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P008/60A 11.6.2015 CLARITY CHROMATOGRAPHY SOFTWARE USER TRAINING - ADVANCED
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Customization Calculations Using Sequences Export Data Archive and Restore Productivity skills Advanced Features
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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
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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
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Overlay mode – 3D View Arange overlaid chromatograms
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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
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Table customization options Context menu invoked by right mouse click in table
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User Columns – Relative Retention Times Setup User Column using the Special Values, Compound option Calculated RRT Force Peak Identification
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Common columns in Summary table Independent setting of columns Common – for all compounds Summary – compound specific
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Summary table options
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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
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Colored peak area in chromatogram Highlight peaks selected in Results table or Graph (signal color used) Peak Color set in Calibration file
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Graph display properties Context menu invoked by right mouse click in the graph in Chromatogram window Graph properties setting Axis properties setting
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Chromatogram display options Signal scaling Individual Signal settings Scale and Move
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Chromatogram display options Auxiliary Signals options Gradient display options
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Customizing toolbars Invoked by right click in toolbar area Reset All restores original settings
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Report Setup - logo
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Report Setup – tiled signals
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Customizable order of Report sections Right click the tab and adjust its position
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Performance parameters Calculation type Values used for Capacity ratio and Efficiency calculation Performance tab Results, Performance Parameters
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Noise monitoring Actual noise monitoring in the Data Acquisition window
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Noise and Drift Drift and Noise can be used in User column calculations Drift and Noise displayed for selected intervals in Result table header
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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
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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
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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
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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
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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).
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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
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Calibration Command Calibration/Show Details displays data used for selected level Residual sum of deviation squares
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Calibration options Calibration curve check Failure displayed in the Peak Type column in Result Table New Calculation types NORM STDADD
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Export data - example
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Export of data in Excel (.xls) format
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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
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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
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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!!)
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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)
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Shortcuts – command locking Ctrl while invoking command will lock it for repeated use
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Most popular shortcuts
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Tables - function Fill series Sequence Calibration Gradient Both numeric and text fields Fill Series
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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
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