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Chromatography software

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1. e A general overview of the PrimeView system e Information about the user documentation for PrimeView and how to use it This chapter contains the following sections Topic See About PrimeView 1 1 About this manual 1 2 ep3 1 Introducing PrimeView 1 1 About PrimeView 1 1 Introduction What is Prime View Operating environ ment Windows func tions Help functions 03 0014 96 ep4 About PrimeView This section is a general overview of the Prime View system PrimeView is a complete control software package for supervision of AKTAprime automated liquid chromatography systems PrimeView runs on a PC under Microsoft Windows 2000 or Microsoft Windows XP It is designed to run under English keyboard settings Note Microsoft and Windows are registered trademarks of the Microsoft Corporation in the United States and or other countries Most Windows functions are also available in PrimeView including e cut and paste e right click short cut menus Note Drag and drop is not available File and folder handling in PrimeView also differs from the general Windows file manager standard An online help utility is included in the PrimeView 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
2. 03 0014 96 e p14 Field Match whole word only Search from top of docu ment Direction Description Select the check box if you only want complete string matches not partial matches Select the check box if you only want matches which correspond according to upper case and lower case letters Select the check box to start the search from the top of the document otherwise the search will start from the cursor position Choose whether to search upwards or downwards in the document Commands Use the commands below to find more occurrences of a text string after you have found the first one e Press F3 to search for the next occurrence of the string or right click and choose Find next e Right click and choose Find previous to search for a previous occurrence The default setting is to search in all result files or chromatograms e 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 automatically saved and stored within user profiles e Click All to return to the default setting to search in all result files or chromatograms PrimeView concepts 2 2 2 4 Help functions Introduction There are different ways to get help and instructions in PrimeView e From the Help menu in each module e From t
3. Result The PrimeView Evaluation module opens The table below describes how to open a result file in the PrimeView Evaluation module Step Action e Select File Open or e Click the Open icon 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 Note By default the chromatograms in a run are shown as opened windows The chromatogram window on top is the active window There is also a minimized Temporary chromatogram window See 6 2 Basic presentation of chromatograms on page 49 for further information about chromatograms How to view results 6 6 2 Basic presentation of chromatograms Introduction This section describes how to access result files and optimize the presentation of a chromatogram and its curves via the Chromatogram Layout dialog box In this section This section contains the following sub sections Topic See Introduction and temporary chromatograms 6 2 1 The chromatogram window 6 2 2 ep 49 6 How to view results 6 2 Basic presentation of chromatograms 6 2 1 Introduction and temporary chromatograms 6 2 1 Contents of a chromatogram Temporary chro matograms How to copy curves into Tem porary How to clear a temporary chroma togram 03 0014 96 ep50 Introduction and temporary chromatograms Chromatograms can be viewed in the Ev
4. Step Action Choose File Exit Result If there are unsaved changes a dialog box opens with an option to save the changes before exit Select Yes if you want to save the changes Result The result file is closed Introduction In this chapter Peak integration 8 Peak integration Peak integration is used to identify and measure a number of curve characteristics including peak areas retention time and peak widths This chapter describes e How to perform peak integrations e How to optimize peak integrations This chapter contains the following sections Topic Baseline calculation How to perform a peak integration How to optimize the baseline with a morphological algorithm How to optimize the baseline with a classic algorithm How to edit the baseline manually How to edit the peaks How to integrate part of a curve and how to exclude or skim peaks Measurements See 8 1 8 2 8 3 8 4 8 5 8 6 8 7 8 8 ep 87 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 Cal
5. Result The Templates menu is displayed e Choose the Application template menu e Press the OK button Result The first application template is displayed e Step through the list of application templates with the up or down buttons until the desired template is displayed e Press the OK button Result The Sample appl volume menu is displayed 4 e Set the sample volume with the up or down buttons e Press the OK button Result The Press OK to start run prompt is displayed e Press the OK button Result The purification run starts ep 33 5 How to perform method runs 5 1 How to start a method run Note If needed the sample volume should include the sample wash out volume AKT Aprime The four most common purification techniques are available as method templates 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 The table below describes how to start a method template run on the AKTAprime ae template nit 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 Templates menu e Press the OK button Result The Templates menu is displayed 2 e Choose the Method template menu e Press the OK button Result The first method template is displayed 3 e Step through the
6. 126 How to measure noise level 127 Curves How to copy into the Temporary chromatogram 50 Run curves default appearance 53 How to choose the Y axis scale 53 Default curve names 58 Peak labels 59 Fraction text alignment options 59 Logbook text alignment options 59 How to change the color and style 59 How to set a hatched background 59 How to change and fix the Y axis 61 How to add a second Y axis 61 How to change and fix the X axis 62 How to save a layout 63 How to apply a layout 63 How to use the zoom function 65 How to rename 81 Export options 82 How to export 82 How to export in AIA format 84 How to delete unwanted curves 86 Curves pane in PrimeView Description 40 03 0014 96 p ii How to display a vertical marker 40 How to set a reference point 40 How to change curve colors and styles 41 How to change scale of the Y axis 41 How to change scale of the X axis 42 How to zoom in regions of the pane 42 Reduce scale of zoom 42 How to select curve pressure units 43 How to select text alignment 43 How to display complete Logbook information 44 Delete files and folders 30 Documentation How to view 78 How to export 85 E Evaluation How to start the Evaluation module 48 Chromatogram window views 52 How to display peak table information 52 Chromatogram window shortcut menu 53 How to optimize the chromatogram workspace 54 How to display a vertical marker 54
7. Default button to restore the default values Shortest baseline If a too high Shortest baseline segment value is set short curve segments between segment peaks in the middle of the chromatogram are not identified as baseline segments The calculated baseline does not follow the source curve see below e p99 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm Slope limit 03 0014 96 ep 100 The Shortest baseline segment value is decreased by 50 in this example A changed Slope limit will often improve the baseline calculation The Slope limit sets the maximum slope of the curve to define when a peak is recognized A too high Slope limit will cause the up slopes of the peaks to be recognized as baseline segments The example above was improved by the shorter baseline segments but the high slope of the short segments in the region between the second and the fourth peak still makes the baseline unacceptable In the example below the Slope limit is increased by a factor of 2 5 which produces a correct baseline Peak integration 8 Too high slope A too high Slope limit value can cause peak limits too high up on the peaks This limit 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
8. How to set a reference point 54 How to make chromatogram layout changes general 57 How to exit the module 86 Evaluation logs How to export 85 F Files and folders Copy to external 29 How to copy from external 30 Folders How to create 25 Index e piii Index Installation Software 19 Prerequisites 19 Software license agreement 20 L Logbook How to display an overlay in the Curves pane in PrimeView 44 How to display an overlay in the chromatogram window 55 Logbook pane Description 45 Autoscroll function 45 How to filter the contents 45 Search function 46 M Manual runs How to run the system manually 36 Measurements How to make direct 121 Method runs Logbook pane description 45 Method templates How to start a run 34 Methods How to run a saved method 35 Morphological algorithm Description 94 How to set 94 Structure width 95 Incorrect structure width 96 Noise window 96 Minimum distance between points 97 Definition 124 03 0014 96 p iv P Peak integration How to perform 89 Differences between to filter peaks and to reject peaks 91 How to display peak labels 92 How to select part of a curve for peak integration 116 Peak skim Compared to drop lines 118 How to select a ratio 118 Peak table How to display information 52 How to rename 81 How to export 84 How to select contents 122 Peaks How to filter from view 91 Labels 92 How to display p
9. Integrate Edit Baseline to display the dialog box The Edit Baseline dialog box displays the baseline and the curve it was calculated from The baseline points are marked with green squares Hold the cursor above the baseline point to display its coordinates See the illustration below How to use the The table below describes how to use the zoom function in the Edit Baseline dialog zoom function bx Step Action e Click the Zoom icon Result The cursor is changed into a magnifying glass 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 03 0014 96 ep 106 How to edit and insert data points Peak integration 8 The table below describes how to edit and insert baseline data points Step 1 Action Select Integrate Edit Baseline Result If there are more than one baseline available the Select Baseline to Edit dialog box opens If not proceed to step 2 e Select the baseline you want to edit from the list e Click OK Result The Edit Baseline dialog box opens e Click the Set Curve Points icon Result The cursor is changed into a cross Add a data point e Click the left mouse button to place a new baseline point in the chromatogram Result A new point is created marked by a green square The baseline curve is red
10. PrimeView 4 2 How to open and preview files 4 2 How to open and preview files Introduction This section describes how to open your saved result files You can also preview your result files to identify the correct file before you open it saat ee a The table below describes how to open result files in the Evaluation module result file Action e Choose File Open Result or e Click the Open icon Result The Open Result dialog box opens e Double click the result file or e Select the result file and click the OK button Result The file is opened in the Evaluation module Quick View Quick View is a preview function for result files to make it easier to select the correct result file You can preview the first curve in the first chromatogram 03 0014 96 ep 26 Files and folders in PrimeView o to use Quick The table below describes how to preview result files in Quick View iew Step Action 1 Select a result file in the Open Result dialog box 2 e Right click and choose Quick View from the short cut menu Result The Quick View dialog box opens 3 e Click the Open button Result The result file that is displayed in the dialog box opens in the Evaluation module e p27 4 Files and folders in PrimeView 4 3 How to arrange and locate your files 4 3 Introduction Different view modes How to change the view mode Sort order How to change the sorting order 0
11. Select the appropriate object e Type anew name in the Name field e Click OK Note The original raw data curves cannot be renamed They will not be listed as options in the dialog box e p81 7 How to edit results 7 3 How to export results 7 3 Introduction Data formats Export options How to export curves 03 0014 96 ep82 How to export results This section describes how to export curves in different formats and how to copy data and curves to the clipboard You can export data in the following formats AIA cdf ASCII asc Lotus 1 2 3 wks Excel xls XML xml Select File Export in the Evaluation module to export data from an open result file The following export options are available Curves Export curve to AIA Peak table Documentation Evaluation log The table below describes how to export curves in the Evaluation module Step Action Choose File Export Curves Result The Export Curves dialog box opens How to limit the exported curves How to edit results 7 Step Action e Select the curve s you want to export e Enter parameters to limit the curve s if necessary e Click the Select button e Repeat Step 2 to select more curves Click the Export button Result The Export Curves to File dialog box opens Select the export file format from the Save as type droplist e ASCII files asc e Lotus 1 2 3 files wks e Excel fi
12. Step Action 1 Open the relevant result file How to view results 6 Step Action e Select Edit Clear Temporary Chromatogram e Click the Yes button to confirm epodl 6 How to view results 6 2 Basic presentation of chromatograms 6 2 2 The chromatogram window 6 2 2 The chromatogram window Main views The chromatogram window is divided into two main views e curves e peak tables The displayed areas for the views can be adjusted by dragging the borders with the mouse cursor between the views How to view peak The table below describes how to display peak table information if the result has table information been integrated Step Action Open a result file 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 03 0014 96 ep52 Run curves de fault appearance and information Run curves short cut menu How to view results 6 The first time a result file is opened and viewed a default layout is applied to display all the original curves The default layout can be changed by the user see 6 3 5 How to save and apply a layout on page 63 Information for each curve Each curve is automatically assigned a default col
