<h3>Introduction</h3>This document presents:<ul><li>a comparison of integration algorithms (IAs) available in <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/products/999">Clarity</a>,</li><li>a generally proposed workflow for integrating chromatograms,</li><li>description of functions that are available only in the Wave algorithm.</li></ul>Integration algorithms are a crucial component of any chromatography software. They identify peaks in a raw chromatographic curve, assign integration marks (starts, ends, apexes), and determine the peak baseline. Although it is the operator's responsibility to verify the correct peak integration after the analysis is finished, an automated peak detection facilitated by the integration algorithm can significantly streamline the workflow.Clarity since version 9.0 offers two IAs: the original algorithm, renamed Legacy, and a newly introduced algorithm named Wave, which evolved from an experimental algorithm present since version 7.0. The Wave algorithm will be regularly updated with new functions, settings, and bug fixes (updates for Legacy will only be released if a critical bug is discovered). Changes in IAs are always versioned and distinguishable by records in the audit trail.<h3>Choosing an integration algorithm</h3>Users can select either the Legacy or Wave integration algorithm for peak detection. The IA drop-down selection has been relocated to the Integration tab in both the Chromatogram window and the Method Setup dialog, highlighting the interconnection between the algorithm and the integration table.The introduction of Wave does not affect existing results or methods, as they will remain set to Legacy unless manually altered. Suppose a method was created using an older version of any integration algorithm and was not changed after the Clarity update to a newer version. In that case, the latest version of the same algorithm will be used in any newly measured chromatograms. This change will be logged in these chromatograms upon creation. To address potential issues, DataApex aims to use the algorithm version with the most bug fixes. Users are not required to re-save their methods, but if they do, the change will be logged in the method audit trail.One way to apply an integration algorithm to multiple chromatograms simultaneously is through the Batch dialog (not applicable to Clarity Lite).<h3>General Comparison</h3>Neither algorithm can be universally deemed superior; some situations may warrant using one IA over the other. Below are some examples of performance differences between the two IAs. At least the Global Peak Width and Global Threshold operations were presumed to be performed on the signal. If you encounter any issues with either of the integration algorithms, please inform DataApex via <a>support@dataapex.com</a>. This datasheet further contains an overview of a basic integration workflow.<h4>Advantages of Wave IA:</h4><ul><li>Handling of negative spikes/peaks with regard to baseline placement.</li><li>Handling of shifting baseline/signal.</li><li>Separation of unresolved peaks.</li></ul><h4>Disadvantages of Wave IA:</h4><ul><li>More sensitive to noise, requiring the use of Bunching or another filter in some cases.</li><li>Incorrect integration when peaks of significantly different widths are present (typical for GPC or EA).</li></ul><h4>Negative spikes/peaks</h4>When a chromatogram contains significant negative peaks or spikes that should not be evaluated, the default integration in the Wave algorithm will produce satisfactory results, while the Legacy algorithm will not. (In Legacy, this problem could be solved by applying several Integration Intervals.)<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_4b4372d5b8.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 1. Integration by Legacy IA considers the negative spike to be the start of the peak (or peak cluster)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_4b4372d5b8.jpg 245w," sizes="100vw" width="1063" height="548"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_11_e51da3eb48.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 2. Integration by Wave IA with the same parameters." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_11_e51da3eb48.jpg 245w," sizes="100vw" width="1061" height="554"><h4>Shifting signal/baseline</h4>Similar to the negative peaks/spikes, the same situation may arise with a shifting baseline where the peaks should be evaluated to that baseline. Legacy IA will provide unsatisfactory integration. In Legacy, this could be solved by applying Baseline Valley to several places and combining them with Integration Interval.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_13_d44f34c303.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 3. Integration by Legacy IA." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_13_d44f34c303.jpg 245w," sizes="100vw" width="1064" height="551"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_14_8c3d2772fe.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 4. Integration by Wave IA with the same parameters. The fairly high number of peaks is caused by the low value of the Global Threshold." