEADESS5 767E 4905 A1 54 BOFFSOFIBSES 0 00 min Base Time O00minPeuse 0 0 2003 12 01 14 4403 W Europe Standerd Time Manuel 0 00 rnin Eror 62 Chack thot tube positionis OK 0 00 min Concertration 0 B 0 00 min injoction Valve Wasto 0
17. be exported may be set by the Export param eter for example every fifth point EX Exports the documentation in the current result file in PORT_DOC_400_ASCII ASCII format to the file defined in Export to file If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in an swer to the question If all parameters to this function are OFF then no documentation is exported If at least one of them is ON then the documentation will be exported and the corresponding parts will be included in the export ed file 184 PrimeView 5 31 User Manual 28 9972 43 AA A Evaluation functions and instructions A 3 Procedure instructions Instruction Description EXPORT_DOC_400_WKS Exports the documentation in the current result file in WKS format to the file defined in Export to file If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in an swer to the question If all parameters to this function are OFF then no documentation is exported If at least one of them is ON then the documentation will be exported and the corresponding parts will be included in the export ed file EXPORT_DOC_400_XLS Exports the documentation in the current result file in MS Excel XLS format to the fil
18. click in the chromatogram window and choose Properties on the shortcut menu Result The Chromatogram Layout dialog box opens 2 e Choose the Curve tab e Select the Logbook curve 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 End Block Block Start_Conc_B Base SameAsMain i 0 00 B 0 000 C7 Block Column_Yalve Base SameAsMain ColumnPosition Position Bypass End Block Block System_Volume_Compensation Base Volume ml Wl PrimeView 5 31 User Manual 28 9972 43 AA 83 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 Howto optimize the presentation of a chromatogram Introduction This section describes some of the ways you can optimize the presentation of a chro matogram In this section This section contains these sub sections Section See page 6 3 1 How to make changes in the Chromatogram Layout dialog box 85 6 3 2 The Curve tab and Curve Names tab 86 6 3 3 The Curve Style and Color tab 88 6 3 4 How to change and fix the axes 90 6 3 5 How to save and apply a layout 92 6 3 6 How to show part
19. 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 Q Eda Bascline iS x Pp Example sexult 003 4 UV Example sexult 003 4 UVGOI BASEM Example 1eralt 003 4 Edhe sBaseline AU o g O g g g g J C O B C Q CHO o 100 200 300 oo wo 000 70 0 30 0 mn 17 233 min Dee 637 976 mAU Diaw straight to pest point ceed e How to use the zoom function 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 PrimeView 5 31 User Manual 28 9972 43 AA 143 8 Peak integration 8 5 How to edit the baseline manually Step Action 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 restore the full view How to edit and insert data points 144 The table below describes how to edit and insert baseline 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 Base
20. 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 baseline Too high slope limit A too high Slope limit value can cause peak limits too high up on the peaks This can 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 PrimeView 5 31 User Manual 28 9972 43 AA 137 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm The example below has a much lower Slope limit and a lower Noise window 138 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm Noise window 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 sl
21. for the peak table 5 Confirm the name and location and click OK PrimeView 5 31 User Manual 28 9972 43 AA 147 8 Peak integration 8 6 How to edit the peaks How to adjust the baseline The baseline can be adjusted graphically see also Section 8 5 How to edit the baseline manually on page 143 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 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 Delete 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 negative peaks must be selected before the peak integration if you want to be able to drag a data point to move the baseline above the curve How to calculate a new baseline The baseline can be recalculated in the Edit Peak Table dialog box The table below de scribes how to do this 148 Step Action 1 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 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integrati
22. is 90 How to apply a layout 93 How to change and fix the X axis 91 How to change and fix the Y axis 90 How to change the color and style 88 PrimeView 5 31 User Manual 28 9972 43 AA How to choose the Y axis scale 80 How to copy into the Tempo rary chromatogram 77 How to delete unwanted curves 118 How to export 116 How to rename 114 How to save a layout 92 How to set a hatched back ground 89 How to use the zoom func tion 94 Logbook text alignment op tions 88 Peak labels 88 Run curves default appear ance 80 Curves pane in PrimeView Description 64 How to change curve colors nd styles 65 ow to change scale of the axis 67 ow to change scale of the axis 66 ow to display a vertical arker 65 ow to display complete ogbook information 69 ow to select curve pres ure units 68 ow to select text align ent 69 ow to set a reference oint 65 ow to zoom in regions of the pane 68 Reduce scale of zoom 68 Curves pane in System Control How to select curves to be monitored 64 How to select text align ment 69 D Delete files and folders 53 Documentation How to export 117 How to view 110 3 Ir rr r3grtKirixiiea 2U I PrimeView 5 31 User Manual 28 9972 43 AA Index E Evaluation Chromatogram window shortcut menu 81 Chromatogram window views 79 How to display a vertical marker 82 How to display peak table information 80 How to exit the module 119 How to m
23. of a curve 94 84 PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 1 How to make changes in the Chromatogram Layout dialog box 6 3 1 Howto make changes in the Chromatogram Layout dialog box Instruction 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 Features regarding peak tables are described in Section 8 2 How to perform a peak inte gration on page 123 The table below describes how to make changes in the Chromatogram Layout dialog box Step Action 1 Open a result file 2 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 chromatograms Click OK PrimeView 5 31 User Manual 28 9972 43 AA 85 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 2 The Curve tab and Curve
24. table data Step Action 1 Click the Chromatogram Layout icon Result The Chromatogram Layout dialog box opens 2 Click the Peak Table tab 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 166 PrimeView 5 31 User Manual 28 9972 43 AA A Evaluation functions and instructions Appendix A Evaluation functions and instructions Introduction This appendix describes the functions that are implemented in the Evaluation module In this appendix This appendix contains these sections Section See page A 1 Baseline calculation theory 168 A 2 Peak table column components 173 A 3 Procedure instructions 178 PrimeView 5 31 User Manual 28 9972 43 AA 167 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 definition Baseline parameters are used to find the baseline segments The default values for 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 Inte
25. the following e Logbook or Fraction curve in the Curve list as appropriate e Select the appropriate Logbook text alignment or Fraction text align ment option Horizontal Vertical Fly over displays the text if you place the mouse pointer over the generated mark Click OK 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 Curves pane 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 PrimeView 5 31 User Manual 28 9972 43 AA 69 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane 0 0 0 2 04 0 6 0 8 For Help press F1 Run 70 PrimeView 5 31 User Manual 28 9972 43 AA 5 How to perform method runs 5 2 How to monitor a method run 5 2 3 The Logbook pane 5 2 3 The Logbook pane Introduction Illustration Autoscroll 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
26. the two points in the point list 2 Click the Draw straight to next point button Result The baseline is drawn through the points as a straight line 146 PrimeView 5 31 User Manual 28 9972 43 AA 8 6 Introduction 8 Peak integration 8 6 How to edit the peaks How to edit the peaks 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 peak table for editing The table below describes how open the peak table for editing The editing options are described below this table Step Action 1 e Select Integrate Edit Peak Table Result If there are more 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 2 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 integration 5 Perform the changes described in the instructions below 4 Click OK Result The Save Edited Peak Table dialog box opens The dialog box displays a suggested name and location
27. to and from retention points The actual curve value is compared to a set amplitude parameter If the difference exceeds a set Delta value the test is failed A print parameter may be set to On to generate printed results PrimeView 5 31 User Manual 28 9972 43 AA A Evaluation functions and instructions A 3 Procedure instructions Instruction Description TEST_INFO Adds selected information items to the output file e g system name UNICORN version etc Also a specified free text can be added A print parameter may be set to On to generate printed results TEST_LOG Verifies if a specified text is present in the logbook curve be BOOK_EVENT tween the defined to and from retention points The test can be defined to be passed either if the text is present or not A failed or passed text will be added to the output file A print parameter may be set to On to generate printed results UV_RESPONSE_IN Sets the level intervals for the UV_RESPONSE_TEST TERVALS UV_RESPONSE_TEST The amplitudes for the 0 and 100 levels are calculated and the difference between the values are calculated The results of 1 Curve2_Difference Curvel1_Difference and 2 Curve2_Difference Curve3_Difference are calculated The calculated points are checked if they are outside the defined limits from the 50 level PrimeView 5 31 User Manual 28 9972 43 AA 189 Index Index 190 A Application templates How to start a run
28. to folders that are specific to your user name e You can also copy files to and from the folders that you have access to on the net work 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 Select File Copy or e Right click and select Copy from the short cut menu Result The Copy dialog box is opened 3 Select a target folder or USB memory 4 Click OK PrimeView 5 31 User Manual 28 9972 43 AA 51 4 Files and folders in PrimeView 4 4 How to copy delete rename and backup files and folders How to Copy to External The table below describes how to use the function Copy to External Step Action 1 Select the file you want to copy 2 e Select File Copy to External or 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 How to use Copy from External The table below describes how to use the function Copy 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 fil
29. to this Folder or click Change to install to a dif ere Install Siield PrimeView 5 31 User Manual 28 9972 43 AA 33 3 Software Installation 3 2 How to install PrimeView for the first time Step 5 Select the COM port You must define the COM port which the AKTAprime system is connected to e Select the appropriate COM port e Click the Next button to proceed jz Prime iew 5 31 InstallShield Wizard Select COM port Choose the setup type that best suits your needs InstallSiield Step 6 Perform the installation The wizard is ready to perform the installation If the settings are correct click the Install button to copy the files Tip If you want to make any changes you can click the Back button one or more times 34 PrimeView 5 31 User Manual 28 9972 43 AA 3 Software Installation 3 2 How to install PrimeView for the first time Step 7 Installation completed The software installation wizard is now completed Click the Finish button to close the wizard and re start the computer Prime iew 5 31 InstallShield Wizard The InstallShield Wizard has successfully installed PrimeView 5 31 Click Finish to exit the wizard The computer will be restarted for the configuration changes to take effect PrimeView 5 31 User Manual 28 9972 43 AA 35 3 Software Installation 3 3 Updating installations 3 3 Updating installations Repair or remove PrimeView 5 31 installations 3
30. 00 rnin Cornus 2003 12 01 14 44 09 W Europe Standard Tine Manual 0 00 min Flow 40 0 ml irin 0 87 min Breek point 2 0 87 rnin Flow 5 0 ymin 0 89 min Injection Valve Load 04 min End 2003 12 01 14 43 12 W Europe Standard Tima 5 04 nin Flow 0 0 mnyinin The Status bar The Status bar in the bottom of the PrimeView module displays the current status of the separation run See the illustration below TET Ch Tn i 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 Toolbar icons in the PrimeView module The table below describes the toolbar icons in the module Icon Function The Customize Panes icon opens the Customize Panes dialog box which ki is used to select the display panes that are open 14 PrimeView 5 31 User Manual 28 9972 43 AA 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 1 The PrimeView module Icon Function 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 used to Lu control the data display in the PrimeView panes a PrimeView 5 31 User Manual 28 9972 43 AA 15 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 2 Th
31. 6 The PrimeView 5 31 installation procedure may also be used to either repair or to remove a PrimeView 5 31 installation When the InstallShield Wizard detects a previous installation of PrimeView 5 31 it will suggest repair or remove options Installation repair or removal can either be initiated using the installation CD or by using the Add or Remove Programs procedure from the Windows Control Panel ji Prime iew 5 31 InstallShield Wizard Program Maintenance Remove or Repair the program Instalsmield PrimeView 5 31 User Manual 28 9972 43 AA 3 Software Installation 3 4 Windows 7 post installation settings 3 4 Windows 7 post installation settings Introduction Power save settings in the default Windows 7 Power Options may interfer with the performance of PrimeView 5 31 It is essential to ensure that Windows will not put either the computer or the computer network interface cards to sleep while a run is in progress This section describes how to disable power save settings that are in conflict with PrimeView operations Disable the computer power save setting The table below describes how to disable the Windows 7 power save settings Step Action 1 e Click the Windows Start button and e Choose the Control Panel 2 Click the Systems and Security heading 3 Click the Power Options heading PrimeView 5 31 User Manual 28 9972 43 AA 37 3 Software Installation 3 4 Windows 7 post installation set
32. 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 PrimeView 5 31 User Manual 28 9972 43 AA 129 8 Peak integration 8 3 How to optimize the baseline with a morphological algorithm Step Action 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 Morphological algorithm parameters The parameters for the Morphological algorithm are e Structure width e Noise window e Minimum distance between points Structure width 130 Structure width determines the length of the straight line that follows the chromatogram The default 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 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 3 How to optimize the baseline with a morphological algorithm ATIMIOOO 1_UVI_2ISAn ATIMTO0O 1_UV1_21SANGOTBASEM The correct structure width settings Too low settings Too low Structure width settin
