1. P008/60A 11.6.2015 CLARITY CHROMATOGRAPHY SOFTWARE USER TRAINING - ADVANCED

2.  Customization  Calculations  Using Sequences  Export Data  Archive and Restore  Productivity skills Advanced Features

3. User settings User settings are stored in individual users desktop *.dsk files. For this reason they are set in the instrument window and not in the main Clarity window

4. OverlayOverlay In overlay, several chromatograms can be compared. Maximum number can be set in user options Summary table displays results for several chromatograms or signals simultaneously Overlay could be activated also from File open dialog Ctrl + click will hide/show the signal

5. Overlay mode – 3D View Arange overlaid chromatograms

6. Additional Labels Text Label and Lines for legends and arrows Chromatogram/Create Label Label Assignement Math operations Moving and Scaling of Chromatograms – active only in Overlay

7. Table customization options Context menu invoked by right mouse click in table

8. User Columns – Relative Retention Times Setup User Column using the Special Values, Compound option Calculated RRT Force Peak Identification

9. Common columns in Summary table  Independent setting of columns  Common – for all compounds  Summary – compound specific

10. Summary table options

11. Colored peak area in chromatogram Peaks in calibration can have a color assigned. When these peaks are identified in chromatogram they will be automatically colored Peak selected in result table will be highlighted in chromatogram line color

12. Colored peak area in chromatogram Highlight peaks selected in Results table or Graph (signal color used) Peak Color set in Calibration file

13. Graph display properties Context menu invoked by right mouse click in the graph in Chromatogram window Graph properties setting Axis properties setting

14. Chromatogram display options Signal scaling Individual Signal settings Scale and Move

15. Chromatogram display options Auxiliary Signals options Gradient display options

16. Customizing toolbars Invoked by right click in toolbar area Reset All restores original settings

17. Report Setup - logo

18. Report Setup – tiled signals

19. Customizable order of Report sections Right click the tab and adjust its position

20. Performance parameters Calculation type Values used for Capacity ratio and Efficiency calculation Performance tab Results, Performance Parameters

21. Noise monitoring Actual noise monitoring in the Data Acquisition window

22. Noise and Drift Drift and Noise can be used in User column calculations Drift and Noise displayed for selected intervals in Result table header

23. Calculations  ISTD calculations  Normalized % calculations  Groups  calibration of peak group like single compound example - isomers (xylen)  Scale factor  recalculation of result to other units  Uncalibrated response  quantification of unidentified peaks using Uncalibrated response factor  Injection volume  Injected volume correction for manual injection in GC

24. ISTD calculations Up to 5 ISTD compounds allowed in calibration. If the conditions are not met, no results will be calculated ISTD compound amount in standard ISTD compound amount in sample ISTD calculations are performed: a) Amount for ISTD is set in both calibration and sample b) both are zero

25. Normalized % calculations Amount % column gives the normalized % if all integrated peaks are calibrated and Sample amount is zero Calculation type NORM just checks those conditions are met, calculations are same as for ESTD If Sample amount is non-zero, it will replace the sum in the Amount column and serve as a base for Amount % calculation

26. GroupsGroups 1 st step Adding peaks to a group in the integration table 2 nd step Setting a Group in Calibration table. The compound name and amount is set as for ordinary peaks

27. Scale Factor and Uncal. Response Scale factor and Units after scaling: Multiplies values in Amount column and changes the units in column header. Method specific parameter, multiplies also the entered Sample Amount value Unidentified peaks Used for quantification of unidentified compounds. For universal response detectors (ELSD, FID, RI) Dilution: Multiplies values in Amount column. Sample specific parameter (entered from Sequence or Single Analysis window).

28. Injection Volume Correction Setting Default Injection Volume in calibration Setting Injection Volume for sample and standard  Default Injection Volume must be set first in calibration and Injection Volume set in standards before calibrating  Supposes linear detector response  Can lead to incorrect results, if used improperly

29. Calibration Command Calibration/Show Details displays data used for selected level Residual sum of deviation squares

30. Calibration options Calibration curve check Failure displayed in the Peak Type column in Result Table New Calculation types NORM STDADD

31. Retention indexes, LOD, LOQ Column for Retention (Kovats) indexes is hidden in default settings. Use setup columns to display it. Amounts lower then specified LOD or LOQ limits are marked in Peak type column