13. chroma togram window e Ifthe same layout is to be applied to all chromatograms on the Evaluation workspace select the Apply to all chromatograms checkbox e Click OK 03 0014 96 ep 64 6 3 6 Introduction How to use the zoom function How to view results 6 How to show part of a curve You can select a part of a curve in order to examine details more closely It is also possible fix the axes see 6 3 4 How to change and fix the axes on page 61 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 Action Open a result file e Place the mouse pointer in any corner of the area you want to magnify e Press and hold the left mouse button A magnifying glass icon will be added to the mouse pointer arrow on the screen e Drag a box to cover the area to be magnified and release the mouse button Result The selected region is now displayed in the entire chromato gram window together with appropriate scales for the Y and X axes Use the arrow keys on the keyboard to move around in the chroma togram at the current zoom scale 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 e p65 6 Ho
14. color and style e Click OK The table below describes how to display a hatched background in the chromatogram window Step Action 1 Open a result file e p59 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 3 The Curve Style and Color tab Step Action e Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed 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 03 0014 96 ep60 6 3 4 How to change and fix the Y axis How to add a second Y axis How to view results 6 How to change and fix the axes 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 4 e Select the appropriate curve from the list e Click the Fixed option 5 e Type the desired minimum and maximum values e Click the All with this unit button if you want other curves with the same Y axis units as the current scaled curve to be similarly scaled Note The values will only be applied to existing curves They will not be applied to new curves created after this
15. e Release the mouse button Result The area is enlarged Right click and select Reset zoom to restore the full view If needed you can use the selections on the Integrate menu to perform a peak integration in the Edit Peak Table dialog box This is useful for example if you want to re integrate the curve using different settings or integrate only part of a curve with different settings See 8 7 How to integrate part of a curve and how to exclude or skim peaks on page 116 for more information ep1l15 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 unsatisfactory This section describes e How to select only part of a curve for integration e How to exclude peaks e How to skim peaks These operations can be performed both in the Integrate dialog box in preparation for the peak integration or in the Edit Peak Table dialog box to adjust an unsatisfactory peak integration This section describes both alternatives How to select part The table below describes how to select only a part of a curve for peak integration of a curve in the Integrate dialog box Step Action e Choose Integrate Peak Integrate Result The Integrate dialog box opens e Click the Peak Window button Result The Peak window
16. function was last used e Click the appropriate Pressure unit MPa psi bar option to change Y axis units for pressure curves e Click OK The table below describes how to add a second Y axis to the chromatogram Step Action Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed Click the Y Axis tab 3 e Select the appropriate curve from the Right Axis droplist e Click the OK button ep l 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 The table below describes how to change and fix the X axis and fix the X axis Step Action Open a result file Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed Click the X Axis tab Select the appropriate option in the Base field e Time of retention e Volume Note Some calculated curves for example baselines exist in only one base and might seem to disappear when the base is changed Curves are collected in time and recalculated for display in volume Thus switching the base between Time and Volume can slightly alter the resolution e Click the Fixed option in the Axis scale field to set the axis limits manually e Type the desired minimum and maximum values e Click OK 03 0014 96 ep6 2 How to view results 6 6 3 5 How to save and apply a layout Introduction
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18. have all information in either the header or footer or split informa tion between the header and footer as required e Click OK How to view results 6 How to add ob The table below describes how to add objects to the report The various objects jects to the report re described below this table Step Action e Click the appropriate icon in the Report items toolbar or e Choose an object from the Insert menu e Press and hold the left mouse button on the report page and drag out a box to the size of the item you want to insert Note The mouse pointer shows a symbol for the type of item you have selected e Release the mouse button Result A Setup dialog box opens The dialog is specific to the type of item that you want to insert 3 e Select the desired options and click OK Result The object is inserted onto the page Note If you want to edit an object later double click the object box How to add free The table below describes how to add free text to the report text Step Action e Click the Free Text icon 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
19. is complete at any time by pressing the End button 03 0014 96 p36 How to perform method runs 5 5 2 How to monitor a method run Introduction This section describes how to monitor a method run by using the PrimeView module and how to customize the different panes In this section This section contains the following sub sections Topic See How to customize PrimeView panes 5 2 1 The Curves pane 5 2 2 The Logbook pane 5 2 3 e p37 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 The PrimeView module displays the status of the AKTAprime system run The ee mod primeView module can be open on the Windows desktop before a run is started in which case it will either display a blank Curves pane or show the curves from the previous run The PrimeView module can also be opened after the run has been started in which case it will display the whole progress of the run from the beginning The list below describes how to open the PrimeView module e Click the PrimeView icon Result The PrimeView module opens Illustration The illustration shows the PrimeView module with the Curves and Logbook panes displayed How to select The PrimeView module displays one or two panes for monitoring different aspects tie panes to dis of the run To select what panes to display either e click the Customi
20. 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 03 0014 96 ep 34 How to run a saved method How to perform method runs 5 Step Action 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 e Press the OK button at the Press OK to start run prompt Result The method runs starts The table below describes how to run a saved method on the AKTAprime unit All parameters are selected with the arrow buttons on the unit The selections are confirmed with the OK button Step 1 Action e Choose the Run Stored Method menu e Press the OK button Result The Run Stor
21. negative peaks are important 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 The table below describes how to set a Classic algorithm and define a baseline Step Action Click the Baseline settings button in the Integrate dialog box Result The Settings dialog box opens 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 Peak integration 8 Test your paramet The best way to optimize the baseline is to change the baseline parameters step by er changes step and then check the resulting baseline after each change When the desired effect is accomplished it is best to go back and try a parameter value in between the two last settings to avoid an unnecessarily low or 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
22. sufficient to select the Curve Name option if only one chromatogram is being evaluated However confusion can arise when more than one chromatogram is shown so more complete names might be necessary 03 0014 96 ep58 6 3 3 Introduction Peak label settings Fraction text and Logbook text alignment settings How to change the color and style of a curve How to display a hatched back ground How to view results 6 The Curve Style and Color tab All curves within a chromatogram are represented by a default color and line style Curves imported into the chromatogram or newly created curves are automatically assigned a color and line style Peaks can be labeled on the Curve Style and Color tab of the Chromatogram Layout dialog box Use a combination of the following labels e Retention the default label e sequential Number e user defined Peak name Both Fraction text and Logbook text can be set to the following alignment options e Vertical e Horizontal e Fly Over which sets text labels as hidden text that appears only when the cursor is carefully positioned over a fraction mark The table below describes how to change the color and style of a curve Step Action 1 Open a result file 2 Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed 3 Click the Curve Style and Color tab 4 e Select the curve you want to change from the list e Select the desired
23. view of the chromatogram window and select Add text from the menu or e Choose Edit Text Add e Click where you want to insert text in the chromatogram Result A text box opens e Type the text e Click outside the text box to set the text How to edit the The table below describes how to edit inserted text text Step Action Choose Edit Text Edit Result The Edit Texts tab of the Chromatogram Layout dialog box is displayed e Select the text that you want to edit and make the appropriate changes in the Selected text field e Click the Change text button or the Delete text button e Use the Font and Set Orientation buttons if needed and make the desired changes in the resulting dialog boxes e Click OK to apply the changes Shortcut option You can also right click outside the text box and select Edit Text Mode from the shortcut menu This activates all the text boxes in the chromatogram The list below describes how to edit the text e Click the text and type the new text e Click outside the text box to set the text 03 0014 96 ep80 7 2 Instruction How to edit results 7 How to rename chromatograms curves and peak tables The table below describes how to rename chromatograms curves or peak tables in the Evaluation module Step Action Choose Edit Rename and the relevant option Chromatogram Curve or Peak Table Result The Rename dialog box opens 2 e
24. 3 0014 96 ep 28 How to arrange and locate your files 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 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 If you want to change the view you e Right click and select View and the option that you want from the shortcut menu The files can be sorted in different orders The table below shows the options Sorted by Order Alphabetical order or reverse alphabet ical order type Most recent creation dates first Select one of the methods below to change the sorting order 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 4 4 Introduction How to copy or move files and folders The function Copy to External How to Copy to External Files and folders in PrimeView 4 How to copy delete rename and backup files and folders PrimeView has some file and folder handling functions that are slightly different from the general Windows functions This section focuses on the differences If you copy a folder you will also at the same time cop
25. All configurations that you make in the Chromatogram Layout dialog box can be saved as a layout It is possible to apply saved layouts to other chromatograms All saved layouts are user specific How to save a The table below describes how to save a layout layout Step Action 1 Open a result file 2 Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed 3 Make the appropriate layout configuration within the various tabs View your changes Click OK if you want to return to the chromatogram window to see the applied affects of a given configuration Return to the Chromato gram Layout dialog box to perform further changes 4 e Select the Layout Library tab e Click the Save current layout as button Result The Save Layout dialog box is displayed 5 e Type 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 e Click OK ow toapplya The table below describes how to apply a layout ayout 1 Select the Layout Library tab on the Chromatogram Layout dialog box ep63 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 5 How to save and apply a layout 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
26. Snapshot functionality is available in the Evaluation module where you can take Snapshots from a result file using the Marker the PrimeView module where you can take Snapshots during a run using the Marker The table below describes how to take Snapshots in the Evaluation module Step Action e Open a result file in the Evaluation module e Right click and select Marker in the menu Result A vertical line indicating a certain point is displayed 2 Click the marker line and drag it to the desired point where you want to take a Snapshot Right click and select Snapshot in the menu Result The Snapshot is displayed in the Snap Shot dialog box e Click the Save to File button if you want to save the information as an Excel file xlS or a tabbed text file txt e You can also copy the information to the clipboard Click and drag the mouse in the table to select the information you want to copy Press CTRL C The information can now be pasted in a text editor e Click the Print button if you want to print the information e Click the Close button 1 Repeat steps 2 to 4 if you want to view more Snapshots How to view Snapshots during a method run PrimeView concepts 2 The table below describes how to view Snapshots in the PrimeView module during a method run Step 1 Action A method is running and the PrimeView module is running Right click in the Curves pane and select Mar