33. Customize Panes icon or e choose View Panes 62 PrimeView 5 31 User Manual 28 9972 43 AA 5 How to perform method runs 5 2 How to monitor a method run 5 2 1 How to customize PrimeView panes How to customize PrimeView 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 PrimeView 5 31 User Manual 28 9972 43 AA 63 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane 5 2 2 The Introduction Curves pane The Curves pane of the PrimeView module displays monitor signal values graphically The figure below shows an example of the Curves pane aa See a a Cres n 145 mn 308 157 10 mA How to select curves to be displayed 64 You can decide which curves you want to display in the Curves pane Curves will only be shown for components present in the system The table describes how to select the curves to be displayed on the screen Step Action il In the PrimeView module select View Properties Result The Properties dialog box is displayed 2 Select the Curves tab Note The curves in the list are those for which Store is set to On in the system settings together with any reference curves defined in the method 3 In the Display curves list select the curves you want to displa
34. GE Healthcare Life Sciences PrimeView 5 31 User Manual Table of Contents Table of Contents 1 Introducing PrimeView 1 1 About PrimeView m MAS VABOUE tIS MANUA sana ae ao AR n A EAE oE e r Me OIC SPE STII NS cenene e a a A 2 2 The PrimeView user interfaces 2 2 1 The PrimeView module oc 2 2 2 The PrimeView Evaluation module T 225 SCORCH TUNCUONS ianu n a E RAN ENNA ZEA Held TUNCHONS yneninsansemunn n n EEE E EEA TE 225 SnApPSNOtS ir E ARE TT TENETE Software MINS BO IO e scsscsessdiectvatacsesces excecsteerscpaseeicamssoiadeapcaiacsciwterisetnrectesncenuens 3 1 Preparations before installing PrimeView 5 31 ON WINGOWS 7 un eecscssssssssessesscssscsssssessees 3 2 How to install PrimeView for the first time ne ecccscsscssssssssssssessessccssssssssssssessssseessesssssussseesees 3 3 Updating installations oecccccssssssssseeessssecssen 3 4 Windows 7 post installation settings Files and folders in PrimeView s ssssesssssssessssssesssseressssessssesesssseoresseseseseesessese 4 1 HOW to create folders ssssssssss1100ses1resssstreseeerreeeesrreseeerreeesrrsseeerrsseenrnssteerssseetrnssneosssetanssetssasnnnns nnne 4 2 HOW to open and preview files oe cecsssscccsssssssssssessessscssssssssssssssssssessessssssssssssecsessecsssssssssunseesees 4 3 HOW to arrange and locate your files o eessssssssssesssssscsssssssssssssessssssssecsssssssssssecssssecesstsssssssseesees 44 How to copy delete re
35. 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 chro matogram and click OK Curve name appearance You select options for the curve name appearance on the Curve Names tab This is 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 Result Chromatogram name Number given automatically duringarunora 11 name defined by the New_Chromatogram instruction Curve name Curve type for example detection ofaneluted UV component How to choose curve name appearance You can choose to view only part of the curve name The table below describes how to do this Step Action a Open a result file 2 Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed 3 Click the Curve Names tab 86 PrimeView 5 31 User Manual 28 9972 43 AA 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 Step Action 4 e Select the appropriate boxes for Curve name appearance e Select the appropriate Curve legend position e Click OK Note It is usually sufficient to select the Curve Name option if onl
36. 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 Minimum distance between points 132 The Minimum distance between points is a measure of the distance between the 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 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 3 How to optimize the baseline with a morphological algorithm Zoomed C PrimeView 5 31 User Manual 28 9972 43 AA 133 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm 8 4 Introduction How to optimize the baseline with a classic 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 classical algorithm What is the Classic algorithm The Classic algorithm searches for all parts of the source curve that are longer than a defined minimum baseli
37. Open Result dialog box PrimeView 5 31 User Manual 28 9972 43 AA 45 4 Files and folders in PrimeView 4 2 How to open and preview files 4 2 Howto 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 result file The table below describes how to open result files in the Evaluation module Step Action 1 46 e Choose File Open Result or e Click the Open icon Result The Open Result dialog box opens Open Result B x Prev Folder Result File 2002 04 24 08 46 Result File 2002 04 24 08 51 Result File 2002 04 24 08 52 a Example Result004 Result File 2002 04 24 08 51 ai ExampleResult GFOO1 Result File 2002 04 24 08 41 ai ExampleResult GF002 Result File 2002 04 24 08 35 PrimeView 5 31 User Manual 28 9972 43 AA 4 Files and folders in PrimeView 4 2 How to open and preview files Step Action 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 How to use Quick View The table below describes how to preview result files in Quick View Step Action al Select a result
38. Press the OK button Result The Templates menu is displayed PrimeView 5 31 User Manual 28 9972 43 AA 5 How to perform method runs 5 1 How to start a method run Step Action 2 e Choose the Method template menu e Press the OK button Result The first method template is displayed 5 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 4 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 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 PrimeView 5 31 User Manual 28 9972 43 AA 57 5 How to perform method runs 5 1 How to start
39. See Section 8 6 How to edit the peaks on page 147 See Section 8 7 How to integrate part of a curve and how to exclude or skim peaks on page 157 Peak integration results The peak table is displayed underneath the active chromatogram The start point 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 Primenew Evaluation Example ReswOOirt v UNICORN Local il Nklas result iDcample Result002 example Result0di res i be hy No Retention min Width min Area mAU min Height maU 0 75 62 1651 337 439 44 0967 275 224 60 5619 351 079 115 9646 472 670 169 208 9306 201 7053 0 912141 124 PrimeView 5 31 User Manual 28 9972 43 AA Note 8 Peak integration 8 2 How to perform a peak integration Peak tables can be copied from one chromatogram to another with the Ed it 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 How to display peak characteristics The peak retention times and several other peak characteristics are calculated automat ically The table below describes how to
40. a method run How to run a saved method The table below describes how to run a saved method on the AkKTAprime unit All param eters are selected with the arrow buttons on the unit The selections are confirmed with the OK button Step Action 1 e Choose the Run Stored Method menu e Press the OK button Result The Run Stored Method menu is displayed 2 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 5 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 How to run the system manually 58 The table below describes how to run the AKTAprime unit manually All parameters 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 PrimeView 5 31 User Manual 28 9972 43 AA 5 How to perform method runs 5 1 How to start a method run Step Action To edit the method base press OK and select the base with the arrow buttons Proceed to select parameters with the arrow buttons in the subsequent menus and press OK to continue After the last parameter selection
41. ake chro matogram layout changes general 85 How to optimize the chro matogram workspace 81 How to set a reference point 82 How to start the Evaluation module 74 Evaluation logs How to export 117 F Files and folders How to copy 51 How to move 51 Folders How to create 45 L Logbook How to display an overlay in the chromatogram win dow 83 How to display an overlay in the Curves pane in PrimeView 69 Logbook pane Autoscroll function 71 Description 71 How to filter the con tents 71 Search function 72 M Manual runs How to run the system manually 58 191 Index 192 Measurements How to make direct 164 Method runs Logbook pane descrip tion 71 Methods How to run a saved method 58 Method templates How to start a run 56 Morphological algorithm Definition 168 Description 129 How to set 129 ncorrect structure width 131 Minimum distance between points 132 oise window 132 Structure width 130 P Peak integration Differences between to filter peaks and to reject peaks 126 How to display peak la bels 127 How to perform 123 How to select part of a curve for peak integra tion 158 Peaks Drop lines description 152 Edit integration for part of a curve 161 How to add a fill color and pattern 150 How to add peak names 154 How to delete a peak 150 How to display peak la bels 127 How to exclude before inte gration 159 How to filter fr
42. alley 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 e 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 PrimeView 5 31 User Manual 28 9972 43 AA 159 8 Peak integration 8 7 How to integrate part of a curve and how to exclude or skim peaks Drop line How to skim peaks 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 2 Determine the ratio when peak skimming should be applied based on the relationship in the illustration below hp hy gt skim ratio hp2 hy Note The default ratio value is 10 5 Type the ratio value in the text box 160 PrimeView 5 31 User Manual 28 9972 43 AA 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 Part of a curve can be selected in the Edit Peak Table dialog box and integrated
43. am Layout icon opens the Chromatogram Layout dialog box which is used to select and format curves and display items in the chromatogram PrimeView 5 31 User Manual 28 9972 43 AA 17 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 3 Search functions 2 2 3 Search functions Introduction 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 Search the Folder list The search will take place in the displayed folder only To select another folder click the Browse button and open the desired folder Search the Result list e The search will take place in all result files within the 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 Lex will search only 4 character names that end with iex Search the Chromatogram list The asterisk indicates that all chromatograms with
44. areas EXPORT_TEST_RE SULT_TO_FILE Finishes the current result and saves the output file as an ASCII file in a destination and with a file name specified in the variable DestFilename txt A complete search path may be incluede in the file name GRADIENT_TEST_IN TERVALS Sets the level intervals for the GRADIENT_TEST GRADIENT_TEST The theoretical straight line between the 0 and 100 levels are calculated The deviation between the curve and the ideal straight line is compared in both directions from the center position 50 until the deviation exceeds the defined maximum deviation The calculated deviation points are checked against the defined limits STEP_RESPONSE_IN TERVALS Sets the level intervals for the STEP_RESPONSE_TEST STEP_RE SPONSE_TEST The relative amplitude is calculated at the specified retentions The 0 and 100 amplitudes are used for reference The calculated relative amplitudes are checked against the specified error margins The 0 level amplitude is verified to be within the specified interval from the absolute 0 level TEST_CURVE_AMPLI TUDE_CHANGE Verifies that the curve amplitude has changed more than or equal to the value of the Delta parameter between the de fined to and from retention points A print parameter may be set to On to generate printed results TEST_CURVE_AMPLI TUDE_STABLE Verifies that the curve amplitude is stable between the de fined
45. ast 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 e The curve parts are lower than the Max baseline level This parameter determines the highest acceptable signal level for the baseline Baseline parameters The baseline parameters can be illustrated as a rectangular box that the source curve has to fit into in order to be identified as a baseline segment where e The length of the box corresponds to the Shortest baseline segment e The height of the box corresponds to the maximum level of noise on the baseline segments This is referred to as the Noise window e The box is allowed to be tilted with a maximum slope corresponding to the Slope limit e The box is not allowed to move up above the Max baseline level PrimeView 5 31 User Manual 28 9972 43 AA 169 A Evaluation functions and instructions A 1 Baseline calculation theory Baseline parameters illustration The illustrations below shows the baseline parameters graphically Shortest baseline segment C _ Noise Window Max baseline level Slope limit 170 PrimeView 5 31 User Manual 28 9972 43 AA A Evaluation functions and instructions A 1 Baseline calculation theory Baseline segment identification The table below describes the baseline segment identification process Stage Description 1 The bo
46. ble below contains a list of instructions for file operations Instruction Description CURVE_OPEN Opens the curve specified in the Result file defined in File name and stores it in target curve position If is entered as File name the current result file will be used The File name param eter may include a path from the users root folder IMPORT_CURVE Imports a curve to the current chromatogram from another chromatogram in the current file and stores it in the target curve position IMPORT_PEAK Imports a peak table to the current chromatogram from another TABLE chromatogram in the current file and stores it in the target curve position PEAK Opens the specified Peak table in the Result file defined in File TABLE_OPEN name and stores it in the Resulting peak table If is entered as File name the current Result file will be used The File name parameter may include a path from the current users root folder PrimeView 5 31 User Manual 28 9972 43 AA 181 A Evaluation functions and instructions A 3 Procedure instructions Export The table below contains a list of instructions for export operations Instruction Description EXPORT_CURVE_AIA Exports the curve in AIA format EXPORT_CURVE_ASCII Exports the Source curve to the file defined in Export to File in ASCII format If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name
47. chromatograms PrimeView 5 31 User Manual 28 9972 43 AA 75 6 How to view results 6 2 Basic presentation of chromatograms 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 these topics Section See page 6 2 1 Introduction and temporary chromatograms 77 6 2 2 The chromatogram window 79 76 PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 2 Basic presentation of chromatograms 6 2 1 Introduction and temporary chromatograms 6 2 1 Introduction and temporary chromatograms Contents of a chromatogram 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 Temporary chromatograms 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 How to copy curves into Temporary Curves can be copied into Temporary and compa
