Basic operations

1. Basic operations Clarity User Training

2. Basic Operations • Method development • Integration parameters • Calibration • Reports

3. Opening the station Status table Instrument window Analysis(Single run/Sequence) Method Setup Data Acquisition Clarity Main window Chromatogram Report Calibration

4. Template method concept • Template Method opened on Instrument serves as a template for new chromatograms • The content is copied to chromatogram after acquisition or batch reprocessing • Chromatogram method • Changes in chromatogram methoddo not affect the template method • Linked Calibration • Calibration file is linked to method (template or chromatogram) by its name Template Method opened on Instrument Template Method used for current run

5. Clarity Method development • Template Method parameters • Sample information • Acquisition of a typical chromatogram (standard) • Integration parameters setting • Creating a calibration file • Acquisition of other standards and unknown samples • Printing and export of results

6. Measurement conditions • Measuring conditions • informative, quite useful after time (when filled in) • Autostop setting • necessary for Active Sequence External start signal options

7. Acquisition - xxx • Data acquisition parameters • Range, Sampling Rate – individual for each detector • Range and Sample Rate • critical settings, if wrong, analysis must be repeated Select/enable signal (detector) Caution: this parameters cannot be changed later!

8. Range and Sample Rate • Range • according to detector output • signal outside range is lost, wrong areas and heights • signal sometimes limited by detector • Sample Rate • for capillary GC set 25-50 Hz, otherwise 10 Hz • when low, insufficient data points for peak description

9. Method Setup - Integration Editable Integration table with default parameters Individual table for each signal To set up this table properly measured chromatogram is necessary. Easiest way is to use the graphical tools in Chromatogram window

10. Method - Calculation Set name of existing calibration file(or create new file) The Calibration file is linked to method and chromatograms by its name. It is advisable to set it in the method even before any chromatogram is measured.

11. Sample info Sample description and Sample ID informative fields Values used in calibrated calculations Snapshot – process the data acquired so far without finishing the running analysis Store file in CALIB or DATA subdirectory Recalibrate selected level File Name %variables for automatic name composing Existing files will be overwritten without warning RAW data processing from TMP subdirectory Initiall value for %n

12. Chromatogram acquisition • Inject sample • Start the data acquisition • automatically, by external start cable connected to valve • manually, by button on instrument or start cable • manually, the RUN button in Single Analysis dialogor icon in Data Acquisition window • Watch the acquired signal in the Data acquisition window • Stop the data acquisition • automatically, after set Autostop time • manually, the Stop button in Single Analysis dialogor icon in Data Acquisition window

13. Data Acquisition Baseline monitoring (before analysis) Analysis monitoring Display only, not influencing collected data

14. Integration Table Parameters • Optimize Peak Width and Threshold • basic parameters for integration algorithm • Baseline and peak modifications • integration area, integration lock • peak separation, peak starts and ends • Store to template method • parameters will be applied to newly acquired chromatograms • Manual chromatogram modifications • only actual chromatogram is affected • store to template method • copy to other chromatograms • batch reprocess

15. Basic integration parameters Integration interval

16. Integration parameters Chromatogram method Integration table individual for each detector Template method All operations editable and programmble in time(including Peak Width and Threshold)

17. Toolbars Autointegration tools Global Peak Width Global Threshold Integration Tools integration parameters settings Peak Tools peak operations Baseline Tools baseline modification The crossing of chromatogram and baseline is not allowed. In such case, the peak start or end is moved automatically

18. Integration Tools Detector delay 1) first click peak on active signal 2) then click corresponding peak on first signal Rejections: area, height, peak width

19. Peak Tools Groups several peaks can be quantitated as single compound Solvent Peak not included in result table

20. Baseline Tools

21. Rejection and Separation • Rejection • limits for rejection of already integrated peaks • peaks bellow set limits could not be added manually • Separation • functions only from menu or integration table • Valley to Valley Slope • sensitivity for automatic Valley to Valley separation • Tangent Area Ratio, Tangent Slope Ratio • sensitivity for automatic tangent separation • default values = baseline separation