27. The Page Setup dialog box opens e p69 6 How to view results 6 5 How to create and print a customized report 03 0014 96 e p70 Step Action e Type new values for the Margins if necessary e Select the appropriate Settings and Unit Note An extra Header tab will appear if you de select the option to have the same header on all pages The First Header tab is used for the first page header only and the Header tab is used for all sub sequent pages e Click the First Header tab e Select all the items you want to include in the header from the Select Items list e Click the Font button to change the font for all items if necessary e Type header text in the Free text box and click the Font button to alter the default font if necessary e Type the report title in the Report title box and click the Font button to alter the default font if necessary e Select the Logo check box and click the Browse button if you want to locate and select a logo image file e Select the Alignment for the logo if necessary Note The logo file must be in bitmap format bmp and smaller than 64 kB Larger logo files or files in other formats must be inserted as Picture objects If you want to have a line under or over the header select the appro priate option in the Layout field e Repeat steps 3 to 6 on the Footer tab and the subsequent pages Header tab Note All Header and Footer tabs contain the same options You can
28. View for the first time Step 2 License This table describes how to complete step 2 of the PrimeView Setup Program agreement and user information Step Action The Welcome dialog box is displayed Click the Next button to continue The PrimeView Software License Agreement dialog box is displayed You must accept the license agreement to install PrimeView Click the Yes button to continue 3 e The User Information dialog box is displayed Type your name company and the product serial number of the software The serial number can be found on the License Agreement that is shipped with the CD e Click the Next button to continue Poe Select the You must define the COM port which the AKTAprime system is connected to ort p e Select the appropriate COM port e Click the Next button to proceed 03 0014 96 ep 20 Software Installation 3 Step 4 Select In the Select Drive dialog box you choose the installation folder for the PrimeView software Drive Follow the instructions in the table to select a disk drive Step Action Select the disk drive where the program is to be installed This should be a physical disk drive usually C on the computer where you in stall PrimeView not a network disk drive e Click the Next button to continue e Click the Yes button if asked whether Setup should create the UNICORN program folder Note The UNICORN folder will contain all Prime View file
29. X axis and Y axis values are displayed at the top right corner of the pane Note Right click and select Snapshot to record the marker position values See 2 2 5 Snapshots on page 16 for more information about the Snapshot function The table describes how to set a reference point Step Action e Display a Marker in the Curves pane e Right click and select Set Marker Ref Point to define a reference point for the marker position 2 When the marker is moved from the reference point the X axis and Y axis values for the new position are displayed together with e the new position in relation to the reference point e the minimum maximum and average values for the curve interval between the reference point and the new position How to display the logbook over lay How to view results 6 The table below describes how to display the logbook entries as an overlay in the chromatogram Step Action 1 e Right 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 cu
30. a baseline calculation Description The baseline segments are defined The baseline points are selected The baseline is drawn 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 Integrate Calculate baseline function You can also click the Baseline settings button in the Integrate Peak integrate dialog box The Morphological algorithm searches for all parts of the source curve where 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 forma curve with a plateau The center point in the plateau formed by the horizontal line will be the data point for the baseline 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 The Classic algorithm searches for all parts of the source curve where The curve parts are longer than the Shortest baselin
31. age and drag out a box to the size of the chromatogram Release the mouse button Result The Setup Chromatogram dialog box opens Select which chromatogram s to insert from the Selected chromato gram s droplist e Active chromatogram inserts the chromatogram that currently is active in the Evaluation module e All chromatograms inserts all chromatograms that are open in the Evaluation module e 1 2 etc inserts the corresponding chromatogram 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 ep 73 6 How to view results 6 5 How to create and print a customized report Step Action e Click the Define button in the Layout field if you want to re define the layout of the chromatogram Result The Report Chromatogram Layout dialog box opens e Make the appropriate changes and click OK to return to the Setup Chromatogram dialog box Note The changes that you make will only affect the report and not the view of the chromatograms in the Evaluation module Click OK Result The chromatogram is inserted onto the page Note All curves can be de selected in the Report Chromatogram Layout dialog box leaving only the selected peak table s in the report How to add docu The table below describes how to add documentation to the report mentation Step Action e Click the Documentation
32. aluation module A chromatogram includes a number of curves that have been created during a method run such as UV conductivity pH fraction marks etc A chromatogram also contains the curves created and saved during an evaluation session The original raw data curves cannot be deleted or modified A Temporary chromatogram is essentially an empty chromatogram that is specific to the Evaluation module Information contained within a Temporary chromatogram is automatically saved from one evaluation session to the next but is not saved within the result files Curves can be copied into Temporary and comparisons or evaluations can be performed This is particularly useful if you do not want to clutter up your original chromatograms with a large number of curves It can also be used to keep blank run curves or curves to compare when you open different result files The table below describes how to copy curves into Temporary Step Action Open a result file Select Edit Copy Curves Result The Copy Curve dialog box is displayed Select a source chromatogram and a curve to be copied in the Source Chromatogram fields Select Temporary as the target chromatogram and a position for the new curve in the Target Chromatogram fields Click the Copy button Result The curve is copied into the Temporary chromatogram Click the Close button The table below describes how to clear the contents of a temporary chromatogram
33. ance between the data between points 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 e p 97 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm 8 4 Introduction What is the Clas sic algorithm Classic algorithm parameters How to set a Clas sic baseline 03 0014 96 ep 98 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 The Classic algorithm searches for all parts of the source curve that are longer than a defined minimum baseline 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
34. ard software end user license agreement Copyright Amersham Biosciences AB 2004 All rights reserved Table of Contents Table of Contents 1 Introducing Prime ViGW isi fiscevccs icaedets cormsassevnn st andeanccrens terse iteensessceasonncinlaoatinrenirnnentta 3 TAL ABOUT PRIMO VIGW suck cocee EE A E 4 1 2 Abo tthis man a lesena e a a a E a e tsi 5 2 Prime View CONO E D S a e a a a a eaaa araa E a Aa A aaa aa aaant 6 Zl Concept defiNitiONS eesi ecinneniirne arane e e E EAE T ETE E ee 7 2 2 The PrimeView user iNterfaCes cccccesssssseceeeeeeeeseeeeeeeeneessseeeeeeeeneesseeeeeeeeesennaaes 8 2 2 1 The PrimeView AOC UTE amuse tuinchaa caileaeah iota a tudaaed aac aan tens telia wasn onsunnatacecenausceste 9 2 2 2 The PrimeView Evaluation IMOOUIC icsxccccy snc Crnniy sine Senvenusy ined uweuiwerareuinrimecars 11 Zi Sa S6C PUNCU ON Sienose snes aie E EE R ERA EEE etd Raclinen nantes 13 22 aA TACUS OTACA ATOI NERE EE E E EE 15 2 A0 SNAPS hotsi a Gavan a N E a E E a 16 3 Software INSTAN ATION sco205 ate acaeisanccuarcast cstcawe cased cachcw saravasamtcuatstniasatargGarttuatcuenauaumeatace 18 3 1 How to install PrimeView for the first IMG sesessceacoureststcwrdrvaedudauaenterndeonwuta Wdvewate 19 4 Files and folders in Prim VieW ccccssssssseceeeeeeesseneeeeeeessesseeeeeeeeseesseeeeeeeeeenseaeeeeeeneees 24 4 1 How to create TOMES osetia cas estat anc auduntine sui waistectnnean vaste naga taheraaaea couiolns
35. 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 available on the installation CD 1 2 Introduction Document struc ture Typographical representations Introducing PrimeView 1 About this manual This section is a general description of the manual the contents and the pre requisites for the examples and instructions that are presented in the PrimeView User Manual The manual is divided into chapters Each chapter starts with a brief overview that presents the contents and the headings for the sections that the chapter contains Most sections begin with an introduction that summarizes the content Some sections are divided into sub sections A section is divided into blocks of information with separating lines The blocks are identified by a label in the margin This makes it easier for you to quickly scan a page to find the exact topic you are looking for Menu commands field names and other text items from the software are quoted exactly as they appear on the screen in a bold typeface Example Run Setup Search paths are shown in a bold typeface with a separating colon between each level 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 Connect
36. ck 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 Note The color of the Marker is the same as the selected curve Move the Marker with your mouse to display the peak data Click the curve name legend above the chromatogram to change to another curve Result The Y axis is changed to the one corresponding to the new curve Right click and select Marker again to de select the function e p 121 8 Peak integration 8 8 Measurements How to set a refer The table describes how to set a reference point ence point Step Action 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 between the reference point and the new position on i recorda The table below describes how to record a Snapshot of the current curve values napshot Step Action e Right click in the chromatogram and select Snapshot from the shortcut menu Result The Snaps
37. correct struc Too low settings ture width settings Noise window 03 0014 96 ep 96 Too low Structure width settings can result in a baseline that reaches too high up in the peaks of the curve Sometime a wider peak is not recognized because it contains a cluster of smaller peaks The Structure width is then set to a value according to the largest width of the identified narrower peaks and must be increased Too high settings Too high Structure width settings mean that narrower peaks especially in fluctuating curves are not properly followed This happens when an artifact in a curve is identified as the widest peak by the morphological algorithm and then is used to set the default Structure width value The illustration below is an example of baselines using the default morphological algorithm settings A and a morphological algorithm with an increased Structure width value B Sometimes you get too many peaks after the peak integration usually because noise on the baseline is erroneously detected as peaks The solution to this is to increase the Noise window parameter However this can result in peak limits too high up on the peak slopes Note You can also use the Reject peaks function in the Integrate dialog box to reduce the number of peaks based on the total number of accepted peaks or the minimum peak height Peak integration 8 Minimum distance The Minimum distance between points is a measure of the dist
38. culate baseline function e To create a baseline based on a blank curve e To use a Zero baseline e To reuse an existing baseline pee ey The Calculate baseline instruction provides automatic calculation of the baseline aseline function 1 most cases the measurement is very accurate The calculation can be performed using the Morphological algorithm or the Classical algorithm Baselines basedon A blank curve can be used as the baseline for peak integration a blank curve i sr e You can use a blank curve with the same chromatographic conditions as the corresponding sample or e You can subtract the blank run from the source curve and then perform peak integration on the resulting curve with the Calculate baseline instruction Note In addition to blank run curves it is also possible to select any curve from the current chromatogram as the baseline e g an edited baseline Zero baseline To use a Zero baseline means that there is no baseline subtraction at all aed an existing To reuse an existing baseline for the selected curve is the default alternative ASEE whenever there is an existing baseline available The option Correlated baseline is selected if this is the case 03 0014 96 e p88 8 2 Peak integration 8 How to perform a peak integration How to performa The table below describes how to perform a basic peak integration peak integration Step 1 2 Action Open a result file in the E
39. destination folder e Type a file name e Click OK How to export The table below describes how to export peak tables peak tables Step Action Choose File Export Peak Table Result The Export Peak Table dialog box opens e Select the source chromatogram and the peak table you want to export e Click the Export button Result The Export Peak Table to File dialog box opens Select the export file format from the Save as type drop list e ASCII files asc e Lotus 1 2 3 files wks e Excel files xIs e XML files xml e Select a destination folder e Type a file name e Click OK Note Peak tables are exported as text strings in ASCII format and numerical values in the Lotus 1 2 3 formats All possible columns in the peak table are exported 03 0014 96 e p84 How to export documentation and evaluation logs Copy to the clip oard How to edit results 7 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 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 tabl