48. ck and ch Find p t hf p PrimeView 5 31 User Manual 28 9972 43 AA 19 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 3 Search functions General information about searches The default setting is to search in all result files or chromatograms User entered search filters to a maximum of 10 will be saved in the drop down 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 automat ically saved and stored within user profiles Click All to return to the default setting to search in all result files or chromatograms 20 PrimeView 5 31 User Manual 28 9972 43 AA 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 4 Help functions 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 F1 key The Help menu e By choosing the Help menu item from the Help menu in each module you can access the Help file e By choosing the Manuals menu item from the Help menu in each module you can access the installed manuals in PDF format The illustration below shows the Help menu of the Evaluation module Help t Help For Evaluation About The Help file The table below describes how to open and use the Help file St
49. ck the Select icon e press and hold the Ctrl key while you click the objects to move the selected click on the objects hold down the left mouse button and object s drag the objectis to the new position to resize the selected click one of the object border anchors either in the corners object s or in the middle of a border and drag the box to the new size Note Some Text objects cannot be resized Alignment toolbar icon functions 106 Objects can be placed in exact positions and sized in relation to other objects The table below describes the function of the Alignment toolbar icons in the Report Editor Toolbar Function icon Align left IE Matches the left alignment of all selected objects to that of the highlighted am object Align right gt Matches the right alignment of all selected objects to that of the highlighted gt object PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 5 How to create and print a customized report Toolbar Function icon Align top RF Matches the top alignment of all selected objects to that of the highlighted object Align bottom 4 4 Matches the bottom alignment of all selected objects to that of the highlight O ed 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 B Adjusts the selecte
50. computer to tum off this device t Aligw this device to wake the computer Only allow a magic packet to wake the computer Waming F this is a laptop computer and you run it using battery power allowing the network adapter to wake the computer could drain the battery more quickly t might also cause the laptop to become very hot f t wakes up while packed in a camying case 6 e Choose the Power Management tab e uncheck the Allow the computer to turn off this device to save power option and e click the OK button 7 Close all dialogs PrimeView 5 31 User Manual 28 9972 43 AA 41 3 Software Installation 3 4 Windows 7 post installation settings Restore UAC After the PrimeView installation is completed follow the instruction below to restore the UAC setting to the default state Step Action 1 e Click the Windows Start button and e Choose the Control Panel 2 Click the Systems and Security heading 3 Under the heading Action Center click the Change User Account Control settings option gt Control Panel System and Security p Search Contro Panel Pp Control Panel Home Action Center System arid Security Review your computer s status and resolve issues tate rol setti Troubleshoot common computer problems Restore your computer to an earlier ti Pg Windows Firewall Check firewall status Allow a program through Windows Firewall Network and Internet Hardware and Sou
51. ction contains these topics Section See page 3 1 Preparations before installing PrimeView 5 31 on Windows 7 27 3 2 How to install PrimeView for the first time 30 3 3 Updating installations 36 3 4 Windows 7 post installation settings 37 26 PrimeView 5 31 User Manual 28 9972 43 AA 3 Software Installation 3 1 Preparations before installing PrimeView 5 31 on Windows 7 3 1 Preparations before installing PrimeView 5 31 on Windows 7 User Account Control on Windows 7 The User Account Control UAC feature in Windows 7 may cause problems during the PrimeView installation Due to this the UAC should be temporarily disabled before the installation However it is recommended that the UAC is restored immediately after the installation and system setup is completed This is described in Restore UAC on page 42 Disable UAC The table below describes how to disable the Windows 7 User Account Control feature Step Action 1 e Click the Windows Start button and e Choose the Control Panel 2 Click the Systems and Security heading PrimeView 5 31 User Manual 28 9972 43 AA 27 3 Software Installation 3 1 Preparations before installing PrimeView 5 31 on Windows 7 28 Step Action 3 Under the heading Action Center click the Change User Account Control settings option O gt Control Panel p system and Security s Search Controt Panel Control Panel Home System and Security Network and Internet Har
52. d object s to the right margin Adjust to center z Adjusts the selected objects to the center of the page Make same size object Make same width Adjusts the selected objects to the same width as the highlighted reference at Adjusts the selected objects to the same size as the highlighted reference object PrimeView 5 31 User Manual 28 9972 43 AA 107 6 How to view results 6 5 How to create and print a customized report Toolbar Function icon Make same height f 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 How to print the report The table below describes how to print the report Step Action 1 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 3 Click OK Note You can also print the report from the Generate Report dialog box 108 PrimeView 5 31 User Manual 28 9972 43 AA How to save the report format The table below describes Step Action 6 How to view results 6 5 How to create and print a customized report how to save the finished report format 1 e Choose File Save or e Click the Save icon Result The Save Report
53. dialog box opens e Click the Peak Window button Result The Peak window dialog box opens Leit PS aime pa OK caret He 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 3 Click OK Result The baseline will be calculated from the whole curve but the calcula tion of the peak areas is only performed on the selected section 158 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 7 How to integrate part of a curve and how to exclude or skim peaks How to exclude peaks 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 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 How to include negative peaks Select the Accept negative peaks checkbox of the Integrate dialog box to include neg ative 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 The area under a peak can be calculated either using separating drop lines or peak skimming e Drop lines are vertical marks that split two peaks at the v
54. display other peak characteristics Step Action 1 e Right click in the active chromatogram e Select Properties from the shortcut menu Result The Chromatogram Layout dialog box opens Click the Peak Table tab e Select options from the Select peak table columns list Result The selected items will be displayed in the peak table How to filter peaks from view Peaks can be removed from display in a peak table The table below describes how to filter the peaks Step 1 Action e Right click in the active chromatogram or peak table e Select Properties from the shortcut menu Result The Chromatogram Layout dialog box opens Click the Peak Table tab PrimeView 5 31 User Manual 28 9972 43 AA 125 8 Peak integration 8 2 How to perform a peak integration Step Action 3 e Click the check boxes in the Filter Peaks field to select the filter criteria e Specify filter values To filter peaks vs to reject peaks The table below describes the major differences in the effect of filtering peaks compared to excluding the peaks by rejection Filter peaks Reject peaks excludes the peaks from display permanently excludes peaks from the in tegration does not exclude the peaks from the excludes the peaks from the calculation calculation of the total peak area of the total peak area can be reversed cannot be reversed Peak labels Peaks can be labelled with their r
55. dware and Sound Programs User Accounts and Family Safety Appearance and Personalization Clock Language and Region Ease of Access PRE CS ER F Action Center Review your computer s status and resolve issues Chan count Troubleshoot common computer problems Restore your computer to an earlier ti Windows Firewall Check firewall status Allow a program through Windows Firewall System View amount of RAM and processor speed Check the Windows Experience Index Allow remote access Seethe name of this computer Device Manager Windows Update Turn automatic updating on or off Checkforupdates View installed updates Power Options Require a password when the computer wakes Change what the power buttons do Change when the computer sleeps Backup and Restore Back up your computer Restore files from backup Windows Anytime Upgrade Get more features with a new edition of Windows 7 Administrative Tools Free up diskspace Defragment your hard drive Create and format hard disk partitions View event logs Schedule tasks PrimeView 5 31 User Manual 28 9972 43 AA 3 Software Installation 3 1 Preparations before installing PrimeView 5 31 on Windows 7 Step Action 4 e Click and drag the slider control down to the position Never notify and e Click the OK button 3 Choose when to be notified about changes to your computer User Account Control helps prevent potentially harmful progra
56. e Result The selected part of the curve is peak integrated based on the changed parameters 162 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 8 Measurements 8 8 Measurements Introduction 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 Measurement options Coordinates can be obtained in two ways e Through direct measurement e From peak table data PrimeView 5 31 User Manual 28 9972 43 AA 163 8 Peak integrati 8 8 Measurements How to make direct on measurements The table below describes how to make direct measurements in a chromatogram Step Action i 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 uo uo 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 fu
57. e current default chromatogram a run time error will be caused OPEN_CHROM Opens the specified chromatogram from the specified file RENAME_CHROM Renames the specified chromatogram If is used as From then the current default chromatogram is used RESTORE_DESTINA Resets the destination for the subsequent curve and peak TION_ CHROM table operations to the default chromatogram Used in pair with the SET_DESTINATION_CHROM instruction SET_DESTINA Opens the named chromatogram as destination for the TION_CHROM subsequent curve and peak operations Used in pair with the RESTORE_ DESTINATION_CHROM instruction 186 PrimeView 5 31 User Manual 28 9972 43 AA Other instructions A Evaluation functions and instructions A 3 Procedure instructions The table below contains a list of instructions for other operations Instruction Description BASE Sets the X axis base that the following calculations will be made in If the value of the X axis base is DEFAULT then the default base is used usually the base the method was run in This instruc tion should be the first in the evaluation procedure otherwise it will have no effect at all Comment Inserts a comment below the marked instruction ENDLOOP Marks the end of a LOOP statement LOOP The instructions between this statement and the ENDLOOP statement are repeated n times It is possible to have loops within loops as long as the number of
58. e CD ROM or decompress the files 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 at tempt to decompress the files using any other file decompression utility Step 1 Insert the Setup CD Follow the instructions in the table below to begin the installation Step Action 1 For network installations log on to the network and check that you have access to the server disk and folder where the UNICORN network components are to be installed 30 PrimeView 5 31 User Manual 28 9972 43 AA 3 Software Installation 3 2 How to install PrimeView for the first time Step Action 2 e Insert the CD ROM disk into the CD ROM drive The PrimeView InstallShield Wizard should start automatically If not follow the applicable instruction in the table below If you are using Windows XP If you are using Windows 7 e click the Windows Start but e click the Windows Start button ton and select Run e Inthe Search programs and files e typethe command d set field type d set up where d up where d is the unit for is the unit for your CD ROM your CD ROM drive drive e click OK e Press the Enter key 3 The PrimeView 5 31 InstallShield Wizard is launched Continue with the setup below Step 2 Install prerequ
59. e PrimeView Evaluation module 2 2 2 The PrimeView Evaluation module Introduction The PrimeView Evaluation module provides extensive facilities to present and to evaluate curve data The module window Opened result files are displayed in the Evaluation module window See the illustration below G Prise ew vabselion Durple Ren ROH I v UNICORN Local if Nidan renit Cxarnple Renit brangia Rewet0 Lres Ei trarnele Ren AOH E VAPON Local A Nidar rend Example Result Exarple PersktoLres E A E a T T Samo UNAS y M 2 2 CC 19 wo w 16 PrimeView 5 31 User Manual 28 9972 43 AA 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 2 The PrimeView Evaluation module Toolbar icons in the Evaluation module The table below describes the toolbar icons in the module Icon Function Y The Open icon displays all available result files and result folders in the Open Result dialog box The Save icon saves the edited result file u Mp 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 TEE 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 Chromatogr
60. e after each change When the desired effect is ac complished it is best to go back and try a parameter value in between the two last settings to avoid an unnecessarily low or high 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 PrimeView 5 31 User Manual 28 9972 43 AA 135 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm Shortest baseline segment If a too high Shortest baseline segment value is set short curve segments between peaks in the middle of the chromatogram are not identified as baseline segments The calculated baseline does not follow the source curve see below The Shortest baseline segment value is decreased by 50 in this example 136 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm Slope limit 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
61. e 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 How to add a second Y axis The table below describes how to add a second Y axis to the chromatogram Step Action 1 Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed 2 Click the Y Axis tab e Select the appropriate curve from the Right Axis droplist e Click the OK button 90 PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 4 How to change and fix the axes How to change and fix the X axis The table below describes how to change and fix the X axis Step Action 1 Open a result file 2 Choose Edit 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 vol ume Thus switching the base between Time and Volume can slightly alter the resolution PrimeView 5 31 User Manua