22. Storing to Template method Set Model/Copy from Model • copy parameters from actual chromatogram to other chromatograms Save as Template • use parameters from current chromatogram to new chromatogram • actual method could not be overwritten

23. Integration results • Integration results are peak retention times, areas and heights • Calibration must be constructed to assign compound names and concentrations

24. Calibration • Relationship between retention time and compound identity • Global calibration table • Identification windows • RT area, in which peak is identified as a given compound • Reference peaks • the biggest peak is identified in identification window (instead of nearest), identification windows for other peaks are shifted accordingly

25. Calibration • Relationship between response and compound quantity • Response • height or area • Calibration curve fit • point to point-linear-quadratic-cubic-sigmoid • Zero usage • not used-used as a point-forced through zero • Recalibration • replace-weighed average-average • Response weighing • none-1/amount-1/response-1/amount^2-1/response^2

26. Calibration window Open Calibration Active signal selection Calibration options Transfer data from chromatogram to calibration Open Standard Set level Use compound on active signal Global calibration table Individual compounds tabs Current level table

27. Calibration options calculation mode Calibrate new level for each opened chromatogram Recalibrate current level Units used in the result table Recalibration mode Enable editing of responses Actualization of retention times during recalibrations

28. Calibration options Default response base Calibration Curve fit type Response weighting Zero usage Indentification windows Set for all compounds in calibration table for current signal

29. Compound table Use point Curve fit: Free calibration Point to point Linear Quadratic Cubic Sigmoid Response base setting Compound type Odinary Reference Internal Standard Reference ISTD Zero usage: Ignore Origin, Compute with Origin, Curve passes through Origin

30. Creating calibration file • Create new calibration in Calibration window • command menu File - New • Set calibration options • command menu Calibration - Options or icon • Open integrated chromatogram of a standard • command menu File - Open primary or icon • Transfer data from chromatogram to a calibration file • command menu Calibration - All or icon

31. Creating calibration file • Identify peaks • fill in the peak names and concentrations for first level • Repeat for all standard levels • Check calibration curves for all compounds • click on compound tab • set options (curve fit, zero usage, exclude points) • Save calibration • command menu File - Save

32. Calibrated calculations • Linked calibration • Calibration file is common to all files linked to it and all changes in calibration are immediately progressed to all opened linked files • Copy of actual calibration state is stored within chromatogram, when saved • Calibration selection • Calibration file and calculation type is selected in method (template or chromatogram) • Those parameters should be set in template method before starting data acquisition

33. Repeated use of calibration • Each serie of samples should be linked to an unique calibration file • Create copy of calibration using Save as or Clone • Clone creates a copy linked to the method • Clear responses option is available • Acquire standards • Recalibrate (by automatic, recalibrate, replace) • Acquire samples (with linked actual calibration)

34. Template method settings Jump to the linked calibration Calibration file selection Calculation type selection Result table display options Create and attach copy of calibration file to template method (option Clear responses) Calculation Tab

35. Chromatogram settings Select a calibration file Select the calculation type Jump to the linked calibration Response base indication

36. Calculation types • UNCAL • uncalibrated, only areas and heights • ESTD • external standard, most common • ISTD • internal standard, calculated from the ratio of ISTD and unknown compound • A) same amount of ISTD in samples and standards • Internal standard must not be calibrated • ISTD amount must be set to zero • B) different amount of ISTD in samples and standards • Internal standard must be calibrated • ISTD amount must be given • When those conditions are not met, no results are calculated

37. Results display Peak type Error calibration curve could not be used Free when response factor and Free Calibration is used Calculation type If the conditions are not met, no results are displayed, the reason indicated in table header Amount in % a) base Total Amount b) base Sample Amount Amount calculated from calibration curve Response and response base

38. Printing of results

39. Report