40. dialog box opens 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 03 0014 96 ep116 How to exclude peaks How to include negative peaks Peak integration 8 Step Action 3 Click OK Result The baseline will be calculated from the whole curve but the calculation of the peak areas is only performed on the selected section You can define criteria to exclude peaks from integration The table below describes how to define peaks to be excluded in the Integrate dialog box Step Action Click the Reject peaks button Result The Reject Peaks dialog box opens 2 e Select the appropriate checkboxes and type values for height width and area e Define how many of the largest peaks you want to include e Click OK Select the Accept negative peaks checkbox of the Integrate dialog box to include negative peaks in the integration Result The negative peaks will be reported as negative areas in the peak table By default negative peaks are not included in the integration epll7 8 Peak integration 8 7 How to integrate part of a curve and how to exclude or skim peaks Peak skimming vs The area under a peak can be calculated either using separating drop lines or peak drop lines How to skim peaks 03 0014 96 e p118 skimming e Drop lines are vertical marks that split two peaks at the
41. e The Morphological algorithm does not work well if there are negative peaks or if quantitative data from negative peaks are important in the run Note The Morphological algorithm is the default baseline setting The table below describes how to choose a Morphological algorithm and define baseline settings Step Action Select Integrate Peak Integrate Result The Integrate dialog box opens Click the Baseline settings button in the Integrate dialog box Result The Settings dialog box opens e Select the Morphological algorithm e Change the Baseline parameters if necessary See more information about the parameters below this table e Click OK Note The same settings can be edited in the Calculate Baseline dialog box when a new baseline is created Choose Integrate Calculate Baseline to open the dialog box Peak integration 8 Morphological al The parameters for the Morphological algorithm are gorithm paramet i ers e Structure width e Noise window e Minimum distance between points Structure width Structure width determines the length of the straight line that follows the chromatogram The default 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 ep95 8 Peak integration 8 3 How to optimize the baseline with a morphological algorithm The
42. e columns that are selected in the spreadsheet will be copied e p85 7 How to edit results 7 4 How to save results and exit the Evaluation module 1 4 Introduction How to delete un wanted curves How to save the results How to exit the Evaluation mod ule 03 0014 96 ep 86 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 All the curves that you created during your manipulations will be saved in the chromatogram 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 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 e select File Save file or e click the Save toolbar icon in a new result file e select File Save as Note The previous version of the result file will be overwritten if you save the changes This cannot be reversed However the raw data curves remain unchanged The table below describes how to exit the Evaluation module
43. e curve with the same color as the axis markings To get the correct Y axis click the legend The table below describes how to fix the scale of individual curves Step Action 1 e Select View Properties Result The Properties dialog box is displayed e Select the Y axis tab 2 e Select the appropriate curve e Select Fixed and type a minimum and maximum range in the fields within the specified limits 3 Repeat step 2 for other curves if needed 4 Click OK ep4l 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane How to change The table below describes how to change the scale of the X axis the scale of the X axis Step Action e Select View Properties Result The Properties dialog box is displayed e Select the X axis tab Select the appropriate base Time or Volume Note Curves are collected in time and recalculated for display in volume Thus the resolution of the two bases may appear slightly different Select the appropriate Axis scale e Total will show the curves as far as they have come in the run e Window allows you to set the portion of the total pane to be dis played either in minutes or ml depending on the selected base e Click OK How to switch e Click the legend of the X axis between time and volume units or e right click and select Base Type to switch the display between time and volume units The run is controlled accordin
44. e segment This parameter determines the minimum length for a part of the source curve to be considered a possible baseline segment The curve has no point outside the Noise window The noise window is defined as a rectangular corridor parallel to the slope of the curve and centered on the first and last points within the currently inspected segment The slope is less than the Slope limit This limits the maximum slope of the baseline to differentiate baseline segments from peaks The curve parts are lower than the Max baseline level This parameter determines the highest acceptable signal level for the baseline Evaluation functions and instructions A Baseline paramet The baseline parameters can be illustrated as a rectangular box that the source crs 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 Baseline paramet The illustrations below shows the baseline parameters graphically ers illustration ep 125 A Evaluation functions and instructions A 1 Baseline calculation theory Baseline segment identification Baseline points C
45. eak labels 92 How to open the peak table 109 How to delete a peak 111 How to add a fill color and pattern 112 Drop lines description 113 How to split a peak 113 How to join peaks 114 How to add peak names 114 How to exclude before integration 117 Include negative peaks in integration 117 How to select a skim ratio 118 Edit integration for part of a curve 119 Peak parameters 128 PrimeView module How to open 38 How to select the displayed panes 38 How to customize the panes 39 Q Quick View How to preview result files 27 Index epv Index R Rename files and folders 30 Reports How to create a blank customized report 68 Edit mode toolbar buttons 68 How to add or delete pages 69 How to change the page setup 69 How to add objects to a report 71 How to add free text 71 How to add picture objects 72 How to include chromatograms 73 How to include a peak table 73 How to add documentation 74 How to add the Evaluation log 75 Toolbar icons in Report Edit Mode 76 How to print 77 How to save the report format 77 Result files How to open 26 How to save 86 S Searches General functions 13 Security Backup 31 Snapshots How to view 16 System Control module Description 9 T Templates How to start a run from an application template 33 How to start a run from a method template 34 Temporary chromatogram Description 50 03 0014 96 p vi Toolbar icons In the PrimeView modu
46. ed Method menu is displayed e Select System or PC e Press the OK button e Choose the method number e Press the OK button Result The Press OK to start run menu is displayed 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 e p35 5 How to perform method runs 5 1 How to start a method run How to run the The table below describes how to run the AKTAprime unit manually All parameters system manually are selected with the arrow buttons on the unit The selections are confirmed with the OK button Step Action e Choose the Manual Run menu e Press the OK button Result The Set Method Base menu is displayed e To edit the method base press OK and select the base with the arrow buttons e Proceed to select parameters with the arrow buttons in the sub sequent menus and press OK to continue e After the last parameter selection navigate to the Start run menu e Press the OK button Result The method runs starts Note Refer to the AKTAprime User Manual for instructions on how to select the parameters if needed How to finish the Press the OK button to finish the run at the Method Complete prompt This will a cause all valves to return to the default position 1 The run can be aborted before it
47. effect and be caused by the same situation often also in combination with a high Slope limit Peak limits are defined on peaks in the example below due to the high Slope limit The example below has a much lower Slope limit and a lower Noise window ep 101 8 Peak integration 8 4 How to optimize the baseline with a classic algorithm Noise window 03 0014 96 ep 102 Sometimes you get too many peaks after the peak integration usually because noise on the baseline is erroneously detected as peaks The solution to this is to increase the Noise window parameter However this can result in peak limits too high up on the peak slopes The illustration below is an example of noise detected as peaks A and the result of a second peak integration with an increased Noise window B Note You can also use the Reject peaks function in the Integrate dialog box to reduce the number of peaks based on the total number of accepted peaks or the minimum peak height Peak integration 8 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 All peaks are detected if the Noise window is decreased see example below Note Missing peaks can also be caused by improper settings for Reject peaks in the Integrate dialog box or Filter peaks in the Chromatogram layout dialog box ep 103 8 Peak integration 8 4 How to
48. efore you start the installation procedure the following prerequisites have to be met e The operating system Windows 2000 XP must be correctly installed on your computer See the operating system documentation for details Also notice the following e Youcan exit the installation at any point by clicking on either the Cancel button or the Exit button If you do this however the installation will be incomplete and the software cannot be used Installing a new version of the PrimeView software over an existing Prime View installation is no problem You do not have to uninstall the previous version before installing the new version PrimeView is supplied on a CD ROM Files on the CD ROM are compressed and cannot simply be copied onto the hard disk During the installation procedure the required folder structure is created on the hard disk and the files are decompressed Do not attempt to decompress the files using any other file decompression utility Follow the instructions in the table below to begin the installation Step Action 1 e Insert the CD ROM disk into the CD ROM drive The PrimeView Setup Program should start automatically If not e click the Windows Start button and select Run e type the command d setup where d is the unit for your CD ROM drive e click OK 2 The PrimeView Setup Program is launched Continue the setup be low e p19 3 Software Installation 3 1 How to install Prime
49. er of the pane Note Right click and select Snapshot to record the marker position values See 2 2 5 Snapshots on page 16 for more information about the Snapshot function How to set arefer When the vertical marker is displayed you can set a reference point to display ence point curve data The table describes how to set a reference point 03 0014 96 ep 40 How to change the curve colors and styles How to change the scale of the Y axis How to perform method runs 5 Step Action 1 e Display a Marker in the Curves pane e Right click and select Set Marker Ref Point to define a reference point for the marker position 2 When the marker is moved from the reference point the X axis and Y axis values for the new position are displayed together with e the new position in relation to the position of the reference point e the minimum maximum and average values for the curve interval between the reference point and the new position The Curves pane displays graphs for the selected curves in different colors The table below describes how to change the curve colors and styles Step Action 1 Select View Properties Result The Properties dialog box is displayed 2 Select the Curve Style and Color tab 3 e Select a curve from the Curve list e Select an appropriate color and style In most cases the Y axis is automatically scaled for each of the curves Values on the Y axis apply to th
50. es How to change the page layout How to view results 6 Toolbar button Prev Page One Page Two Pages Zoom In Zoom Out Add Page Delete Page Exit Function This button displays the previous page or pair of pages where there are more than one page This button toggles between single page view and pairs of pages view when there is more than one page This button increases the magnification of the view This button decreases the magnification of the view This button adds a blank page to the report This button deletes the current page from the report This button closes the Customize Report window The table below describes how to add or delete report pages in the Report Editor If you want to add new pages to delete a page while in One Page mode to delete a page in Two Page mode then e click the Add Page toolbar button Result A new page is added after the last page e select the page with Next Page or Prev Page e click the Delete Page toolbar button and confirm the deletion e select the page with Next Page or Prev Page e click an object on the page e click the Delete Page toolbar button and confirm the deletion 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
51. es and text strings in Prime View These functions can be used in several program modules dialog boxes and wizards The search will take place in the displayed folder only To select another folder click the Browse button and open the desired folder 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 3 iex will search files named iex gt iex will search all files with names that begin with iex xiex will search all files with names that end with iex iex will search only 4 character names that end with iex The asterisk indicates that all chromatograms within a result file will be selected Click Browse to select one or several specific chromatograms The UV curves are identified by number To search for all UV curves select UV in the Curve name text field The Find command is used to search for text strings Field Description Find what Type the text string you want to find ep13 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 3 Search functions General informa tion about searches