62. e defined in Export to file If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in an swer to the question If all parameters to this function are OFF then no documentation is exported If at least one of them is ON then the documentation will be exported and the corresponding parts will be included in the export ed file EXPORT_DOC_WKS Exports the documentation in the current result file in WKS format to the file defined in Export to file If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in an swer to the question If all parameters to this function are OFF then no documentation is exported If at least one of them is ON then the documentation will be exported and the corresponding parts will be included in the export ed file EXPORT_DOC_XLS Exports the documentation in the current result file in XLS format to the file defined in Export to file If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question If all parameters to this function are OFF then no documentation is exported If at least one of them is ON then the doc
63. e 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 How to take Snapshots in the Evaluation module The table below describes how to take Snapshots in the Evaluation module Step Action 1 24 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 PrimeView 5 31 User Manual 28 9972 43 AA 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 5 Snapshots Step Action Click the Save to File button if you want to save the information as an Excel file xls or a tabbed text file txt 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 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 PrimeView 5 31 User Manual 28 9972 43 AA 25 3 Software Installation 3 Software Installation In this section This se
64. e name a full search path must be entered in answer to the question EXPORT_METHOD_ASCII Exports a method to the file defined in Export to file in ASCII format If is entered as File name the current Result file will be used If all parameters are OFF then no method is exported If Main is ON then the main method is included and if Blocks is ON then all blocks are included in the exported file 182 PrimeView 5 31 User Manual 28 9972 43 AA A Evaluation functions and instructions A 3 Procedure instructions Instruction Description EXPORT_METHOD_WKS Exports a method to the file defined in Export to file in WKS format If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question If all parame ters are OFF then no method is exported If Main is ON then the main method is included and if Blocks is ON then all blocks are included in the exported file EXPORT_METHOD_XLS Exports a method to the file defined in Export to file in XLS format If is entered as File name the current Re sult file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question If all parameters are OFF then no method is exported If Main is ON then the main method is included and if Blocks is ON then a
65. e options Sorted by Order Name Alphabetical order or reverse alphabetical 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 PrimeView 5 31 User Manual 28 9972 43 AA 49 4 Files and folders in PrimeView 4 3 How to arrange and locate your files How to change the sorting order Select one of the methods below to change the sorting order e Select View Sort and the option that you want or e 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 Note Only the currently active window is affected 50 PrimeView 5 31 User Manual 28 9972 43 AA 4 Files and folders in PrimeView 4 4 How to copy delete rename and backup files and folders 44 Howto copy delete rename and backup files and folders Introduction PrimeView has some file and folder handling functions that are slightly different from the general Windows functions This section focuses on the differences Note You need explicit authorization in your user profile to copy move and delete files How to copy or move files and folders There are some restrictions to how you can copy or move files and folders e Files and folders can only be copied or moved
66. e unit The selections are confirmed with the OK button Step Action 1 e Choose the Templates menu e Press the OK button Result The Templates menu is displayed PrimeView 5 31 User Manual 28 9972 43 AA 55 5 How to perform method runs 5 1 How to start a method run Step Action 2 e Choose the Application template menu e Press the OK button Result The first application template is displayed 3 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 Note If needed the sample volume should include the sample wash out volume AKTAprime method templates 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 How to start a method template run 56 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 con firmed with the OK button Step Action 1 e Choose the Templates menu e
67. eak is displayed Type a name in the Peak name textbox and click OK 154 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 6 How to edit the peaks How to adjust peak areas with drop lines The table below describes how to move the drop lines to adjust the peak area in the Edit Peak Table dialog box Step Action 1 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 2 Drag the bars to define the new limits for the selected peak Result The drop lines are moved and the peak areas are automatically re calculated Note A drop line can never be moved beyond another drop line or beyond a point where the peak meets the baseline How to use the zoom function 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 td Result The cursor is changed into a magnifying glass PrimeView 5 31 User Manual 28 9972 43 AA 155 8 Peak integration 8 6 How to edit the peaks Step Action 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 restore the full view The In
68. en 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 lt gt DEMO System Cortiol 1 Explorer t00 Method c Defauk Quoues _Example700002 E xampte7 m Dt Rosuh c Deloult Example7001 105 Fale ES Be Yew Houd Syten Heb Fun e oe ea i Gal a ami ice Block Volume Ace Time _ a a a a oe Cond cH SangleFow wi ns a Cord Come Pessue Pow Jef Sangeres Aint a00 AWeno ray 0 00 min Ruan started 1 58 min Pouse 1 68 min Cor nue Fox Help geess FI Orn Block I No waich Controlled By dolya Result The PrimeView module opens PrimeView 5 31 User Manual 28 9972 43 AA 61 5 How to perform method runs 5 2 How to monitor a method run 5 2 1 How to customize PrimeView panes Illustration The illustration shows the PrimeView module with the Curves and Logbook panes dis played Me Ven Help a C al mag UVi_2is Cond pH Pressure Temp cone EmN i min 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20 DOO ren Ran stented For Help prosa rt Rn Bek i i Jew ertsaed Dy prime How to select what panes to display 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
69. ep Action 1 Choose Help Index Result The Help file is displayed with the Index panel selected PrimeView 5 31 User Manual 28 9972 43 AA 21 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 4 Help functions Context sensitive help 22 Step Action 2 Search for topic in the Help Index Type a keyword you want help on in the text box in the panel Result The alphabetically closest matches are displayed in the list Select a match and click the Display button Result The associated help text is displayed in the right pane Search for topic using text search Click the Search tab Type one or more keywords you want help on in the keyword text box Result A number of topics containing the keywords are listed Select a match and click the Display button Result The associated help text is displayed in the right pane You can also click the Contents tab to view the contents of the Help file divided into sections Click the plus signs to expand the tree structure Click a topic to read the associated help text In each dialog box there is a Help button If you press that button either of the following will be displayed e Amessage box with relevant information for example the dialog box options e The Help file with relevant information displayed in the right pane PrimeView 5 31 User Manual 28 9972 43 AA 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 5 Snapshots 2 2 5 Snapsh
70. er 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 How to select curve pressure units 68 If the Pressure curve is displayed in the Curves 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 PrimeView 5 31 User Manual 28 9972 43 AA 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane How to edit text in the Curves pane You can select the way that text is aligned for the Logbook curves You can also select to show only part of the Logbook information The table below describes how to do this You can select the way that text is aligned for the Logbook and Fraction curves You 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 2 Select the Curve Style and Color tab 3 Select
71. es are copied into the open folder in the Open Results dialog box How to rename files and folders 52 The table below describes how to rename files and folders in the Open Results dialog box Step Action I Select the item that you want to rename PrimeView 5 31 User Manual 28 9972 43 AA 4 Files and folders in PrimeView 4 4 How to copy delete rename and backup files and folders Step Action 2 e Select File Rename or e Right click and select Rename from the shortcut menu Result The Rename dialog box opens 3 Type a new name 4 Click OK How to delete files and folders The table below describes how to delete files and folders in the Open Results dialog box Note Home folders cannot be deleted this way Step Action iL Select the item that you want to delete 2 e Select File Delete or 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 security Backup copies should be taken regularly to avoid data loss in the event of hard disk failure or accidental 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 PrimeView 5 31 User Manual 28 9972 43 AA 53 5 How to perform method runs 5 How to perform m
72. es or in the biochemical process industry PrimeView is a trademark of GE Healthcare Operating environment PrimeView 5 31 runs on a PC using the following operating systems e Microsoft Windows xP Professional 32 bit e Microsoft Windows 7 Professional 32 bit e Microsoft Windows 7 Professional 64 bit It is designed to run under English keyboard settings Windows functions Most Windows functions are also available in PrimeView including e cutand paste e right click short cut menus Note Drag and drop is not available File and folder handling in PrimeView also differ from the general Windows file manager standard 6 PrimeView 5 31 User Manual 28 9972 43 AA 1 Introducing PrimeView 1 1 About PrimeView Software modules The PrimeView control software consists of two integrated modules Function PrimeView System Control To monitor the separation processes online PrimeView Evaluation To evaluate and present stored results from separation processes Help functions An online help utility is included in the PrimeView software 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 or e press the F1 key on your keyboard Note An online version of the PrimeView User Manual is ava
73. etention 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 126 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 2 How to perform a peak integration Chromatogram Layout 1 01 id148Quantitate001 1_UV1_ 280nm 02 id1 48Quantitate001 1_U 2_Onm 03 id1 48Quantitate001 1_U 3_Onm 04 id 48Quantitate001 1_Cond 05 id1 48Quantitate001 1_Cond O6 id1 48Quantitate001 1_Cone OF 08 id 48Quantitate001 1_Pressure How to display peak labels The table below describes how to display peak labels Step Action 1 e Choose Edit Chromatogram Layout or e Click the Chromatogram Layout icon Result The Chromatogram Layout dialog box opens 2 Click the Curve Style and Colour tab PrimeView 5 31 User Manual 28 9972 43 AA 127 8 Peak integration 8 2 How to perform a peak integration 128 Step Action 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 Section 8 6 How to edi
74. ethod 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 The chapter contains these sections Section See page 5 1 How to start a method run 55 5 2 How to monitor a method run 60 54 PrimeView 5 31 User Manual 28 9972 43 AA 5 How to perform method runs 5 1 How to start a method run 5 1 Howto start a method run Before you start Before you start a method make sure that e the correct system is connected in control mode e the correct system for the method is selected in the system selector of the System Control module e the system is prepared according to the system user manual e the AKTAprime system is prepared according to the instructions in the AKTAprime system documentation Four ways to start an AKTAprime run 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 How to start an application template run Application templates are available for the most frequent purifications All process pa rameters except the sample volume are preset The table below describes how to start an Application template run on the AKTAprime unit All parameters are selected with the arrow buttons on th
75. ew button Result The Report Editor opens in Edit mode The Edit mode window The illustration below shows the Report Editor window in Edit mode with a blank report open PrimeView 5 31 User Manual 28 9972 43 AA 97 6 How to view results 6 5 How to create and print a customized report Toolbar button functions in the Report Editor 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 report and the Edit mode Next Page This button displays the next page or pair of pages where there are more than one page 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 magnification 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 How to add and delete report pages The table below describes how to add or delete report pages in the Report Editor If you want then to add new pages e click the Add Page toolbar button Result A new page i
76. ew concepts Introduction 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 terminology are not explained here In this chapter This chapter contains these sections Section See page 2 1 Concept definitions 10 2 2 The PrimeView user interfaces 12 PrimeView 5 31 User Manual 28 9972 43 AA 9 2 PrimeView concepts 2 1 Concept definitions 2 1 Concept definitions Introduction 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 Chromatogram Curves Method Result files 10 A chromatogram is a collection of data represented by a number of curves that have been created during a 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 an evaluation session The monitor signals from the run are displayed graphically as curves Note Log text entries and similar events from the run are treated as curve data in PrimeView even though they are not shown graphically as curves in the chromatogram The program ins
77. file The illustration below shows an example of the Logbook pane 0 00 min Mead Run 2003 12 01 14 4403 W Europe Standard Time Method Retut prime AT2003dec0 no001 RES Leabook 0 00 min Borch ID BEADESIS 767E 4005 A1 S4 BOFFSOFI BEES 0 00 min Bose Time O00minPeuse 0 02003 92 01 14 44 03 W Europe Standerd Time Menuet 0 00 min Eror 62 Chack thet tube positionis OK 0 00 min Concertration 0 B 0 00 min injection Valve Wasto 0 00 rnin Conmnue 2003 12 01 14 44 09 W Europe Standard Tine Manuo 0 00 min Flow 40 0 mljirin 0 87 min Broek point 2 0 87 min Flow 5 0 ralirin 0 89 min Injection Valve Load E04 min End 2003 12 01 144312 W Europa Standard Tima 5 04 nin Flow 0 0 nyinin 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 How to filter the logbook contents You can choose to display only selected items in the logbook The table below describes how to activate the filter Step Action i e Right click in the Logbook pane and choose Properties Result The Properties dialog box opens PrimeView 5 31 User Manual 28 9972 43 AA 71 5 How to perform method runs 5 2 How to monitor a method run 5 2 3 The Logbook pane Step Action Z e Choo