32.  Defines a series of samples to be measured  Essential for working with autosamplers  For controled autosamplers the Vial number and Injection volume are loaded from this table  Allows modifications during a run for not yet processed samples  Simply add samples by filling any field in the last empty row. Other fields will be copied from previous. Several samples can be added by copying from a table  Allows the import of sample data from text files  Allows reprocessing of last measured sample set Sequence table

33. Sequence table window Start, End vial and Injections number. Several vials and/or injections defined on single row File name, automatic %variables for SV, EV, IV Automatic recalibration from sequence Individual Post- Run settings for each row ImprovedRow status indicator Use row, add new rows during sequence run Tooltip with actual file name

34. Sequence options Pasive sequence Clarity only expects Start signal, analysis time is set on autosampler Active sequence Clarity sends a Ready signal to autosampler and waits for Start signal AS control (Active sequence) Autosampler injects according to SV, EV, IV and Inj. Volume in sequence table Editation of template method used on selected row Pasive sequence Clarity only expects Start signal, analysis time is set on autosampler Active sequence Clarity sends a Ready signal to autosampler and waits for Start signal AS control (Active sequence) Autosampler injects according to SV, EV, IV and Inj. Volume in sequence table Initial value for %n

35. Sequence control Run sequence starts complete sequence (resets the status) Resume sequence continues from last injection Status of the sequence. Stored at Pause, Abort, Stop Can be changed by Edit/Reset Status for selected rows Repeat Injection and Skip Vial only in active sequence Stop sequence will stop the sequence run. Repeated Stop will stop the current analysis Check Sequence

36. Sequence import Assign the respective fields to be imported Only Start vial (SV) and file name must be set (marked in bold) Other fields will be filled by default values Select the file to import

37. SequenceSequence Bypass to perform run without injection for startup and shutdown methods New file name variables %P – Project %s – Sequence %J – Method New columns: Include in SST – perform SST test when injection is finished Stored Calib. – chromatogram will be opened with stored calibration Close All – close all currently opened chromatograms in overlay to prepare for next summary report

38. Bracketing and Standard Addition Calibration and Sequence Usage Clone calibration at each Sequence start Standard Addition Bracketing This calibration will be used with Calibration used as specified by user Copy of the Example Calibration will be created according to Sequence options, Calibration and Sequence Usage

39.  Export data to other programs to prevent typing errors  Simple Copy and Paste (Ctrl C – Ctrl V)  Export Data settings common for  manual export from chromatogram window  automatic export from postrun at the end of each run  automatic export by batch reprocess of chromatograms or sequence  Export of chromatograms in common formats Export data

40. Export data - simplest Copy a selected part of table using Copy (Ctrl C) and Paste (Ctrl V) Copy a picture to MS Office (including labels) via Clipboard or store it in *.emf format

41. Export data - options Export automatic – Postrun, Export data manual – from Chromatogram window batch - from Analysis/Batch Export time/signal data pairs (import to other programs – for example graphics) Headers: Column headers and chromatogram info Full format: Filename, date and time before each row blank field = actual chromatogram name +.txt extension Path can be used All exported data are in single file

42. Export data - example

43. Export of data in Excel (.xls) format

44.  Print  Report style from Report Setup dialog will be used  do not forget to switch off the Overlay mode  Export  Reprocess of chromatograms according to instrument method  Reprocess whole sequence  Electronic signature Batch processing Export according to Settings - Export Data File type Chromatograms Calibration standards Sequence Files Open exported data in selected program

45.  To reduce the data size, compressed archive *.dgz files should be used  *.dgz archives always replace all data (files deleted from project will be also deleted from the archive during archiving).  It is advantageous to archive whole projects – should be considered when planning project structure Archiving and Backup

46. Archive data  Archive and Restore for copying or moving selected file types  Without compressing = original format and structure  Compressed *.dgz archives = single file, always created new (no appending!!)

47. Clarity – Perform postrun Dialog will appear only if nothing is filled in or when invoked from menu. Sequential opening of chromatograms Icon to perform postrun actions (Use Customize to reveal)

48. Shortcuts – command locking  Ctrl while invoking command will lock it for repeated use

49. Most popular shortcuts

50.  Tables - function Fill series  Sequence  Calibration  Gradient Both numeric and text fields Fill Series

51. Force Peak Identification Select new Peak Identification  Name peaks without calibration file  Override identification by calibration  Name peaks without calibration file  Override identification by calibration Force Peak Identification Select Peak to Force