52. ess and hold the lt Ctrl gt key while you click the objects to move the selected object s click on the objects hold down the left mouse button and drag the object s to the new position to resize the selected click one of the object border anchors either in the object s corners or in the middle of a border and drag the box to the new size Note Some Text objects cannot be resized e p75 6 How to view results 6 5 How to create and print a customized report Alignment toolbar Objects can be placed in exact positions and sized in relation to other objects The icon functions table below describes the function of the Alignment toolbar icons in the Report Editor Tool Function bar icon Align left Matches the left alignment of all selected objects to that of the highlighted object Align right Matches the right alignment of all selected objects to that of the highlighted object Align top Matches the top alignment of all selected objects to that of the highlighted object E Align bottom E Matches the bottom alignment of all selected objects to that of the highlighted object Adjust to margins Stretches the selected object s to the left and right margins Adjust to left margin Adjusts the selected object s to the left margin a Adjust to right margin E Adjusts the selected object s to the right margin Adjust to centre Adjusts the selected object s to the center
53. ets aunnvates tome 52 6 3 How to optimize the presentation of a ChromatOgram ccssssssecceeeessessseeeeeeeeesseeees 56 6 3 1 How to make changes in the Chromatogram Layout dialog DOX c 0ceeeees 57 6 3 2 The Curve tab and Curve Names ta bined iin iets ae acted eaveaanntenaaues 58 6 3 3 The Curve Style and Color tab x victescncscanatan san venaetulaewtheiatstaswenantaavicnsevautwnaundays 59 6 3 4 How to change and fix the axes icccies seed sce des saec gcekss canedake Geeeeddes deisel Weds deanest 61 6 3 5 How to save and apply a lAVOUliisicuiesiencinuncntenedatevieuarenteuletlarterawesasdati laters 63 Table of Contents 6 3 6 How to show part of a CUIVE A siccterrgieriasigned isatevendnccaecatheresbammorbetsloabentiansedans 65 6 4 How to print active chromatogramsS sssssssrssrrersrrrrrerterrrrrtrerrsrrnrrsrrrrrreern 66 6 5 How to create and print a customized report sssssseresrrsrrrrrererrsrrsrrererrrrrerren 68 6 0 R n documentation issaraen en e e a e EE Te a ated 78 7 How to edit POSING soot cosieindarsiavcnadceschevnccisualgenmsvswsadsbenctenendinscateutiad anteondinceenbestearxintemtines 79 7 1 How to enter and edit text in the Chromatogram ccccccessecsseeseeeeeeeeereeenseeeenes 80 7 2 How to rename chromatograms curves and peak tables ccsceceeeeeeeeeeeeeeeeeees 81 Jor HOW to export results rissie a a a haere ale cea ancient 82 7 4 How to save results and exit the E
54. g to the time volume base defined in the current block regardless of the base in the curves display How to zoomin The table below describes how to zoom in on a selected region of the curve pane the Curves pane Step Action 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 Repeat the process for further magnification of selected areas How to zoom out To reduce the scale of the zoom right click in the Curves pane and select one of the following options 03 0014 96 ep 42 How to perform method runs 5 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 If the Pressure curve is displayed in the Curves pane you can set the displayed units e pee The table below describes how to do this Step Action 1 Right click in the Curves pane and select Properties in the displayed menu Result The Properties dialog box is displayed 2 Select the Y Axis tab 3 Select the Pressure curve and select the appropriate Pressure unit button Click OK How to edit text You can select the way that text is aligned for the Logbook and Fraction curves in the Curves pane You can also select to show only part of the Logbook information The table below describes how to do t
55. he context sensitive help in each dialog box e By pressing the lt F1 gt key The Help menu e From the Help menu in each module you can access the Help file The illustration below shows the Help menu of the Evaluation module The Help file The table below describes how to open and use the Help file Step Action 1 Choose Help Index Result The Help file is displayed 2 e Type a word you want help on in the text box in the left pane Result The closest matches are displayed in the list e Select a match and click the Display button Result The associated help text is displayed in the right pane 3 e You can also click the Contents tab to view the contents of the Help file divided into sections e Click the plus signs to expand the tree structure e Click a topic to read the associated help text Context sensitive In each dialog box there is a Help button If you press that button either of the ep following will be displayed e A message box with relevant information for example the dialog box options e The Help file with relevant information displayed in the right pane epl15 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 5 Snapshots 2 2 9 Introduction How to take Snapshots in the Evaluation mod ule 03 0014 96 ep16 Snapshots A Snapshot provides information about a method run at a certain point in time It contains monitor values at the selected point
56. his 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 the following e Logbook or Fraction curve in the Curve list as appropriate e Select the appropriate Logbook text alignment or Fraction text alignment option Horizontal Vertical Fly over displays the text if you place the mouse pointer over the generated mark Click OK ep 43 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane How to view the At some breakpoints there can be more logbook information than what is possible complete logbook o conveniently display in the Curves pane The additional information that is not information bes sock be 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 03 0014 96 ep 44 9 2 3 Introduction Illustration Autoscroll How to filter the logbook contents How to perform method runs 5 The Logbook pane All actions including method start and end base instruction method instructions and manual interventions such as Pause or Hold and unexpected conditions such as warnings and alarms are logged for every run with date time and current user name where a
57. hot dialog box opens 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 How to select The retention time and amplitude of any peak can be viewed directly in a peak peak table data table after an integration This data and more is selected in the Chromatogram Layout dialog box The table below describes how to select peak table data Step Action Click the Chromatogram Layout icon E Result The Chromatogram Layout dialog box opens 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 03 0014 96 ep 122 Evaluation functions and instructions A A Evaluation functions and instructions Introduction This appendix describes the functions that are implemented in the Evaluation module In this chapter This chapter contains the following sections Topic See Baseline calculation theory AG Peak table column components A2 e p 123 A Evaluation functions and instructions A 1 Baseline calculation theory A 1 Overall process Baseline segment definition Morphological al gorithm Classic algorithm 03 0014 96 ep 124 Baseline calculation theory The table below describes the overall process of
58. hromatogram Layout dialog box opens 2 Click the Peak Table tab 3 e Click the check boxes in the Filter Peaks field to select the filter criteria e Specify filter values e Click OK To filter peaks vs The table below describes the major differences in the effect of filtering peaks to reject peaks compared to excluding the peaks by rejection Filter peaks Reject peaks excludes the peaks from display permanently excludes peaks from the integration does not exclude the peaks from the calculation of the total peak area excludes the peaks from the calcula tion of the total peak area can be reversed cannot be reversed e p91 8 Peak integration 8 2 How to perform a peak integration Peak labels How to display peak labels 03 0014 96 ep92 Peaks can be labelled with their retention sequentially numbered or be marked with specific identification names See table below for an instruction on how to display peak labels The label type can be selected on the Curve Style and Colour tab in the Chromatogram Layout dialog box De select all label options to hide the labels e g for presentations The illustration below shows the Chromatogram Layout dialog box with the Curve Style and Colour tab opened The table below describes how to display peak labels 1 e Choose Edit Chromatogram Layout or e Click the Chromatogram Layout icon Result The Chromatogram Layout d
59. ialog box opens Click the Curve Style and Colour tab Peak integration 8 Step Action Select one or more of the following labelling options in the Peak label field e Number Result The peaks will be numbered sequentially e Peak Name Result Peak names will be displayed See 8 6 How to edit the peaks on page 109 for information about how to name the peaks e Retention Result The retention volume or time will be displayed e Click OK ep 93 8 Peak integration 8 3 How to optimize the baseline with a morphological algorithm 8 3 Introduction The Morphologic al algorithm How to set a Morphological baseline 03 0014 96 ep 94 How to optimize the baseline with a morphological algorithm The first choice when you want to optimize the peak integration is to change the baseline parameters This section describes how to optimize the baseline with a morphological algorithm The Morphological algorithm can be described as a line that follows the chromatogram parallel to the X axis Data points for the baseline are created whenever the line touches the curve and the points are joined at the end 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 baselin
60. icon L 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 Select the items to be included in the report e Select All includes all items in the report e Clear All removes all selections e If desired change the Fonts e Select if the documentation should start on a new page e If was selected make the necessary changes to the Base and Log book filter settings e Click OK Result The selected documentation items are inserted into the report 03 0014 96 ep74 How to add the Evaluation Log How to view results 6 The table below describes how to add the Evaluation Log to the report Step Action 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 2 e If desired change the Fonts e Select if the Evaluation Log should start on a new page e Click OK Result The Evaluation Log is inserted into the report How tomoveand The table below describes how to select move and resize objects freely resize objects freely If you want then to select a single object click the Select icon e click the object of interest to select several ob e click the Select icon jects e pr
61. ime or volume base A and G in the diagram above Name of the peak Peak area as a percent of the total area under the curve above the baseline Time or volume base Note This value can differ in time and volume base if the flow rate is not constant throughout the method Peak area as a percent of the sum of all integrated peaks Note This value can differ in time and volume base if the flow rate is not constant throughout the method Peak resolution See definition below this table Retention at the peak maximum time or volume base C in the diagram above Standard deviation for a Gaussian shaped peak See definition below this table ep 129 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 intersec tion or dropline to the baseline or skim line Difference in retention between the peak end and peak start time or volume base G A in the diagram above 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 dia gram above where BD bisects CF Sigma formula The formula below is used to calculate Sigma Where e nis the number of data points e x is the volume or time value Xymax is the vol
62. ion change ep5 2 PrimeView concepts 2 PrimeView 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 chromatography terminology are not explained here In this chapter This chapter contains the following sections Topic See Concept definitions The Prime View user interfaces 2 03 0014 96 ep6 2 1 Introduction Chromatogram Curves Method Result files Template PrimeView concepts 2 Concept definitions This chapter contains explanations and definitions of a number of PrimeView concepts that are used in this manual The concepts are organized in alphabetical order A chromatogram is a collection of data represented by a number of curves that have been created during a separation run including UV conductivity pH fraction marks etc The original raw data curves cannot be deleted or modified They can be used as a basis for evaluation procedures and subsequent creation of new curves A chromatogram can also contain curves that have been created and saved during an evaluation session The monitor signals from the chromatography run are displayed graphically as curves The program instructions for a run are defined in a Method The Method is programmed in the AKTAprime system The AKTA
63. ker in the menu Result A vertical line is displayed Click the marker line and drag it to the desired point where you want to take a Snapshot Right click in the Curves pane and select Snapshot in the menu Result The Snapshot is displayed in the Snap Shot dialog box 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 Repeat steps 2 to 4 if you want to view more Snapshots epl7 3 Software Installation 3 Software Installation Introduction The PrimeView software is normally pre installed by a Amersham Biosciences representative Follow the instructions in this chapter to install the program yourself if your system is not pre installed In this chapter This chapter contains the following section Topic See How to install Prime View for the first time 31 03 0014 96 ep18 3 1 Installation pre requisites Installation notes Upgrading a Prime View install ation Do not copy the CD ROM or de compress the files Step 1 Insert the Setup CD Software Installation 3 How to install PrimeView for the first time B
64. ks will then be renumbered and the peak values will all be recalculated How to open the The table below describes how open the peak table for editing The editing options vie for 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 integ ration 3 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 for the peak table 5 Confirm the name and location and click OK How to adjust the The baseline can be adjusted graphically see also 8 5 How to edit the baseline baseline manually on page 106 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 ep 109 8 Peak integration 8 6 How to edit the peaks Step Action 2 Perfor