78. file in the Open Result dialog box 2 e Choose File Quick View or e Right click and choose Quick View from the short cut menu Result The Quick View dialog box opens prime Example Result001 res Example Result001 1_UV1_215nm Cancel Help PrimeView 5 31 User Manual 28 9972 43 AA 47 4 Files and folders in PrimeView 4 2 How to open and preview files Step Action 3 e Click the Next and Previous buttons to move between the result files if more than one is selected e Click the Open button Result The result file that is displayed in the dialog box opens in the Evalua tion module 48 PrimeView 5 31 User Manual 28 9972 43 AA 4 Files and folders in PrimeView 4 3 How to arrange and locate your files 4 3 Howto arrange and locate your files Introduction This section 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 modes You can choose how the files and folders are displayed in the Open Results dialog box The options are the standard Windows alternatives e Details e List e Large icons e Small icons How to change the view mode If you want to change the view you e Select View and the option that you want or 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 th
79. grate Calculate baseline function You can also click the Baseline settings button in the Integrate Peak integrate dialog box Morphological algorithm The Morphological algorithm searches for all parts of the source curve where 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 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 168 PrimeView 5 31 User Manual 28 9972 43 AA A Evaluation functions and instructions A 1 Baseline calculation theory Classic algorithm 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 e 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 l
80. gs 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 algo rithm settings A and a morphological algorithm with an increased Structure width value B PrimeView 5 31 User Manual 28 9972 43 AA 131 8 Peak integration 8 3 How to optimize the baseline with a morphological algorithm app 104 I VILIA omaro 10A I UVI ZION EASEC enn Tape IOA L UVI ISAM OS BASEME iz 98 1990 e00 p 194 1400 13 haco at joo i n 178 19 z 309 rad 000 3m C on 1214 200 k i ee LL a gt o B a g g wo wo wo 100 Hg Ey 220 mi Noise window 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
81. ides two curves to produce a third curve which is the quo tient of the two curves The two source curves can have any Y axis unit The threshold values are used to avoid division of numbers close to zero At those points where source curve 1 has an amplitude less than Threshold1 or the source curve 2 has an amplitude less than Threshold2 the result of the division is defined to be 1 0 Integration The table below contains a list of instructions for integration Instruction Description CALCULATE_BASE Calculates a baseline from the source curve The baseline is LINE stored in the target curve position DEFAULT can be selected in the Baseline parameters which will then calculate default baseline parameters for each new curve CALCULATE_BASE Calculates a baseline from the curve crvSrc using a morpho LINE_MORPH logical method DEFAULT can be selected in the Baseline parameters which will then calculate default baseline param eters for each new curve The baseline is stored in curve crvDst CLEAR_PEAKTABLE Clears the peak table in Peak table source from the computer memory COPY_PEAKTABLE Copies a peak table from Peak table source to Resulting peak table NEGATIVE_PEAKS Controls the baseline behavior in subsequent baseline calcu lations If ONOFF is ON then the baseline can be drawn above the curve and negative peaks can be detected by PEAK_IN TEGRATE If ONOFF is OFF then the baseline is never drawn abo
82. iew 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 recalculated for display in vol ume 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 displayed either in minutes or ml depending on the selected base e Adjust retention zero to injection sets the retention value to zero at the point of the first injection e Click OK How to switch between time and volume units e Click the legend of the X axis or 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 PrimeView 5 31 User Manual 28 9972 43 AA 67 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane How to zoom in the Curves pane 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 furth
83. ilable on the installation CD PrimeView 5 31 User Manual 28 9972 43 AA 7 1 Introducing PrimeView 1 2 About this manual 1 2 About this manual Introduction 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 Document structure 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 Typographical representations Menucommands field names and other text items from the software are quoted exactly as they appear on the screen in a bold italic typeface Search paths are shown in a bold italic typeface with a separating colon between each level 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 8 PrimeView 5 31 User Manual 28 9972 43 AA 2 PrimeView concepts 2 PrimeVi
84. in a result file will be selected Click Browse to select one or several specific chromatograms 18 PrimeView 5 31 User Manual 28 9972 43 AA Search the Curve name list 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 3 Search functions The UV curves are identified by number To search for all UV curves select UV in the Curve name text field Find a text string The Find command is used to search for text strings Find Ea Find what HK I Match whole word only T Match case T Search from top of document m Direction t i C Up ste Down 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 let ters Search from top of Select the check box to start the search from the top of document 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 3 ight click and choose Find previous to search for a previous occurrence Right cli
85. isite applications Before the actual PrimeView installation can begin a number of prerequisite applications must be installed if they are not previously installed The applications are available in the folder ISSetupPrerequistes on the installation CD but the installation will proceed automatically for each required application The applications are listed in the table below Note Some of these applications will require a restart of the computer before the installations can proceed This is noted in the table When installing on Then the following applications are required Windows XP e Microsoft Visual C 2008 Redistributable Package x86 e Microsoft Net Framework 2 0 e Windows Installer 4 5 for Windows XP SP2 and later x86 Restart required PrimeView 5 31 User Manual 28 9972 43 AA Si 3 Software Installation 3 2 How to install PrimeView for the first time When installing on Then the following applications are required Windows 7 32 bit e Microsoft Visual C 2008 Redistributable Package x86 e SetSystemPermissions Restart required Windows 7 64 bit e Microsoft Visual C 2008 Redistributable Package x64 9 0 30729 17 e SetSystemPermissions Restart required Note A version of Adobe Acrobat Reader is also distributed on the installation CD Step 3 License agreement and user information This table describes how to complete step 3 of the PrimeView i
86. l 28 9972 43 AA 91 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 Howto 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 layout The table below describes how to save a layout Step Action il 2 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 ap plied affects of a given configuration Return to the Chromatogram Layout dialog box to perform further changes e Select the Layout Library tab e Click the Save current layout as button Result The Save Layout dialog box is displayed e Type a name 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 Click OK 92 PrimeView 5 31 User Manual 28 9972 43 AA 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 How to apply a layout The table below describes how to apply a la
87. le in the Report title box and click the Font button to alter the default font if necessary PrimeView 5 31 User Manual 28 9972 43 AA 99 6 How to view results 6 5 How to create and print a customized report Step Action 5 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 6mp and smaller than 64 kB Larger logo files or files in other formats must be inserted as Picture objects 6 If you want to have a line under or over the header select the appropriate option in the Layout field y 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 infor mation between the header and footer as required 8 Click OK How to add objects to the report The table below describes how to add objects to the report The various objects are de scribed below this table 100 Step Action 1 e Click the appropriate icon in the Report items toolbar or e Choose an object from the Insert menu 2 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 dia
88. lect Split Peak from the shortcut menu or e Select Edit Split Peaks Result A new drop line is inserted at the middle point between the two ex isting 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 How to join peaks It is 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 il e Click the Edit peaks icon a e Click the peak in the curve or in the peak table to select the peak PrimeView 5 31 User Manual 28 9972 43 AA 153 8 Peak integration 8 6 How to edit the peaks Step Action 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 names The table below describes how to add names in the Edit Peak Table dialog box to iden tify the peaks Step Action 1 e Click the Edit peaks icon a e Click the peak in the curve or in the peak table to select the peak 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 retention of the selected p
89. line dialog box opens 2 e Click the Set Curve Points icon pco 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 chro matogram 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 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 5 How to edit the baseline manually Step Action 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 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 A 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 7 e Confirm the location and type a new name if necessary Result The new baseline is saved Edited baseline The illustration below is an example of a baseline before and after editing PrimeView 5 31 User Manual 28 9972 43 AA 145 8 Peak integration 8 5 How to edit the baseline manually How to draw a straight line The table below describes how to force a straight baseline between two points Step Action i Select the first of
90. ll blocks are included in the exported file EXPORT_MUL Exports multiple curves previously defined with EX TI_CURVES_ASCII PORT_SEL_CURVES instructions in ASCII format to the file defined in Export to file If is entered as File name the current Result file will be used If is entered fol lowed by text e g Enter a file name as File name a full search path must be entered in answer to the question EXPORT_MUL Exports multiple curves previously defined with EX TI_CURVES_WKS PORT_SEL_ CURVES instructions in WKS format to the file defined in Export to file If is entered as File name the current Result file will be used If is entered fol lowed by text e g Enter a file name as File name a full search path must be entered in answer to the question EXPORT_MUL Exports multiple curves previously defined with EX TI_CURVES_XLS PORT_SEL_ CURVES instructions in XLS format to the file defined in Export to file If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question EXPORT_NOR Normalizes retention when exporting multiple curves MALISE_RETENTION PrimeView 5 31 User Manual 28 9972 43 AA 183 A Evaluation functions and instructions A 3 Procedure instructions Instruction Description EXPORT_PEAK Exports the peak table in Peak table so
91. log box opens The dialog is specific to the type of item that you want to insert 3 Select the desired options and click OK Result The object is inserted onto the page PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 5 How to create and print a customized report Note If you want to edit an object later double click the object box How to add free text The table below describes how to add free text to the report Step Action 1 e Click the Free Text icon I 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 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 4 Click OK Result The text object is inserted onto the page PrimeView 5 31 User Manual 28 9972 43 AA 101 6 How to view results 6 5 How to create and print a customized report How to add a picture The Picture dialog box is useful to insert logos pictures or other image objects in the report The table below describes how to add a picture object to the report Step Action
92. ms from making changes to your computer Tell me more about User Account Control settings Always notify Never notify me when Programs try to install software or make changes to my computer a J Imake changes to Windows settings Not recommended Choose this only if you need to use programs that are not certified for Windows 7 0 because they do not support User Account Control Never notify 5 e Acknowledge the change in the pop up dialog e close the Control Panel and e proceed with the PrimeView installation as described in Section 3 2 How to install PrimeView for the first time on page 30 PrimeView 5 31 User Manual 28 9972 43 AA 29 3 Software Installation 3 2 How to install PrimeView for the first time 3 2 How to install PrimeView for the first time Installation prerequisites Before you start the installation procedure the following prerequisites have to be met The operating system must be correctly installed on your computer e Windows XP Professional 32 bit with service pack 3 e Windows 7 Professional 32 bit or e Windows 7 Professional 64 bit See the operating system documentation for details about the operating system instal lation Installation notes 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 Do not copy th
93. name and backup files and folders ss 111991151155115111511511101122 How to perform method runs 5 1 How to start a method TUN oe cceceecssssssssssseessssseesssseesssssesssssessnsssssssnsassasnesssnunsnnissnniisnniusnneesnee 5 2 How to monitor a method FUN eeeesssssssseesssssessssseesssssesssssessnsssesssssessnssnssssnnusnsnisnnntessnnssneeeseee 5 2 1 How to customize PrimeView panes i 522 The Curves p ne kirosennnieiaa iaa RRRA RE EA si 5 23 TING Logbook PaN ssnsesnusrisennan aieia AEAN How to view POS NG eire a eeta EEE 6 1 How to open a result file 6 2 Basic presentation of Chromatograms o cccssssssssessssscssecssssssssussesssssessssssssssssseesssseessesessssssseeses 6 2 1 Introduction and temporary Chromatograms eeessssssssssssssssssssssssssssssssssssssssssssssssssssssssssssstse 622 The hromatogram WINDOW samsimieneeneei inen a a aai 6 3 How to optimize the presentation of a ChromMatogram oecseecsscsssssssssssssemesssesecsessessssesees 6 3 1 How to make changes in the Chromatogram Layout dialog box ia 6 3 2 The Curve tab and Curve Names tab eeceeecesssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssset 63 3 The Curve Style and Color tab iasiieirisenininnianrananonannannaiihisaass 6 3 4 How to change and fix the AXES ceceeccsssssssssssssssssssccssssssssssssssssssesssssssssssnusesssssceessassssssssssessssseeeeeee 6 3 5 How to save and apply a layout uececcsssssssssssssssssssscs
94. navigate to the Start run menu Press the OK button Result The method runs starts Note Refer to the AKTAprime User Manual for instructions on how to select the param eters if needed How to finish the run Press the OK button to finish the run at the Method Complete prompt This will cause 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 PrimeView 5 31 User Manual 28 9972 43 AA 59 5 How to perform method runs 5 2 How to monitor a method run 5 2 Howto 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 60 The table shows the topics that can be found in this section Section See page 5 2 1 How to customize PrimeView panes 61 5 2 2 The Curves pane 64 5 2 3 The Logbook pane 71 PrimeView 5 31 User Manual 28 9972 43 AA 5 How to perform method runs 5 2 How to monitor a method run 5 2 1 How to customize PrimeView panes 5 2 1 How to customize PrimeView panes How to open the PrimeView module The PrimeView module displays the status of the AKTAprime 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 be