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_14_8c3d2772fe.jpg 245w," sizes="100vw" width="1062" height="553"><h4>Unresolved Peaks</h4>In Legacy IA, if a peak does not fulfill some criteria (it is too narrow or the valley to other non-resolved peaks is too low), it gets joined to a neighboring bigger peak. Meanwhile, Wave IA evaluates the valley depths much better and separates the peaks automatically, even when the small peak does not fulfill some of the criteria. Small impurities, thus, do not influence the area of the bigger peak of interest.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_10_49fded9390.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 5. Integration by Legacy IA." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_10_49fded9390.jpg 245w," sizes="100vw" width="1062" height="554"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_12_6d8d9a6980.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 6. Integration by Wave IA with the same parameters." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_12_6d8d9a6980.jpg 245w," sizes="100vw" width="1062" height="551"><h4>Significant noise</h4>In some cases, the signal noise may be very significant, and the set threshold value in the Wave algorithm will be so low that one peak will be split into several peaks. The example below shows that neither of the IAs is sufficient with just Global Peak Width and Global Threshold; additional operations must be used.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_9_e020e43a49.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 7. Integration by Legacy IA with the same parameters." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_9_e020e43a49.jpg 245w," sizes="100vw" width="1062" height="552"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_8_1b275412a8.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 8. Integration by Wave IA." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_8_1b275412a8.jpg 245w," sizes="100vw" width="1064" height="552"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_7_4071029dd3.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 9. Integration by Wave IA after applying Global Bunching. Sometimes, small peaks at the start/end of a bigger one may remain." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_7_4071029dd3.jpg 245w," sizes="100vw" width="1061" height="550"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_6_ee88c557f1.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 10. Integration by Wave IA after applying Global Bunching and Minimal Area parameters." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_6_ee88c557f1.jpg 245w," sizes="100vw" width="1063" height="556"><h4>Peaks with significantly different peak widths</h4>Sometimes, chromatograms have very different peak widths; when some peaks cover a significant portion of the chromatogram (e.g., in EA or GPC), Wave IA may fail to evaluate the wide peaks properly. Currently, it is recommended to integrate these chromatograms using Legacy IA.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_3_b833975244.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 11. Integration by Legacy IA with the same parameters." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_3_b833975244.jpg 245w," sizes="100vw" width="1060" height="549"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_4_660685f241.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 12. Integration by Wave IA." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_4_660685f241.jpg 245w," sizes="100vw" width="1060" height="551"><h4>Peaks cut off in the middle</h4>Sometimes, random peaks get integrated strangely in Wave IA, being cut off. This happens only randomly in the Wave IA (in a series of chromatograms, most peaks are OK, but occasional chromatograms may have one or more peaks cut off). The phenomenon results from filtering the data in combination with the signal curve course. There is no 100% solution in the Wave algorithm (applying Global Bunching or other filters helps in most cases). Switching to Legacy IA helps.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_2_ce68c8dc99.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 13. Integration by Wave IA." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_2_ce68c8dc99.jpg 245w," sizes="100vw" width="1064" height="553"><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_5_af9302130f.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 14. Integration by Wave IA after applying Global Bunching." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_5_af9302130f.jpg 245w," sizes="100vw" width="1061" height="549"><h3>Basic integration workflow</h3>Setting at least the Integration Interval and global parameters before resorting to other operations is recommended. This strategy suffices for most chromatograms, and such integration is then applicable to all similar samples. The recommended order of operations is as follows (refer to the User Guide for a detailed description):<ol><li>Set Integration Interval(s) Some areas of the chromatograms are irrelevant to the analysis and may cause wrong integration of the rest of the chromatogram if left in operation, e.g., sudden steep signal rises/drops when lamps are switched on, mobile phase compositions suddenly changing, etc. Make sure that the Integration Interval operation does not define an interval starting or ending inside of a peak slope; in either IA, the expectation is that the chromatogram starts and ends on a baseline.