65. lassic al gorithm Baseline drawing How to measure the baseline seg ment Classic al gorithm 03 0014 96 e p 126 The table below describes the baseline segment identification process Description The box is virtually moved along the source curve in steps of one third of the Shortest baseline segment length to look for baseline segments A baseline segment is found whenever the currently examined part of the source curve fits completely within the box The found baseline segments are joined by connecting adjacent seg ments provided that the slope of the joining lines does not exceed the Slope limit When the baseline segments have been defined and joined they are replaced by baseline points at the start and end of each segment The line between these is also filled with points Note The baseline points are shown as green squares in the Integrate Edit baseline function of the Evaluation module The baseline points are used to create the baseline curve using a spline interpolation The spline function ensures that the baseline curve is guided by the baseline points However the curve does not necessarily pass through the baseline points The baseline will be a smoothly curved function passing close to or through the points 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 base
66. le 10 Y Y axis How to choose the Y axis scale 53 Z Zero baseline Definition 88 Zoom function How to enlarge parts of a curve 65 Index ep vii
67. les xIs e AIA files cdf 5 e Select a destination folder e Type a file name and click OK Note Curves are exported as series of numerical coordinates that refers to the time volume and signal respectively You can optimize the exported curves to only the parts that you want to focus on in the Export Curves dialog box The table below describes how to use these editing options Dialog box option Instruction Enter retention values in the text boxes to limit the curve to only a portion of the original curve Cut curves Cut graphically This button opens the Export Cut dialog box Move the vertical markers to the correct cutoff points Reduce number of samples Adjust the factor value or the maxim um number of samples To reduce the number of samples by a factor of five means that only every fifth point will be sampled for export Normalise retention Select the Normalise retention checkbox to have all exported curves normalized to a common X axis ep 83 7 How to edit results 7 3 How to export results How to export The table below describes how to export curves in AIA format curves in AIA format Step Action Select File Export Export curve to AIA Result The Export curve in AIA format dialog box opens e Select the source chromatogram and the curve you want to export e Click the Export button Result The Export Curves to File dialog box opens e Select a
68. line and the source curve is small enough Choose Integrate Calculate Baseline If the Accept negative peaks option is off the baseline will be forced down to the level of the source curve whenever the created baseline goes above the source curve You can try to measure the Shortest baseline segment length directly on your chromatogram The table below describes how to do this Step Action 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 Evaluation functions and instructions A How to T Curve coordinates can also be used to measure noise levels on the source curve noise level Classic The table below describes how to do this algorithm Step Action 1 Use the Zoom function to focus on a part of the curve that is repres entative for the baseline noise 2 Select an appropriate Y axis scale 3 Measure the Y axis coordinates 4 e Calculate the noise range as the difference between the max and min values e Add an extra 20 e Choose Integrate Calculate Baseline and insert this value as the Noise window value ep 127 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 parameter
69. lt file This section describes e how to view and print the run documentation How to view and The table below describes how to view and print the run documentation print the run docu mentation Step Action Open a result file e Choose View Documentation in the Evaluation module or e Click the view Documentation icon El Result The Documentation dialog box opens e Click the Print button Result The Print dialog box opens e Select the documentation items you want to print and click OK Result The documentation is printed on the default Windows printer 03 0014 96 ep 78 How to edit results 7 7 How to edit results Introduction This chapter describes e how to edit the results that are presented in the Evaluation module e how to export results For more information about how to view results see chapter 6 How to view results on page 47 In this chapter This chapter contains the following sections Topic How to enter and edit text in the chromatogram How to rename chromatograms curves and peak tables How to export results How to save results and exit the Evaluation module e p79 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 e Right click the curves
70. m 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 integ ration if you want to be able to drag a data point to move the baseline above the curve How to calculate The baseline can be recalculated in the Edit Peak Table dialog box The table below a new baseline describes how to do this Step Action e Select Baseline New Calculate or e Right click and select New Calculate from the shortcut menu Result The Settings dialog box opens e Select an algorithm Morphological is default e Adjust the Baseline parameters as desired or e Click the Default Values button for the default values e Click OK Result The baseline is recalculated Note Select Baseline New Zero Baseline to replace the calculated baseline with a zero baseline 03 0014 96 ep110 Peak integration 8 The Edit Peak The illustration below shows the Edit Peak Table dialog box Table dialog box me todeletea The table below describes how to delete a peak in the Edit Peak Table dialog box pea 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 selec
71. me or time wy peak width at half height expressed in the same units as Vp A Application templates How to start a run 33 Baseline Calculation options 88 The Calculate function 88 Reuse existing 88 How to edit manually 107 How to adjust the baseline graphically 109 Definition of a segment 124 Parameters 125 BatchID Logbook illustration 45 Blank curve Calculate baseline based on 88 c Chromatogram Layout Curve tab 58 Default curve names 58 How to choose curve name appearance 58 The Curve Style and Color tab description 59 Chromatogram window Shortcut menu 53 How to optimize the workspace 54 How to display a vertical marker 54 How to display the Logbook overlay 55 Chromatograms Description 50 Temporary chromatogram 50 How to make layout changes general 57 How to change and fix the Y axis 61 How to add a second Y axis 61 How to change and fix the X axis 62 How to save a layout 63 Index epi Index How to apply a layout 63 How to print active chromatograms 66 How to add annotations 80 How to edit annotation text 80 How to rename 81 How to set a reference point 122 Classic algorithm Definition 98 Parameters 98 How to set 98 Shortest baseline segment 99 Slope limits 100 Noise window 102 Missing peaks 103 When to change the Max baseline level 104 How to set Max baseline level 104 Definition 124 How to measure baseline segments
72. nd to evaluate curve data The module win Opened result files are displayed in the Evaluation module window See the dow illustration below Toolbar icons in The table below describes the toolbar icons in the module the Evaluation module Icon Function The Open icon displays all available result files and result folders in the Open Result dialog box a The Save icon saves the edited result file The Print icon opens the Print Chromatograms dialog box The Report icon opens the Generate Report dialog box which is used to select a report format The View Documentation icon opens the Documentation dialog box which is used to view and edit the result documentation epll 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 2 The PrimeView Evaluation module Icon Function The Peak Integrate icon opens the Integrate dialog box which is used to select peaks to integrate in a modified peak table The Chromatogram Layout icon opens the Chromatogram Layout dialog box which is used to select and format curves and display items in the chromatogram 03 0014 96 p12 2 2 3 Introduction Search the Folder list Search the Result list Search the Chro matogram list Search the Curve name list Find a text string PrimeView concepts 2 Search functions This section describes the general search functions that can be used to locate for example chromatograms curv
73. o 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 re tention of the selected peak is displayed Type a name in the Peak name textbox and click OK 03 0014 96 ep114 How to adjust peak areas with drop lines How to use the zoom function The Integrate menu Peak integration 8 The table below describes how to move the drop lines to adjust the peak area in the Edit Peak Table dialog box Step Action 1 e Click the Edit peaks icon 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 automatic ally recalculated Note A drop line can never be moved beyond another drop line or beyond a point where the peak meets the baseline The table below describes how to use the zoom function in the Edit Peak Table dialog box Step Action 1 e Click the Zoom icon Result The cursor is changed into a magnifying glass 2 e Press and hold the left mouse button e Drag the cursor over the area you want to zoom in on
74. of the page Make same size Adjusts the selected objects to the same size as the highlighted refer ence object Make same width Adjusts the selected objects to the same width as the highlighted reference object Make same height Adjusts the selected objects to the same height as the highlighted reference object 03 0014 96 ep 76 How to view results 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 6 How to print the The table below describes how to print the report report Step Action e Choose File Print or e Click the Print icon Result The Print dialog box opens Note The report will be printed on the default Windows printer e Select the printing range e Select the number of copies e Click OK Note You can also print the report from the Generate Report dialog box How to save the The table below describes how to save the finished report format report format Step Action e Choose File Save or e Click the Save icon Result The Save Report Format dialog box opens e Type a name for the format Note The name for the default format will automatically be changed to DEFAULT e Click OK e p77 6 How to view results 6 6 Run documentation 6 6 Run documentation Introduction The full documentation for a method run is stored in the resu
75. ogram and automatically restart the computer ep23 4 Files and folders in PrimeView 4 Introduction In this chapter 03 0014 96 ep 24 Files and folders in PrimeView 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 This chapter contains the following sections Topic See How to create folders How to open and preview files How to arrange and locate your files How to copy delete rename and backup files and folders 44 4 1 Introduction How to create a new folder Files and folders in PrimeView 4 How to create folders This section describes how folders are organized in PrimeView and how to create a new user specific folder for the user s methods and results The table below describes how to create a new folder in the Evaluation module Step Action e Select File Open or e Click the Open icon Result The Open Result dialog box opens e Right click on an empty area of the dialog box e Select New Folder from the shortcut menu Result The Create New Folder dialog box opens 3 e Type a name for the new folder e Click OK Result The new folder is displayed in the Open Result dialog box ep25 4 Files and folders in
76. optimize the baseline with a classic algorithm When to change In rare cases the top of a broad flat peak can be incorporated as a baseline segment oe baseline This is one of the very few situations where it is useful to change the Max baseline level The illustration below is an example How to set the The table below describes how to set the Max baseline level Max baseline level Step Action Right click in the chromatogram and select Marker Result A vertical line is set in the chromatogram A text box in the top left corner of the chromatogram displays the X axis and Y axis values of the curve at the point where the vertical Marker line crosses the curve e Move the Marker with your mouse e Measure the height of the peak you want to exclude from the baseline Choose Integrate Calculate baseline e Select the Classic checkbox as the Chosen algorithm e Type anew value for Max baseline level Set the level slightly lower than the value that you measured in step 2 e Click OK 03 0014 96 ep 104 Peak integration 8 Example of a cor The illustration below is an example of a correct baseline after the Max baseline rect baseline level has been changed ep 105 8 Peak integration 8 5 How to edit the baseline manually 8 5 How to edit the baseline manually The Edit Baseline You can edit the baseline manually in the Edit Baseline dialog box in the Evaluation dialog box module e Select
77. or and style with default information about each curve displayed in the key above the curves This information includes e result file name e chromatogram name e curve name Choose the Y axis scale Each curve has a correspondingly colored Y axis To choose the appropriate Y axis scale e click on the Y axis until the desired scale is displayed or e click on the name of the curve When viewing curves in the Evaluation module you can access a menu that provides a quick alternative to menu commands Right click the run curves view to display the menu shown in the picture below ep 53 6 How to view results 6 2 Basic presentation of chromatograms 6 2 2 The chromatogram window Optimizing the workspace How to display a vertical marker line How to set a refer ence point 03 0014 96 ep 54 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 The table below describes how to display a vertical marker line Step Action Right click the Curves pane and select Marker 2 Drag the marker line with the mouse Result Where the line bisects the curve the