95. nction 164 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 8 Measurements How to set a reference point 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 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 be tween the reference point and the new position How to record a Snapshot The table below describes how to record a Snapshot of the current curve values Step Action 1 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 PrimeView 5 31 User Manual 28 9972 43 AA 165 8 Peak integrati 8 8 Measurements on How to select peak table data 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
96. nd Programs User Accounts and Family Saf Ba System pppesenreand View amount of RAM and processor speed Check the Windows Experience Index Personalization Allow remote access Seethename of this computer I Device Manager Clock Language and Region 8 Windows Update Ease of Access Turn automatic updating on or off Checkfor updates View installed updates B Power Options Require a password when the computer wakes Change what the power buttons do Change when the computer sleeps dia Backup and Restore Back up your computer Restore files from backup Windows Anytime Upgrade Get more features with a new edition of Windows 7 A Administrative Tools Free up disk space Defragment your hard drive Create and format hard disk partitions View eventlogs Schedule tasks 42 PrimeView 5 31 User Manual 28 9972 43 AA Step Action 3 Software Installation 3 4 Windows 7 post installation settings 4 e Click and drag the slider control up to the position Default Notify me only when programs try to make changes to my computer and e Click the OK button Choose when to be notified about changes to your computer User Account Control helps prevent potentially harmful programs from making changes to your computer Tell me more about User Account Control settings Always notify Default Notify me only when programs try to make changes to my computer Don t notify me when I make changes to Wi
97. nd how to exclude or skim peaks 157 8 8 MEGSUREMMS NES ccccsosscsasssasccossccpapvns ed ousavasbucecncetvepresdebsecoesey ncouedecbiyeyeasedcennenapestevessavnvilesteseabannstucecoatenenee 163 A Evaluation functions and instructions s sesssessssesessssessssessessesesesseseossssesessese 167 A1 B s line calculation th on sesssisicssssestassvasausdbesteethinvvvslacescbascssvstccsszassdb aAa 168 A 2 Peak table column components 173 A 3 Procedure INStrUCTIONS oo seesessseessssssesssssssssnssssssntssssntsssssnsesstsssssensssssnssseeseneceeeeeeeeceeeceneeeeceeeeceeeeeeeeeee 178 ut Ca a E E E E ater t tet prt eer nee tere tea tere rrr see 190 4 PrimeView 5 31 User Manual 28 9972 43 AA 1 Introducing PrimeView 1 Introducing PrimeView Introduction This chapter contains e Ageneral overview of the PrimeView software e nformation about the user documentation for PrimeView and how to use it In this chapter This chapter contains these sections Section See page 1 1 About PrimeView 6 1 2 About this manual 8 PrimeView 5 31 User Manual 28 9972 43 AA 5 1 Introducing PrimeView 1 1 About PrimeView 1 1 About PrimeView Introduction This section is a general overview of the PrimeView system What is PrimeView PrimeView 5 31 is a complete control software package for supervision of AKTAprime automated liquid chromatography systems Liquid chromatography is used in separation processes for analytical purpos
98. ndows settings Recommended if you use familiar programs and visit familiar websites Never notify 5 e Acknowledge the change in the pop up dialog and e close the Control Panel PrimeView 5 31 User Manual 28 9972 43 AA 43 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 This chapter contains these sections Section See page 4 1 How to create folders 45 4 2 How to open and preview files 46 4 3 How to arrange and locate your files 49 4 4 How to copy delete rename and backup files and folders 51 44 PrimeView 5 31 User Manual 28 9972 43 AA 4 Files and folders in PrimeView 4 1 How to create folders 4 1 Howto create folders How to create a new folder The table below describes how to create a new folder in the Evaluation module Step Action 1 e Select File Open or e Click the Open icon Result The Open Result dialog box opens 2 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
99. ne segment and fall within limiting parameters Together the parameter values define 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 parameters The parameters for the Classic algorithm are e Shortest baseline segment e Noise window e Max baseline level e Slope limit See more information about the parameters below How to set a Classic baseline 134 The table below describes how to set a Classic algorithm and define a baseline Step Action 1 Click the Baseline settings button in the Integrate dialog box Result The Settings dialog box opens PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm Step Action 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 Test your parameter changes The best way to optimize the baseline is to change the baseline parameters step by step and then check the resulting baselin
100. ned 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 PrimeView 5 31 User Manual 28 9972 43 AA Run curves shortcut menu 6 How to view results 6 2 Basic presentation of chromatograms 6 2 2 The chromatogram window 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 ful Peak Integrate Hatch Marker Marker Re et Mat apshot Copy to Clipboard Copy to Metafile Base Type aa Properties Optimizing the workspace 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 Arrange icons to arrange icons of minimized windows Window Tile to view several chromatogram windows side by side Window Cascade to stack the open windows like a deck of cards PrimeView 5 31 User Manual 28 9972 43 AA 81 6 How to view results
101. nstallation Step Action 1 e The Welcome dialog box is displayed e Click the Next button to continue 2 e The PrimeView Software License Agreement dialog box is displayed You must accept the license agreement to install PrimeView e Click the Next button to continue 3 e The Customer Information dialog box is displayed Type your name organization 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 32 PrimeView 5 31 User Manual 28 9972 43 AA 3 Software Installation 3 2 How to install PrimeView for the first time Step 4 Select Destination Folder In the Destination Folder dialog box you choose the folder where PrimeView will be in stalled The default destination folder is C UNICORN e If this is suitable click the Next button to proceed or e Follow the instruction below to choose another folder Step Action 1 Click the Change button to open the Change Current Destination Volume dialog 2 Select the destination volume where the program is to be installed This should be on a physical disk drive on the computer where you install PrimeView not on a network disk drive 3 e Click the OK button to continue e Click the Yes button if asked whether Setup should create the UNICORN program folder iz Prime iew 5 31 InstallShield Wizard Destination Folder Click Next to install
102. o create a baseline based on a blank curve e To use a Zero baseline e To reuse an existing baseline The Calculate baseline function 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 Baselines based on a blank curve A blank curve can be used as the baseline for peak integration e Youcan use a blank curve with the same chromatographic conditions as the corre sponding sample or e You can subtract the blank run from the source curve and then perform peak inte gration 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 PrimeView 5 31 User Manual 28 9972 43 AA 121 8 Peak integration 8 1 Baseline calculation Zero baseline To use a Zero baseline means that there is no baseline subtraction at all Reuse an existing baseline 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 122 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 2 How to perform a peak integration 8 2 Howto perform a peak integration How to perform a peak
103. om view 125 How to join peaks 153 How to open the peak ta ble 147 How to select a skim ra tio 160 How to split a peak 153 Include negative peaks in integration 159 Labels 126 Peak parameters 174 Peak skim Compared to drop lines 159 How to select a ratio 160 Peak table How to display informa tion 80 How to select contents 166 PrimeView module How to customize the panes 63 How to open 61 How to select the displayed panes 62 Procedure instructions Chromatogram func tions 186 Curve operations 178 Export functions 182 File operations 181 Integration 180 Miscellaneous 187 Test instructions 188 Q Quick View How to preview result files 47 R Rename files and folders 52 Reports Edit mode toolbar but tons 98 How to add documenta tion 104 How to add free text 101 How to add objects to a re port 100 How to add or delete pages 98 How to add picture ob jects 102 PrimeView 5 31 User Manual 28 9972 43 AA How to add the Evaluation log 105 How to change the page setup 99 How to create a blank cus tomized report 97 How to include a peak ta ble 103 How to include chro matograms 103 How to print 108 How to save the report for mat 109 Toolbar icons in Report Edit Mode 106 Result files How to open 46 How to save 118 S Searches General functions 18 Security Backup 53 Snapshots How to view 23 Software installation
104. on 8 6 How to edit the peaks Step Action 4 e Click OK Result The baseline is recalculated Note Select Baseline New Zero Baseline to replace the calculated baseline with a zero baseline The Edit Peak Table dialog box The illustration below shows the Edit Peak Table dialog box Q Edi Peak Table LIS Eie Edt Barsine Integrate Pjg i il Example esult003 1_UW Example 1esult 003 4_UV O1 BASEM PrimeView 5 31 User Manual 28 9972 43 AA 149 8 Peak integration 8 6 How to edit the peaks How to delete a peak The table below describes how to delete a peak in the Edit Peak Table dialog box Step Action 1 e Click the Edit peaks icon 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 renumbered How to add color to a peak The table below describes how to add a fill color and a pattern to a peak in the Edit Peak Table dialog box 150 Step Action 1 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 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 6 How to edit the peaks Step Action e Right click and select Fill Peak from the shortcut menu or e Select Edit Fill Peak
105. opes 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 cer 2 037 1 715 1 311 6 052 No Peak name Retention min Area mAU min Height mav 2 internal st 5 85 60 5051 336 828 2 Peak A 0 2 6 53 14 6032 95 761 fre B 0 2 7 06 20 4377 125 560 a loeser noa 77K ar amn 147 eral a 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 PrimeView 5 31 User Manual 28 9972 43 AA 139 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm Missing peaks 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 ALUA 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 In tegrate dialog box or Filter peaks in the Chromatogram layout dialog box 140 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm When to change the Max baseline level In rare cases the top of a broad flat peak can be incorporated as a baseline segment This is one of the very few situations where it is u
106. ots 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 Method Editor where Snapshot instructions can be inserted in a method to be recorded during the method run e the PrimeView module where you can take Snapshots during a run using the Marker e the Evaluation module where you can take Snapshots from a result file using the Marker How to take Snapshots during a method run The table below describes how to take Snapshots in the PrimeView module during a method run Step Action 1 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 2 Click the marker line and drag it to the desired point where you want to take a Snapshot 3 Right click in the Curves pane and select Snapshot in the menu Result The Snapshot is displayed in the Snap Shot dialog box PrimeView 5 31 User Manual 28 9972 43 AA 23 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 5 Snapshots Step Action e Click the Save to File button if you want to save the information as an Excel file xIls 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 Th
107. ow displayed in the entire chromatogram window together with appropriate scales for the Y and X axes 3 Use the arrow keys on the keyboard to move around in the chromatogram 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 94 PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 4 How to print active chromatograms 6 4 Howto print active chromatograms Introduction This section describes how to print the chromatograms that are open in the Evaluation module The Print Chromatograms dialog box This is an illustration of the Print Chromatograms dialog box Note The selected print format is outlined in red Print Chromatograms Instruction The table below describes how to print active chromatograms on the default Windows printer Step Action 1 Open all chromatograms that you want to print in the Evaluation module PrimeView 5 31 User Manual 28 9972 43 AA 95 6 How to view results 6 4 How to print active chromatograms Step Action 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 4 e Click OK to print or e Proceed with step 5 to preview and edit the layout 5 Click the Preview button Result The Customi
108. ow to view results 6 3 How to optimize the presentation of a chromatogram 6 3 3 The Curve Style and Color tab Step Action 4 e Select the curve you want to change from the list e Select the desired color and style e Click OK How to display a hatched background The table below describes how to display a hatched background in the chromatogram window Step Action 1 Open a result file 2 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 PrimeView 5 31 User Manual 28 9972 43 AA 89 6 How to view results 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 axes How to change and fix the Y axis The table below describes how to change and fix the Y axis Step Action 1 Open a result file 2 Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed 3 Click the Y Axis tab e Select the appropriate curve from the list e Click the Fixed option 5 e Type the desired minimum and maximum values e Clickthe All with this unit button if you want other curves with the same Y axis units as th
109. p Action 1 Choose File Export Curves Result The Export Curves dialog box opens Export Curves E Sasco chomiogarx Cake apa 201 125200101 1_UV1_200nm 1 x 02 125200101 1_U 2_250nm 403 125200101 1_U 3_Onm TOF 1252001 01 1 UVI 20m TOR 1252001 01 1 _UV2_250rm TOR 1252001 01 1 _UV3 na 104 1252001 01 1_Cond 05 125200101 1_ Conds 308 125200101 1_Cone 207 1252001 01 1_sH 08 1252001 01 1_Piessure 308 1282001 01 1_ Flew S10 126200101 1_ Teno Tie ovs Reduce number of sanger Thee Erom i m Reduce by factor ally Maxine samples 905 Io fis 3 m DITE C e e 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 3 Click the Export button Result The Export Curves to File dialog box opens 4 Select the export file format from the Save as type droplist e ASCII files asc e Excel files xls 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 116 PrimeView 5 31 User Manual 28 9972 43 AA 7 How to edit results 7 3 How to export results How to limit the exported curves 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 de