</li><li>Set Global Peak Width If the chromatogram has peaks with significantly differing peak widths, applying the Local Peak Width operation may be useful later.</li><li>Use Global Bunching operation Global Bunching is calculated based on the chromatogram frequency and the set Global Peak Width, so it should be applied after setting the Global Peak Width.</li><li>Set Global Threshold Based on the Threshold value, the smallest peaks are omitted depending on the noise of the signal curve. Since Global Bunching acts as a signal filter, the automatically suggested Global Threshold value will differ after applying Global Bunching higher than 1.</li></ol><h3>Exclusive features in Wave IA</h3>Wave IA contains some Integration Table functions that are unavailable in Legacy IA. If these functions are present in the Integration Table, they will become invisible (not performed) when switching to the Legacy IA but will remain if the algorithm reverts to Wave.<h4>Peak – Show and Peak – Hide</h4>The Peak – Show and Peak – Hide functions provide a convenient way to manage the visibility of specific peaks in your data. These tools allow you to tailor your display by either showing or hiding specific peaks.By default, the Wave algorithm might automatically ignore some of the minor peaks identified during integration. However, completely eliminating these peaks could potentially affect the baseline's trajectory. Therefore, these functions offer a flexible way to handle unwanted peaks without completely removing them.Both the Peak – Show and Peak – Hide features are complemented by the Baseline – Lock function. This tool completely removes all peaks that have their maxima within a set time interval. This could affect other peaks with maxima outside the specified window, particularly if they share the same baseline.The Peak – Hide function has been designed within the Wave algorithm to address this. It merely hides peaks within the selected time interval instead of eradicating them. These peaks are considered when constructing a joint baseline but excluded from the final calculation and the Result Table. The counterpart function Peak - Show allows you to visualize a previously hidden peak or display peaks automatically hidden by the algorithm.In scenarios where a region of the chromatogram contains hidden peaks and the user executes the Peak – Add Positive/Negative operation, all automatically generated but concealed peaks within the defined time interval are replaced by the newly added peak. This could lead to the cancellation of hidden peaks in areas where the manually added peak is not displayed due to baseline crossing limitations.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Integration_Algorithms_in_Clarity_15_b934973f35.jpg" alt="DataApex: Integration Algorithms in Clarity: Figure 15. Difference between Peak Hide (left) and Baseline Lock (right)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Integration_Algorithms_in_Clarity_15_b934973f35.jpg 245w," sizes="100vw" width="1830" height="285"><h4>Global/Local Baseline Slope</h4>Automatic peak generation on a standard signal curve typically comprises three parts: Peak Start, Peak Apex, and Peak End. The highest signal point determines the location of Peak Apex. At the same time, the positioning of Peak Starts and Peak Ends can vary, potentially being either closer or farther from the Peak Apex, based on user preference. Different settings can be more effective depending on the situation.Before the introduction of the Wave IA, the automatic determination of Peak Starts and Peak Ends was governed by the instantaneous peak slope, calculated using the Global/Local Threshold parameter. If users wanted the automatically generated peak borders closer to the Peak Apex, they had to increase the Threshold value. However, this resulted in raising the detection limit for peaks on the baseline, which could prevent the identification of smaller peaks.Wave IA presents an alternative. It allows users to maintain their chosen Threshold value while separately defining the chromatographic curve slope for detecting Peak Starts and Peak Ends through the use of the Global Baseline Slope or Local Baseline Slope operations. This parameter is not mandatory; users can retain the original slope calculation method by leaving the Global Baseline Slope value set to 0. Any value other than zero will cause a shift in the positions of the Peak Starts and Peak Ends.You can find an approximate value for this function using the Chromatogram – Show Slope/Level function in the Chromatogram window menu. However, altering the Baseline Slope value may result in separating peak clusters into individual peaks or merging separate peaks, and some peaks may not be integrated at all.For specific alterations to the start and/or end positions of individual peaks, the Peak – Start and Peak – End operations remain useful. These functions override the automatically calculated positions for peak start and peak end.