78. ow How to split a It is possible to split the peak into two new peaks by inserting a drop line The peak table below describes how to split a peak in the Edit Peak Table dialog box Step Action e Click the Edit peaks icon e Click the peak in the curve or in the peak table to select the peak e Right click and select 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 existing drop lines and the peak is split Note The area under each new peak will not be the same if the symmetry of the original peak was not perfect e p113 8 Peak integration 8 6 How to edit the peaks How to join peaks Itis possible to join the areas of adjacent peaks if they are separated by a drop line The table below describes how to join adjacent peaks in the Edit Peak Table dialog box Step Action e Click the Edit peaks icon e Click the peak in the curve or in the peak table to select the peak e Right click and select Join Left or Join Right from the shortcut menu or e Select Edit Join Left or Edit Join Right Result The original intervening drop line is removed and all peaks are renumbered How to add peak The table below describes how to add names in the Edit Peak Table dialog box to names identify the peaks Step Action e Click the Edit peaks icon e Click the peak in the curve or in the peak table t
79. pages for example as header and footer text ep71 6 How to view results 6 5 How to create and print a customized report Step Action 3 e Click the Font button to change the default font Result The Font dialog box opens e Make the necessary changes and click OK to return e Click OK Result The text object is inserted onto the page How to add a pic The Picture dialog box is useful to insert logos pictures or other figures in the ture report The table below describes how to add a picture object to the report Step Action e Press and hold the left mouse button on the report page and drag out a box to the size of the picture item Release the mouse button e Click the Picture icon Result The Picture dialog box opens e Click the Browse button to locate the desired picture file e Select the picture file and click the Open button Note The file formats bmp emf jpg and tif can be used Result A preview of the selected picture is displayed e Select the desired Settings and click OK Result The picture is inserted onto the page 03 0014 96 ep 72 How to add a chromatogram or peak table How to view results 6 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 1 Action e Click the Chromatogram icon e Press and hold the left mouse button on the report p
80. pens 2 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 Note All operations described below will only affect the selected part of the curve e p119 8 Peak integration 8 7 How to integrate part of a curve and how to exclude or skim peaks Step Action 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 e Choose Integrate Peak Integrate Result The selected part of the curve is peak integrated based on the changed parameters 03 0014 96 ep 120 Peak integration 8 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 op Coordinates can be obtained in two ways tions e Through direct measurement e From peak table data How to make dir The table below describes how to make direct measurements in a chromatogram ect measurements Step 1 Action Right cli
81. ppropriate The logbook thus provides a complete history of any given run The log is saved in the result file The illustration below shows an example of the Logbook pane Note The second logbook line is the BatchID that is automatically generated The Logbook pane can autoscroll to display the latest entries Right click in the pane and select Autoscroll You can also select the Autoscroll option in the Properties dialog box View Properties and select the Logbook tab You can choose to display only selected items in the logbook The table below describes how to activate the filter Step Action 1 e Right click in the Logbook pane and choose Properties Result The Properties dialog box opens 2 e Choose the Logbook tab e Select the items you want to display in the logbook all items are selected by default e Click the OK button Result Only the selected items will be displayed in the logbook The Logbook title in the upper right corner will show the text Filter on to indicate that not all items are visible All items will still be logged in the result file ep 45 5 How to perform method runs 5 2 How to monitor a method run 5 2 3 The Logbook pane How to find log The logbook can be searched for specific text entries The table below describes book text entries he function Step Action Right click in the Logbook pane and choose Find Result The Find dialog box opens e Type
82. prime system creates Result files when a method is run The Result files contain e Run data from the monitors in the chromatography system Example UV absorbance flow rate conductivity etc e Documentation from the run Example Logbook entries settings text method etc e Saved results from evaluations of the run data Example Peak integrations etc Templates are basic methods that can be used as a starting point for developing customized methods The method variables in a suitable Template is adjusted to create a method for another application Method Templates are supplied with the AKTAprime system ep7 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 The PrimeView user interfaces Introduction This section is an overview of the two PrimeView modules with descriptions of some of the elements of the user interfaces The section also contains a description of the search functions in PrimeView In this section This section contains the following sub sections Topic See Snapshots 22 5 03 0014 96 ep8 2 2 1 Introduction The PrimeView panes The Curves pane The Logbook pane The Status bar PrimeView concepts 2 The PrimeView module The PrimeView module is used to monitor separation runs The PrimeView module contains two different display panes that can be opened both at once or one at a time e The Curves pane e The Logbook pane The Cur
83. rawn 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 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 Move a data point e Select the data point and drag it to a new position Result The baseline curve is redrawn Click OK Result The Save Edited Baseline dialog box opens ep 107 8 Peak integration 8 5 How to edit the baseline manually Step Action 7 e Confirm the location and type a new name if necessary e Click OK Result The new baseline is saved Edited baseline The illustration below is an example of a baseline before and after editing How to draw a The table below describes how to force a straight baseline between two points straight line Action Select the first of the two points in the point list Click the Draw straight to next point button Result The baseline is drawn through the points as a straight line 03 0014 96 p 108 Peak integration 8 8 6 How to edit the peaks Introduction Once a peak table has been generated based on an appropriate baseline it is possible to split or join peaks and to manually adjust the peak start and end points The pea
84. rint 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 The table below describes how to open the Report Editor in Edit mode to create a Report Editorin customized report format edit mode Step Action Open a result file in the Evaluation module e Select File Report or e Click the Report icon Result The Generate Report dialog box opens e Click the New button Result The Report Editor opens in Edit mode The Edit mode The illustration below shows the Report Editor window in Edit mode with a blank window report open Toolbar button The table below describes the different functions of the Edit mode toolbar buttons saa os 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 03 0014 96 ep 68 How to add and delete report pag
85. rsor over the break point to display the complete information in a flyover text box as shown in the illustration below ep55 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 How to optimize the presentation of a chromatogram Introduction This section describes some of the ways you can optimize the presentation of a chromatogram In this section This section contains the following sub sections Topic See How to show part of a curve 6 3 6 03 0014 96 ep 56 How to view results 6 6 3 1 How to 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 8 2 How to perform a peak integration on page 89 The table below describes how to make changes in the Chromatogram Layout dialog box Step Action Open a result file e Right click the chromatogram window and select Properties or e Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed The view from which you activate the Properties command determines the tab that is displayed in the Chromatogram Layout dialog box 3 Carry out the changes on the different tabs to get the desired layout for header cu
86. rves 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 e p 57 6 How to view results 6 3 How to optimize the presentation of a chromatogram 6 3 2 The Curve tab and Curve Names tab 6 3 2 The Curve tab and Curve Names tab The Curve tab The Curve tab of the Chromatogram Layout dialog box contains a list of all the curves included in the chromatogram Select the curves you want to display in the chromatogram and click OK Curve name ap You select options for the curve name appearance on the Curve Names tab This is pearance an example of a default curve name Result 11_UV The table below describes the three components that make up the default curve name Component Description Example Result name Name of the result Result Chromatogram name Number given automat 11 ically during a run or a name defined by the New_Chromatogram in struction Curve name Curve type for example UV detection of an eluted component How to choose You can choose to view only part of the curve name The table below describes curve name ap pearance how to do this Choose Edit Chromatogram Layout Result The Chromatogram Layout dialog box is displayed e Select the appropriate boxes for Curve name appearance e Select the appropriate Curve legend position e Click OK Note It is usually
87. s and folders ep2l 3 Software Installation 3 1 How to install PrimeView for the first time Step 5 Select In the Select Program Folder dialog box you choose where to store the program icon Program Folder The table below describes how to select a program folder for the PrimeView icon Step Action In the Select Program Folder dialog box you select the Start menu folder where you want the PrimeView icon to be placed You can either e accept the suggested folder named UNICORN recommended or create a new folder Type the name of the new folder in the text field Program Folders or select a folder that already exists by clicking its name on the list 2 Click the Next button to continue 03 0014 96 ep 22 Software Installation 3 Step 6 Start The Start Copying Files dialog box displays the installation choices made Copying Files The table describes how to start copying the program files from the CD Action The setup program is ready to copy the files The Start Copying Files dialog box displays all the selections that have been made and the components to be installed Note If you want to make any changes you can click the Back button one or more times If the settings are correct click the Next button to copy the files Step 7 Setup The installation is complete and the computer must be restarted Complete i f e Click the Finish button to exit the setup pr
88. s with explanations and calculation formulae when applicable ih ak parameters The diagram below illustrates the peak parameters See the parameter list below illustration for explanations Peak parameter The list below contains descriptions of the peak parameters descriptions Parameter Description Calculated as the area between the curve and baseline between the peak start and peak end time or volume base Gray area in the diagram above 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 03 0014 96 ep 128 Evaluation functions and instructions Parameter Fraction tube id Height Plate height HETP Peak endpoint heights Peak endpoint retention Peak name Percent of total area Percent of total peak area Resolution Retention Sigma Description Fraction number at peak start peak maximum and peak end Maximum amplitude above the baseline C F in the diagram above Height equivalent to theoretical plate and plates meter The column height must be entered in the Integrate dialog box for this parameter to be calcu lated See definition below this table Amplitude above the baseline at left A in the diagram above and right peak limits E G in the diagram above Retention value at peak start and peak end t
89. t Delete Peaks from the shortcut menu or e Select Edit Delete Peaks Result The peak is deleted and the remaining peaks are renumbered eplll 8 Peak integration 8 6 How to edit the peaks How to add color The table below describes how to add a fill color and a pattern to a peak in the to a peak Edit Peak Table dialog box 1 e Click the Edit peaks icon 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 e Right click and select Fill Peak from the shortcut menu or e Select Edit Fill Peak Result The Color and Pattern dialog box opens e Select a color and a pattern e Click OK Result The peak is filled according to the selections Note The color and pattern selections will override the general Fill settings that can be selected for all peaks on the Peak Table tab in the Chromatogram Layout dialog box 03 0014 96 ep112 Peak integration 8 Peak start andend The beginning of each peak is marked with a drop line above the curve and the poms 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 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 bel
90. t were lost as a result of computer failure or other incidents ep3l 5 How to perform method runs 5 How to perform method runs Introduction This chapter describes how to perform and monitor different kinds of runs from the PrimeView module It also describes how to control the system with manual commands and instructions In this chapter This chapter contains the following sections Topic See How to start a method run How to monitor a method run 52 03 0014 96 ep 32 5 1 Before you start Four ways to start an AKTAprime run How to start an application tem plate run How to perform method runs 5 How to start a method run Before you start a method make sure that e the KTAprime system is prepared according to the instructions in the KTAprime system documentation The method runs are all operated from the KTAprime unit There are four different types of KTAprime runs e Application template runs e Method template runs e Operator created method runs e Manual runs Application templates are available for the most frequent purifications All process parameters except the sample volume are preset The table below describes how to start an Application template run on the AKTAprime unit All parameters are selected with the arrow buttons on the unit The selections are confirmed with the OK button Step Action e Choose the Templates menu e Press the OK button