110. risons 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 PrimeView 5 31 User Manual 28 9972 43 AA 77 6 How to view results 6 2 Basic presentation of chromatograms 6 2 1 Introduction and temporary chromatograms Step Action 5 Click the Copy button Result The curve is copied into the Temporary chromatogram Click the Close button How to clear a temporary chromatogram 78 The table below describes how to clear the contents of a temporary chromatogram Step Action 1 Open the relevant result file 2 e Select Edit Clear Temporary Chromatogram e Click the Yes button to confirm PrimeView 5 31 User Manual 28 9972 43 AA 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
111. rs with explanations and calculation formulae when applicable Peak parameters illustration The diagram below illustrates the peak parameters See the parameter list below for explanations PrimeView 5 31 User Manual 28 9972 43 AA 173 A Evaluation functions and instructions A 2 Peak table column components Peak parameter descriptions The list below contains descriptions of the peak parameters Parameter Description 174 Area Calculated as the area between the curve and baseline be tween the peak start and peak end time or volume base Gray area in the diagram above Asymmetry Peak asymmetry indicator of column packing See definition below this table Baseline height Baseline amplitude at peak start peak maximum and peak end A F and G in the diagram above Fraction tube id Fraction number at peak start peak maximum and peak end Height Maximum amplitude above the baseline C F in the diagram above Plate height HETP 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 Peak endpoint heights Amplitude above the baseline at left A in the diagram above and right peak limits E G in the diagram above Peak endpoint reten tion Retention value at peak start and peak end time or volume base A and G in the diagram abo
112. s a dialog box opens with an option to save the changes before exit 2 Select Yes if you want to save the changes PrimeView 5 31 User Manual 28 9972 43 AA 119 8 Peak integration 8 Peak integration Introduction Peak integration is used to identify and measure a number of curve characteristics in cluding peak areas retention time and peak widths This chapter describes e How to perform peak integrations e How to optimize peak integrations In this section This section contains these sub sections Section See page 8 1 Baseline calculation 121 8 2 How to perform a peak integration 123 8 3 How to optimize the baseline with a morphological algorithm 129 8 4 How to optimize the baseline with a classic algorithm 134 8 5 How to edit the baseline manually 143 8 6 How to edit the peaks 147 8 7 How to integrate part of a curve and how to exclude or skim peaks 157 8 8 Measurements 163 120 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 1 Baseline calculation 8 1 Baseline calculation Introduction 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 Baseline options The Evaluation module offers several options for how to create an accurate baseline e To use the automatic Calculate baseline function e T
113. s added after the last page to delete a page while e select the page with Next Page or Prev Page in One Page mode e click the Delete Page toolbar button and confirm the deletion 98 PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 5 How to create and print a customized report If you want 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 The page layout is changed in the Page Setup dialog box The table below describes 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 2 e Type new values for the Margins if necessary e Select the appropriate Settings and Unit 3 e Click the First Header tab 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 is used for all subsequent pages e Select all the items you want to include in the header from the Select Items list e Click the Font button to change the font for all items if necessary 4 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 tit
114. s and instructions A 2 Peak table column components HETP formula The formula below is used to calculate the HETP value HETP L N N 5 54 x Vp Wp 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 wy peak width at half height expressed in the same units as Vp PrimeView 5 31 User Manual 28 9972 43 AA 177 A Evaluation functions and instructions A 3 Procedure instructions A 3 Procedure instructions Introduction This section contains lists of procedure instructions with descriptions These instructions are used in the Procedure Editor Choose Procedures Edit New in the Evaluation module to view the Instruction list Curve operation The table below contains a list of instructions for curve operations Instruction Description ADD Adds two curves to produce a third curve which is the sum of the two curves The two source curves must have the same Y axis unit and not be fraction or injection curves or else a run time error will occur AMP_MUL Multiplies the amplitude of the source curve by the multiplica tion factor and stores the result in the target curve position AMP_SHIFT Shifts the amplitude of the source curve by the shift factor and stores the result in the target curve position CLEAR Clears the specified curve from the working memory of the computer COPY Copies the source curve to
115. scribes how to use these editing options Dialog box option Instruction Cut curves Enter retention values in the text boxes to limit the curve to only a portion of the original curve Cut graphically This button opens the Export Cut dialog box Move the vertical markers to the correct cutoff points Reduce number of Adjust the factor value or the maximum number of sam samples ples To reduce the number of samples by a factor of five means that only every fifth point will be sampled for export Normalize retention Select the Normalize retention checkbox to have all ex ported curves normalized to a common x axis How to export documentation and evaluation logs The table below shows how to export documentation and evaluation logs Step Action 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 clipboard You can also use the Windows clipboard to copy the contents of the active window 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 PrimeView 5 31 User Manual 28 9972 43 AA 117 7 How to edit results 7 4 How to save results and exit the Evaluation module 7 4 Introduc
116. se 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 How to find logbook text entries The logbook can be searched for specific text entries The table below describes the 72 function Step Action 1 Right click in the Logbook pane and choose Find Result The Find dialog box opens 2 e Type the text you want to locate e Select search criteria if necessary e Click OK Result The located logbook entry is highlighted PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 Howto view results Introduction A result file is automatically generated at the end of a method run and contains a com plete record of the method run including method system settings curve data and method run log The Evaluation module offers 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 In this chapter This chapter contains these sections Section See page 6 1 How to open a result file 74 6 2 Basic presentation of chromatograms 76 6 3 How to optimize the presenta
117. seful to change the Max baseline level The illustration below is an example How to set the Max baseline level The table below describes how to set the 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 PrimeView 5 31 User Manual 28 9972 43 AA 141 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm Step Action 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 Example of a correct baseline The illustration below is an example of a correct baseline after the Max baseline level has been changed 142 PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 5 How to edit the baseline manually 8 5 How to edit the baseline manually The Edit Baseline dialog box 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
118. ssssssssssssssssssessssssssssssussssssscesssssssssssssessessseeeesee 6 3 6 How to show part of a CUIVE eececcsssssssssssssssssssssssssssssssssssssssssssssessesssssssususssssssceesssssssssssseesssseeeessee PrimeView 5 31 User Manual 28 9972 43 AA Table of Contents 6 4 How to print active Chromatograms aeeeccscsscsssssssssssssessssscsssssssssusssssssssesssssssssssssessessessecessssessseonees 95 6 5 How to create and print a customized report 97 6 6 RUM d c mentatioN aserne A ENN RR RUNN 110 T How to edit results ssc esscastasceicedescctbasdcanecanatnuiuccieatiaduess 7 1 Howto enter and edit text in the chromatogram 7 2 How to rename chromatograms GANA CULVES csssssssssssssccsscssssssssssusesseseccessssssssusesesseecesssenss 7 3 How to export results 7 4 Howto save results and exit the Evaluation module oe ceeeccsssssssssssessssessssssessssnsesssnsssssies 118 SMD 3 GL 8 2 1 eee nr E ne eee ne ee eee 120 8 1 Baseline calculations iaaiiai 121 8 2 How to perform a peak integration 123 8 3 How to optimize the baseline with a morphological algorithm cssssssseseesecsccccsseeessee 129 8 4 How to optimize the baseline with a classic algorithm oo ecsssssssssssssssssssesesscssscesssesssees 134 8 5 How to edit the baseline manually oo ccecccssssssssssssessessecssssssssusssessessecssssssssssssesseseesseessssessseesees 143 86 H Wwt editthepedkSiscarrssinninrinaumannei u a RA E 147 8 7 How to integrate part of a curve a
119. t results 115 7 4 How to save results and exit the Evaluation module 118 PrimeView 5 31 User Manual 28 9972 43 AA 111 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 How 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 Click where you want to insert text in the chromatogram Result A text box opens 3 Type the text 4 Click outside the text box to set the text How to edit the text The table below describes how to edit inserted text Step Action 1 Choose Edit Text Edit Result The Edit Texts tab of the Chromatogram Layout dialog box is dis played 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 de sired changes in the resulting dialog boxes 3 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 112 PrimeView 5 31 User Manual 28 9972 43 AA 7 How to edit results
120. t the peaks on page 147 for information about how to name the peaks e Retention Result The retention volume or time will be displayed e Click OK PrimeView 5 31 User Manual 28 9972 43 AA 8 3 8 Peak integration 8 3 How to optimize the baseline with a morphological algorithm How to optimize the baseline with a morphological 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 morphological algorithm The 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 to 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 How to set a Morphological baseline The table below describes how to choose a Morphological algorithm and define baseline settings Step
121. tegrate menu 156 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 See Section 8 7 How to integrate part of a curve and how to exclude or skim peaks on page 157 for more information PrimeView 5 31 User Manual 28 9972 43 AA 8 Peak integration 8 7 How to integrate part of a curve and how to exclude or skim peaks 8 7 How to integrate part of a curve and how to exclude or skim peaks Introduction There are several possibilities to improve the results if the peak integration is unsatisfac tory 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 PrimeView 5 31 User Manual 28 9972 43 AA 157 8 Peak integration 8 7 How to integrate part of a curve and how to exclude or skim peaks How to select part of a curve The table below describes how to select only a part of a curve for peak integration in the Integrate dialog box Step Action 1 e Choose Integrate Peak Integrate Result The Integrate
122. the last selected fraction If the source curve is not a fraction curve or First or Last is not an existing identi fication a run time error will occur LATE_PEAK_FRAC RET_MUL Multiplies the retention of the source curve by the Multiplication factor and stores the result in the target curve position RET_SHIFT Shifts the retention of the source curve by the Shift factor and stores the result in the target curve position SIMU Simulates Peak Fractionation SMOOTH_AR Smooths the source curve with an autoregressive filter and stores the result in the target curve position The Filter param eter decides the strength of the filter SMOOTH_MA Smooths the source curve with a moving average filter and stores the result in the Resulting Curve The Filter width param eter decides how many samples wide the filter is SMOOTH_MEDIAN Smooths the source curve with a median filter and stores the result in target curve position The Filter width parameter de cides how many samples wide the filter is SMOOTH_SG Smooths the curve with the Savitzky Golay algorithm SUB Subtracts two curves to produce a third curve which is the difference of the two curves The two source curves must have the same Y axis unit and not be fraction or injection curves PrimeView 5 31 User Manual 28 9972 43 AA 179 A Evaluation functions and instructions A 3 Procedure instructions Instruction Description TDIV Div
123. the target curve position CUT Cuts out the part of the source curve between the Left and Right limits and stores the result in the target curve position DERIVATE Differentiates the source curve first or second order and stores the result in the target curve position The Y axis of the target curve position will be a normalized scale without unit DIV Divides two curves to produce a third curve which is the quo tient of the two curves The two source curves can have any Y axis unit The Y axis of the target curve position will be a nor malized scale without unit 178 PrimeView 5 31 User Manual 28 9972 43 AA A Evaluation functions and instructions A 3 Procedure instructions Instruction Description HISTOGRAM Creates a histogram from any non fraction curve Source curve 1 and a fraction curve source curve 2_frac and stores the result in the target curve position If source curve 2 is nota fraction curve arun time error will occur The Y axis of the target curve position will be the same as that of the first source curve INTEGRATE Performs a mathematical integration of the source curve and stores the result in a Result curve This instruction is not the same as Peak integrate which performs a real peak integration POOL_FRACTIONS Pools fractions from the source curve and stores the result in the target curve position The fractions are pooled from the first selected fraction to
124. tings Step Action 4 Click Change plan settings for the selected power plan I Aor gt Control Panel System and Security Power Options p Search Control Pane Select a power plan Power plans can help you maximize your computer s performance or conserve energy Make a plan active by selecting it or choose a plan and custormize it by changing its power settings Tell me more about power plans Preferred plans Balanced recommended Change plan settings Automatically balances performance with energy consumption on capable hardware Power saver Change pian settings Saves energy by reducing your computer s performance where possible Show additional plans 5 e Choose the option Never for the setting Put the computer to sleep and e click the Save changes button Change settings for the plan Balanced Choose the sleep and display settings that you want your computer to use 38 PrimeView 5 31 User Manual 28 9972 43 AA 3 Software Installation 3 4 Windows 7 post installation settings Step Action 6 Close the Control Panel Disable the network interface card power save setting The table below describes how to disable the network interface card power save settings Step Action 1 e Click the Windows Start button and e Choose the Control Panel 2 Click the Network and Sharing Center heading Result The Network and Sharing Center opens ox 7 5E All Control Panel items