Integration Algorithms in Clarity

<h4>Calculation of biodiesel composition can be done directly in Clarity</h4>This whitepaper explains how to calculate the content of fatty acid methyl esters (FAME) and the linoleic acid methyl ester in biodiesel fuel according to ISO 14103 in Clarity. As stated in the norm, the content of FAME in biodiesel is greater than 90 % (m/m), while the content of the linoleic acid methyl ester is between 1 % and 15 % (m/m). The methyl esters in FAME should be between C14 and C24.<h4>Principle</h4>The determination of the content of FAME employs internal calibration (ISTD – methyl heptadecanoate). The ester content in m/m percent is calculated as:<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Determining_biodiesel_composition_according_to_ISO_14103_2_f900384c97.jpg" alt="DataApex: Determining biodiesel composition according to ISO 14103." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Determining_biodiesel_composition_according_to_ISO_14103_2_f900384c97.jpg 245w," sizes="100vw" width="1064" height="85">where 𝐶 is the ester content, ∑ 𝐴 is the total peak area of the methyl esters from C14 to C24, 𝐴ISTD is the peak area of the ISTD compound, 𝐶ISTD is the concentration of ISTD (in mg/ml), 𝑉ISTD is the volume of ISTD (in ml), 𝑚ISTD is the mass of ISTD (in mg), and 𝑚 is the mass of the sample (including ISTD mass; in mg).The linoleic acid methyl ester content in m/m percent is given as:<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Determining_biodiesel_composition_according_to_ISO_14103_3_1a356fc1f5.jpg" alt="DataApex: Determining biodiesel composition according to ISO 14103." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Determining_biodiesel_composition_according_to_ISO_14103_3_1a356fc1f5.jpg 245w," sizes="100vw" width="1064" height="85">where 𝐿 is the linoleic acid methyl ester content, ∑𝐴 is the total peak area of the methyl esters from C14 to C24, 𝐴ISTD is the peak area of ISTD, and 𝐴𝐿 is the peak area corresponding to the linoleic acid methyl ester.<h4>Preparing chromatogram and calibration</h4>After measuring your sample, open your chromatogram in <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/products/999">Clarity</a>. Group the FAME peaks using the Peak Groups… function (menu Chromatogram – Peak). In the Groups dialog, set an ID, click Add, and select the corresponding peaks. In the example chromatogram (download link below), Group A (FAME) does not contain the ISTD peak – this simplifies the subsequent calculations.Create a new calibration and open the sample chromatogram as a standard. In the Calibration Options, change the Display Mode to ISTD and Mode to Recalibrate. Use the Add Peak function to add the ISTD (methyl heptadecanoate) peak and linoleic acid peak to the calibration. In the Amount column, write the known ISTD amount. To add the group of FAME peaks, use the Add Group function. Then, on the linoleic acid and FAME compound tabs, set the Calculate By option to the ISTD compound name. Save the calibration and link it to the sample chromatogram. To improve clarity, in the Common for All Signals pane, select the All Identified Peaks option in the Report in Result Table section.<h5>Procedure for calculation of FAME content</h5>The desired results can be calculated directly in Clarity using the User Columns: right click anywhere in the Result Table pane in the Results tab of the Chromatogram window and select User Columns – Add… in the context menu. In the Add User Column dialog, fill in the Title and Units (e.g. FAME in %) and uncheck the Calculate Total checkbox. The following expression can be used to calculate the FAME content, if the ISTD peak was not included in the FAME peak group:([FAME$Area] / [ISTD$Area]) * ([ISTD1 Amount] / ([Sample Amount] + [ISTD1 Amount]))*100If the ISTD peak was included in the FAME peak group, its area must be subtracted from the area of the FAME group:(([FAME$Area] - [ISTD$Area]) / [ISTD$Area]) * ([ISTD1 Amount] / ([Sample Amount] + [ISTD1 Amount]))*100<h5>Procedure for calculation of the linoleic acid methyl ester content</h5>Calculation of linoleic acid methyl ester content is analogous to calculation of the FAME content. Add another user column, fil in the Title and Units (e.g., Linoleic Acid in %) and uncheck the Calculate Total checkbox. If the ISTD peak was not included in the FAME peak group, the following expression can be used:[Linoleic acid$Area] / [FAME$Area]*100Analogously, if the ISTD peak was included in the FAME group, it must be subtracted:[Linoleic acid$Area] / ([FAME$Area] - [ISTD$Area])*100<h4>Example of an evaluated chromatogram</h4><h4>Sample data for Clarity</h4><ul><li><a target="_blank" rel="noopener noreferrer" href="https://downloads.dataapex.com/documentation/clarity/other/Biodiesel.zip">Biodiesel.zip</a> – zipped processed chromatogram and calibration.</li></ul>

Determining biodiesel composition according to ISO 14103