91. the text you want to locate e Select search criteria if necessary e Click OK Result The located logbook entry is highlighted 03 0014 96 ep 46 Introduction In this chapter How to view results 6 How to view results A result file is automatically generated at the end of a method run and contains a complete record of the method run including method system settings curve data and method run log The Evaluation module offers extensive facilities for presentation and evaluation of curve data This chapter describes how to present the chromatograms and curves of your result file and how to create and print reports This chapter contains the following sections Topic See How to open a result file 6 1 Basic presentation of chromatograms 6 2 How to optimize the presentation of a chromatogram 6 3 How to print active chromatograms 6 4 How to create and print a customized report 6 5 Run documentation 6 6 e p47 6 How to view results 6 1 How to open a result file 6 1 How to start the Evaluation mod ule How to opena AKTAprime result file 03 0014 96 ep 48 How to open a result file The PrimeView Evaluation module provides facilities for the presentation and evaluation of separation results The module is independent from the PrimeView module and can be started even if the PrimeView module is not operating e Click the PrimeView Evaluation icon on the Windows desktop
92. tive chromatogram The start point results and end point of each peak are marked by vertical marks drop lines in the chromatogram The peaks are automatically labelled according to what is selected in the Curve Style and Color tab of the Chromatogram Layout dialog box This is an illustration of the results after a peak integration Note Peak tables can be copied from one chromatogram to another with the Edit Copy command However to display the table you must right click in the chromatogram choose Properties and then select the new peak table on the Peak Table tab of the Chromatogram Layout dialog box 03 0014 96 ep90 Peak integration 8 How to display The peak retention times and several other peak characteristics are calculated peak characterist automatically The table below describes how to display other peak characteristics 1CS Step Action 1 e Right click in the active chromatogram e Select Properties from the shortcut menu Result The Chromatogram Layout dialog box opens 2 Click the Peak Table tab 3 e Select options from the Select peak table columns list e Click OK Result The selected items will be displayed in the peak table How to filter Peaks can be removed from display in a peak table The table below describes how peaks from view filter the peaks Step Action 1 e Right click in the active chromatogram or peak table e Select Properties from the shortcut menu Result The C
93. to use the function Copy from External from External Step Action e Right click in the Open Results dialog box and select Copy from External Result The Copy from External dialog box opens Select the files you want to copy Click Save Result The result files are copied into the open folder in the Open Results dialog box How to rename The table below describes how to rename files and folders in the Open Results dialog files and folders pox Step Action Select the item that you want to rename e Right click and select Rename from the shortcut menu Result The Rename dialog box opens Type a new name Click OK How to delete files The table below describes how to delete files and folders in the Open Results dialog and folders box Note Home folders cannot be deleted this way Step Action Select the item that you want to delete e Right click and select Delete from the shortcut menu or e Press the Delete key 03 0014 96 ep30 Files and folders in PrimeView 4 Step Action 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 Amersham Biosciences cannot accept responsibility for the replacement of results tha
94. ume 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 a al The peak resolution is calculated with one of the following three algorithms 1 Vr2 Vra Wh2 Wha 2 2 Veo Vra Sigma Sigma x 2 3 Vr2 Vri 2 x Wh Wh1 12 354 03 0014 96 ep 130 Capacity factor formula Asymmetry for mula Evaluation functions and instructions A Where Vki Whi Sigma and Wj are the retention width Sigma and width at half height of the previous peak Vp Wha Sigma and Wj are the retention width Sigma and width at half height of the current peak The formula below is used to calculate the Capacity factor Where e Vp retention volume e V total liquid volume 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 ep 131 A Evaluation functions and instructions A 2 Peak table column components HETP formula 03 0014 96 ep 132 The formula below is used to calculate the HETP value HETP L N N 5 54 x Vp w assuming a Gaussian peak Where e N no of theoretical plates e L bed height in cm e Vp peak retention elution volu
95. user anual c PRIMEVIEW 5 0 User Manual Amersham im 03 0014 96 e e Biosciences PrimeView 5 0 User Manual 03 0014 96 Edition AB 2004 04 Office addresses Amersham Biosciences AB SE 751 84 Uppsala Sweden Amersham Biosciences UK Limited Amersham Place Little Chalfont Buckinghamshire England HP7 9NA Amersham Biosciences Corp 800 Centennial Avenue P O Box 1327 Piscataway NJ 08855 USA Amersham Biosciences Europe GmbH Munzinger Strasse 9 D 79111 Freiburg Germany Amersham Biosciences K K Sanken Building 3 25 1 Hyakunincho Shinjuku ku Tokyo 169 0073 Japan Amersham Biosciences China Limited 13 F Tower I Ever Gain Plaza 88 Container Port Road Kwai Chung New Territories Hong Kong www amershambiosciences com Trademarks UNICORN Dropdesign PrimeView and AKTAprime are trademarks of Amersham Biosciences Limited Amersham and Amersham Biosciences are trademarks of Amersham ple Microsoft and Windows are registered trademarks of the Microsoft Corporation in the United States and or other countries Adobe and Acrobat are trademarks of Adobe Systems Inc Terms and Condition of Sale Unless otherwise agreed in writing all goods and services are sold subject to the terms and conditions of the _ company within the Amersham Biosciences group which supplies them A copy of these terms and conditions is available on request Any use of this software is subject to Amersham Biosciences stand
96. valley Drop lines are used mostly for peaks of relatively similar size When a peak has a shoulder splitting with drop lines will cause the first peak to lose too much of its area to the peak that forms its shoulder 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 The table below describes how to select a ratio to skim peaks in the Integrate dialog box Step Action Select the Peak skim checkbox 2 Determine the ratio when peak skimming should be applied based on the relationship in the illustration below Note The default ratio value is 10 How to integrate part of a curve Peak integration Step Action 8 3 Type the ratio value in the text box Part of a curve can be selected in the Edit Peak Table dialog box and integrated with settings that differ from the rest of the curve The table 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 o
97. valuation module ssssssssrsssesrsrrerrsrerrrrrerrene 86 8 Peak inte oration cist taciceccsatecctarassetessesesareediessessaduscwwendscsteduadeledesescduduebeudestenadeSeundsdedieewnee 87 8 l Baseline Cale lallon sissies sas vestecioae nsastccu EE AEEA EE AEA ERa 88 8 2 How to perform a peak INTER TALION A fads cteas wit race eehies tek Centred veh any tue thera wears 89 8 3 How to optimize the baseline with a morphological algorith c cceeeeeeeeee ees 94 8 4 How to optimize the baseline with a classic algOrithiM ccceeeeeeeeeeeeeeeeeeeeeeees 98 8 5 How to edit the baseline Mmantally viciwsitsraropedncetentgateyeesirertileina tens aebitietan 106 8 6 How to edit the DEAK S aires says ossaa teeta ceedagerercaua gaat un eto aa eeaau urea 109 8 7 How to integrate part of a curve and how to exclude or skim Pe akS ceceeeees 116 8 8 Measurements sssssrsstssrrrtrttstt de vnat casadieehewecenctauie carddetyeet eevee bah ages EEEE EEEE 121 A Evaluation functions and instructions ccccsssssseceeeeeeessseeceeeeeessessseeaeeeeeeneeseeeeeeseeees 123 A 1 Baseline CAlGUlatiOlm TGOLY aexiinciecaily Vncwvaliies lit vaeies aiewutlee is eed weetinedalataiens 124 A 2 Peak table column components cavecscs iacni wear vase aetedudebaswieuvasylcuarsWakoveccumambede 128 03 0014 96 epii Introduction In this chapter Introducing PrimeView Introducing PrimeView 1 This chapter contains M
98. valuation module e Choose Integrate Peak Integrate or e Click the Peak Integrate toolbar icon 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 8 3 How to optimize the baseline with a morpholo gical algorithm on page 94 and 8 4 How to optimize the baseline with a classic algorithm on page 98 e Click the Baseline settings button to change the calculation al gorithm in the Settings dialog box The default algorithm is Mor phological 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 rejec tion if necessary e Edit the Column height or Column V values if necessary e p89 8 Peak integration 8 2 How to perform a peak integration Step Action 6 e Click OK to integrate and close the dialog box or e Click Save and Edit Peak Table to save the integration and open the integrated curve for editing See 8 5 How to edit the baseline manually on page 106 See 8 6 How to edit the peaks on page 109 See 8 7 How to integrate part of a curve and how to exclude or skim peaks on page 116 Peak integration The peak table is displayed underneath the ac
99. ves pane displays monitor signal values graphically See the illustration below 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 The Status bar in the bottom of the PrimeView module displays the current status of the separation run See the illustration below The current system status is represented by the colored dot e A green dot represents a running system e A red 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 epg 2 PrimeView concepts 2 2 The PrimeView user interfaces 2 2 1 The PrimeView module Toolbar icons in The table below describes the toolbar icons in the module the Prime View module Icon Function The Customise Panes icon opens the Customise Panes dialog box which is used to select the display panes that are open The View Documentation icon opens the documentation pages Run notes can be entered in the Notes page and settings can be changed The View Properties icon opens the Properties dialog box which is used to control the data display in the PrimeView panes 03 0014 96 ep 10 PrimeView concepts 2 2 2 2 The PrimeView Evaluation module Introduction The PrimeView Evaluation module provides extensive facilities to present a
100. w to view results 6 4 How to print active chromatograms 6 4 How to print active chromatograms Introduction This section describes how to print the chromatograms that are open in the Evaluation module The Print Chroma This is an illustration of the Print Chromatograms dialog box tograms dialog a box Note The selected print format is outlined in red Instruction The table below describes how to print active chromatograms on the default Windows printer Open all chromatograms that you want to print in the Evaluation module e Select File Print or e Click the Print toolbar icon Result The Print Chromatograms dialog box opens Select print format and layout options 4 e Click OK to print or e Proceed with step 5 to preview and edit the layout 03 0014 96 ep 66 How to view results 6 Action Click the Preview button Result The Customise Report window opens e Click the Edit Mode button to make changes e g change the order of the chromatograms see 6 5 How to create and print a custom ized report on page 68 for more information about how to edit e Click the Preview button to return to preview mode e Select File Print or e Click the Print toolbar icon Result The Print dialog box opens e Select the print range and number of copies e Click OK e p67 6 How to view results 6 5 How to create and print a customized report 6 5 How to create and p
101. y all files and folders that it contains The table below describes how to copy files and folders Note Follow the same steps but select Move to move files and folders Step Action 1 Select a file or folder in the Open Results dialog box 2 e Right click and select Copy from the short cut menu Result The Copy dialog box is opened 3 Select a target folder or floppy disk drive 4 Click OK Use the function Copy to External when you need to copy files and folders outside of your own user folders Copy to External should be used specifically when you need e to copy toa floppy disk drive The files are automatically compressed into a zip file The file will also automatically be spanned across several disks if necessary The table below describes how to use the function Copy to External Step Action 1 Select the file you want to copy 2 e Right click and select Copy to External from the shortcut menu Result the Copy to External dialog box opens 3 Select the destination drive and folder 4 Click the Save button ep29 4 Files and folders in PrimeView 4 4 How to copy delete rename and backup files and folders The function The function Copy from External can be used to import files and folders Copy from Extern al e Ifthe files were saved using the function Copy to External they will automatically be decompressed How to use Copy The table below describes how
102. ze Panes icon 03 0014 96 ep 38 How to perform method runs 5 or e choose View Panes How to customize Change the size PrimeView panes j ig 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 ep 39 5 How to perform method runs 5 2 How to monitor a method run 5 2 2 The Curves pane 5 2 2 The Curves pane Introduction The Curves pane of the PrimeView module displays monitor signal values graphically The figure below shows an example of the Curves pane How to select The table describes how to select the curves to be displayed on the screen curves to be dis played Step Action In the PrimeView module select View Properties Result The Properties dialog box is displayed Select the Curves tab In the Display curves list select the curves you want to display If you want all curves to be displayed click the Select All button If you do not want any curves to be displayed click the Clear All button Click OK How to displaya The table below describes how to display a vertical marker line vertical marker line Step Action 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 corn

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