125. tion How to save results and exit the Evaluation module 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 unwanted curves All the curves that you created during your manipulations will be saved in the chro matogram If some of these curves are not be needed anymore select Edit Delete Curves in the Evaluation module to remove the curves Note The original curves that were created during the run can never be deleted How to save the results 118 You can either save your edited results in the original file or in a new result file The 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 select File Save or e click the Save toolbar icon e in a new result file 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 PrimeView 5 31 User Manual 28 9972 43 AA 7 How to edit results 7 4 How to save results and exit the Evaluation module How to exit the Evaluation module The table below describes how to exit the Evaluation module Step Action ak Choose File Exit Result If there are unsaved change
126. tion of a chromatogram 84 6 4 How to print active chromatograms 95 6 5 How to create and print a customized report 97 6 6 Run documentation 110 PrimeView 5 31 User Manual 28 9972 43 AA 73 6 How to view results 6 1 How to open a result file 6 1 How to open a result file How to start the Evaluation module 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 Evaluation icon on the Windows desktop Primeview Evaluation Result The PrimeView Evaluation module opens How to open a AKTAprime result file 74 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 y lay Result The Open Result dialog box opens e Select the result file and click OK Result All contents of the opened result file are transferred to the Evaluation module PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 1 How to open a result file 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 Section 6 2 Basic presentation of chromatograms on page 76 for further information about
127. tive 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 PrimeView 5 31 User Manual 28 9972 43 AA 103 6 How to view results 6 5 How to create and print a customized report Step Action 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 4 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 documentation The table below describes how to add documentation to the report Step Action 1 e Click the Documentation icon g 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 button Result The Setup Documentation dialog box opens
128. to calculate Sigma Sigmas gt 2 Xma i 1 A peak Where e nis the number of data points e xis the volume or time value Xymax S the volume or time value at the maximum amplitude value Apeak is the area of the peak Note The peak width for a Gaussian peak is 4 x Sigma Peak resolution algorithms The peak resolution is calculated with one of the following three algorithms 1 Veo Vra Wp Wpa 2 2 Vk2 Vex Sigma Sigma x 2 3 Veo Vea 2 x Who Wh 2 354 Where PrimeView 5 31 User Manual 28 9972 43 AA 175 A Evaluation functions and instructions A 2 Peak table column components Vre Wp1 Sigma and W are the retention width Sigma and width at half height of the previous peak Ves Wp Sigma and W are the retention width Sigma and width at half height of the current peak Capacity factor formula The formula below is used to calculate the Capacity factor k VR B Vi Vi Where e Vp retention volume e V total liquid volume Asymmetry formula 176 The formula below is used to calculate the Asymmetry 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 PrimeView 5 31 User Manual 28 9972 43 AA A Evaluation function
129. tructions for a run are defined in a Method The Method is programmed in the AKTAprime system The AKTAprime system creates Result files when a method is run The Result files contain e Run data from the monitors in the system Example UV absorbance flow rate conductivity etc e Documentation from the run Example Logbook entries settings text method etc PrimeView 5 31 User Manual 28 9972 43 AA 2 PrimeView concepts 2 1 Concept definitions e Saved results from evaluations of the run data Example Peak integrations etc Template Templates are basic methods that can be used as a starting point for developing cus tomized 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 PrimeView 5 31 User Manual 28 9972 43 AA 11 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 Note A user profile can be set up so that the user only has limited access to the modules described in this chapter Only the available modules will open when the program is started In this section This section contains these sub sections Section See page 2 2 1
130. umentation will be exported and the corresponding parts will be included in the exported file PrimeView 5 31 User Manual 28 9972 43 AA 185 A Evaluation functions and instructions A 3 Procedure instructions Instruction Description EXPORT_DOC_ASCII Exports the documentation in the current result file in ASCII format to the file defined in Export to file If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in an swer to the question If all parameters to this function are OFF then no documentation is exported If at least one of them is ON then the documentation will be exported and the corresponding parts will be included in the export ed file Chromatogram functions The table below contains a list of instructions for chromatogram functions Instruction Description COPY_CHROM Creates a copy of the specified chromatogram If is used as source then the current default chromatogram is used If is used as destination then a default name will be cre ated for the copy CRE Creates a new chromatogram with the given name If is ATE_NEW_CHROM used for the chromatogram name a default name will be generated and used Note It is a recommendation not to use only numbers as names for new chromatograms DELETE_CHROM Deletes the named chromatogram If trying to delete th
131. urce to the file TABLE_ASCII defined in Export to file in ASCII format If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question EXPORT_PEAK Exports the peak table in Peak table source to the file TABLE_WKS defined in Export to file in WKS format If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question EXPORT_PEAK Exports the peak table in Peak table source to the file TABLE_XLS defined in Export to file in XLS format If is entered as File name the current Result file will be used If is en tered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question EXPORT_PEAK Exports the peak table in Peak table source to the file TABLE_XML defined in Export to file in XML format If is entered as File name the current Result file will be used If is entered followed by text e g Enter a file name as File name a full search path must be entered in answer to the question EXPORT_SEL_CURVES Selects a curve for subsequent export using the EX PORT_MULTI CURVES_ instruction The curve is cut according to the right and left cut limit and the number of points to
132. ve Peak name Name of the peak Percent of total area 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 constant throughout the method Percent of total peak area 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 constant throughout the method Resolution Peak resolution See definition below this table Retention Retention at the peak maximum time or volume base C in the diagram above Sigma Standard deviation for a Gaussian shaped peak See definition below this table PrimeView 5 31 User Manual 28 9972 43 AA A Evaluation functions and instructions A 2 Peak table column components Parameter Description Type of peak limits Identifies the criteria for peak start and peak end as either the baseline intersection or dropline to the baseline or skim line Width Difference in retention between the peak end and peak start time or volume base G A in the diagram above Width at half height 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 displayed Sigma formula The formula below is used
133. ve whenever the created baseline goes above the source curve PrimeView 5 31 User Manual 28 9972 43 AA 171 A Evaluation functions and instructions A 1 Baseline calculation theory How to measure the baseline segment Classic algorithm You can try to measure the Shortest baseline segment length directly on your chro matogram 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 Use the marker box on the chromatogram to measure the length of the segment Choose Integrate Calculate Baseline and insert this value as the Shortest baseline segment value How to measure noise level Classic algorithm Curve coordinates can also be used to measure noise levels on the source curve The table below describes how to do this Step Action il Use the Zoom function to focus on a part of the curve that is representative for the baseline noise Select an appropriate Y axis scale Measure the Y axis coordinates e Calculate the noise range as the difference between the max and min values e Addanextra 20 e Choose Integrate Calculate Baseline and insert this value as the Noise window value 172 PrimeView 5 31 User Manual 28 9972 43 AA 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 paramete
134. ve the curve PEAK_INTEGRATE Performs a peak integration on the source curve and stores the resulting peak table in Resulting peak table It is assumed that the baseline is subtracted PEAK_WINDOW Specifies which part of the source curve that will be integrat ed Peaks between retention Left limit and Right limit will be detected if the ONOFF parameter is set to ON If ONOFF is set to OFF the whole curve will be used for integration 180 PrimeView 5 31 User Manual 28 9972 43 AA A Evaluation functions and instructions A 3 Procedure instructions Instruction Description REJECT_PEAKS Any combination of conditions is allowed If all parameters are OFF then every detected peak is included in the peak table SET_COL Sets the column height for the peak integration calculation UMN_HEIGHT of the HETP value The Column height parameter is the height of the column in centimetres If Column height is OFF then the HETP value is not calculated for the following inte grations SET_COLUMN_VO Sets void volume for Kav peak integration calculation SET_COLUMN_VT Sets the total liquid volume for peak integration calculation of the capacity factor SET_SKIM_SIZE_RA Sets the Skim size ratio to be used in the following peak in TIO tegration s WINDOW_PEAK_IN Integrates the curve within the peak window All curve parts TEGRATE outside the peak window remain unchanged File operation The ta
135. with settings that differ from the rest of the curve The table below 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 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 Q tdt Pesk Table gx Fie Edt Baselne Intoyate AREA Example FeO 1 vt 2160 Eeantle Rena DOr UVI EEDI PASEM 63 1658 3 Peak A 0 5 6 52 6 26 6 34 44 0967 3 Penk b 0 5 7 08 6 84 2 36 60 5619 4 Peak 0 5 774 7 36 3 68 115 5646 No penx pena Retention min peax start min Peak end min Area mA0rmin 4 Internal sti Note All operations described below will only affect the selected part of the curve PrimeView 5 31 User Manual 28 9972 43 AA 161 8 Peak integration 8 7 How to integrate part of a curve and how to exclude or skim peaks Step Action 3 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 Integrat
136. x is virtually moved along the source curve in steps of one third of the Shortest baseline segment length to look for baseline segments 2 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 segments provided that the slope of the joining lines does not exceed the Slope limit Baseline points Classic algorithm 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 points Note The baseline points are shown as green squares in the Integrate Edit baseline function of the Evaluation module Baseline drawing 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 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 nega tive peaks option is off the baseline will be forced down to the level of the source cur
137. y 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 4 Click OK PrimeView 5 31 User Manual 28 9972 43 AA 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane How to display a vertical marker line The table below describes how to display a vertical marker line Step Action 1 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 Section 2 2 5 Snapshots on page 23 for more information about the Snapshot function How to set a reference point 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 be tween the reference point and the new position
138. y one chro matogram is being evaluated However confusion can arise when more than one chromatogram is shown so more complete names might be necessary PrimeView 5 31 User Manual 28 9972 43 AA 87 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 The Curve Style and Color tab Introduction All curves within a chromatogram are represented by a default color and line style Curves imported into the chromatogram or newly created curves are automatically as signed a color and line style Peak label settings 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 Fraction text and Logbook text alignment settings 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 How to change the color and style of a curve 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 88 PrimeView 5 31 User Manual 28 9972 43 AA 6 H
139. yout Step Action 1 Select the Layout Library tab on the Chromatogram Layout dialog box 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 chromatogram window 3 If the same layout is to be applied to all chromatograms on the Evaluation workspace select the Apply to all chromatograms checkbox 4 Click OK PrimeView 5 31 User Manual 28 9972 43 AA 93 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 You can e use the zoom to magnify or e cut the axes It is also possible to fix the axes see Section 6 3 4 How to change and fix the axes on page 90 How to use the zoom function In the active chromatogram window you can zoom in on a designated area of the chromatogram This is the easiest and quickest way to enlarge different parts of a curve 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 n
140. ze Report window opens 6 e Click the Edit Mode button to make changes e g change the order of the chromatograms see Section 6 5 How to create and print a customized report on page 97 for more information about how to edit e Click the Preview button to return to preview mode 7 e Select File Print or e Click the Print toolbar icon Result The Print dialog box opens 8 e Select the print range and number of copies e Click OK 96 PrimeView 5 31 User Manual 28 9972 43 AA 6 How to view results 6 5 How to create and print a customized report 6 5 How to create and print a customized report Introduction 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 customized 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 How to open the Report Editor in edit mode The table below describes how to open the Report Editor in Edit mode to create a cus tomized report format Step Action 1 Open a result file in the Evaluation module 2 e Select File Report or e Click the Report icon a Result The Generate Report dialog box opens e Click the N

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