Clarity's Dual Chromatogram Mode is a specialized configuration designed for analytical systems that require simultaneous acquisition and processing of data from multiple detectors. Most commonly applied in dual tower gas chromatograph (GC) systems, this mode allows for the real-time acquisition of two chromatograms - each representing distinct detector outputs.This guide provides an in-depth look into the configuration, operational mechanics, and benefits of using Dual Chromatogram Mode within <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/products/999">Clarity software</a> by DataApex.<h4>Tools and System Requirements</h4><h5>Prerequisites</h5><ul><li>Clarity Chromatography Software</li><li>Dual Detector System (e.g., Dual Tower GC)</li><li>Properly configured System Configuration files</li><li>Signal Channels connected to respective detectors</li></ul><h4>System Configuration and Activation</h4><h5>Enabling Dual Chromatogram Mode</h5>To enable this mode, the user must access the System Configuration settings and individually activate Dual Chromatogram Mode for each instrument. This configuration determines how signal inputs from multiple detectors are routed.<h5>Assigning Signals</h5>Once activated:<ul><li>Signals are split and assigned to either the Front or Back chromatogram.</li><li>This signal labeling is consistent throughout the Clarity software workflow, ensuring accurate data mapping and separation.</li></ul><h4>Method Setup and Calibration</h4><h5>Method Adaptation</h5>Each method needs to be adapted to work with Dual Chromatogram Mode:<ul><li>Signals are distinctly labeled by position (Front/Back).</li><li>Each method tab includes separate configuration areas for each signal path.</li></ul><h5>Calibration Files</h5><ul><li>If calibration is used, individual calibration files must be assigned to the front and back chromatogram paths within the method settings.</li></ul><h4>Interface and Workflow Adjustments</h4><h5>Chromatogram and Instrument Windows</h5><ul><li>The Instrument Window is visually adapted to display both signal positions side by side.</li><li>The Chromatogram Window clearly labels which detector the chromatogram originated from by indicating position in the Measurement Conditions section.</li></ul><h5>Sequence Window Enhancements</h5><ul><li>Identification columns in the Sequence Window are designated separately for each chromatogram.</li><li>Other columns (like sample names, batch parameters) are shared and applied to both positions.</li></ul><h4>Reporting and Data Processing</h4><h5>Report Customization</h5><ul><li>Generated reports automatically include a dual mode label, indicating the chromatogram's origin (Front/Back).</li><li>All standard report formatting options remain supported.</li></ul><h5>Data Evaluation</h5><ul><li>The mode supports independent processing for each chromatogram.</li><li>All standard reprocessing operations—such as integration, calibration application, and result analysis - are supported independently for each position.</li></ul><h4>Conclusion</h4>Clarity’s Dual Chromatogram Mode offers robust functionality for dual-detector systems, providing synchronized acquisition while maintaining the independence of signal processing. This ensures analytical accuracy, ease of comparison, and flexible evaluation, especially in multi-detector chromatographic setups.<blockquote>For more information, see the Dual Chromatogram Mode manual:<ul><li><a target="_blank" rel="noopener noreferrer" href="https://gcms.cz/paper/30514">Clarity Extension DUAL CHROMATOGRAM MODE</a></li></ul>For further learning, watch more instructional content on the:<ul><li><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/@DataapexPrague">DataApex YouTube channel</a></li></ul></blockquote>

Dual Chromatogram Mode in Clarity: A Technical Overview

<h4>1. Introduction</h4>This article provides a comprehensive and structured troubleshooting guide for <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999">Clarity chromatography software </a>by DataApex. Based on the instructional video titled “What to do when you have issues with Clarity”, it outlines common errors, diagnostic methods, and recommended procedures for addressing technical problems in both software and hardware configurations.<h4>2. Required Tools and Environment</h4>To effectively troubleshoot Clarity, ensure you have access to the following:<ul><li>Clarity Software (version 9.x or 10.x)</li><li>Hardware key (HW key) – for license authorization</li><li>Windows administrator privileges</li><li>Connected instrumentation (GC/LC systems, A/D converters)</li><li>Diagnostic tools:<ul><li>Windows Event Viewer</li><li>Clarity Device Configuration Manager</li></ul></li></ul><h4>3. Common Errors and Solutions</h4><h5>3.1 File Access Errors</h5>Symptom:<ul><li>Error messages such as: "Unknown error accessing ... Temp\Clarity\$ch1run.raw"</li></ul>Cause:<ul><li>Lack of write permissions to the Temp directory.</li></ul>Solution:<ol><li>Ensure the Windows user has full access to the Temp\Clarity folder.</li><li>Run Clarity as Administrator to bypass restricted permissions.</li></ol><h5>3.2 Hardware Key Not Recognized</h5>Symptoms:<ul><li>"Clarity is unable to find HW key"</li><li>"Missing keylock drivers"</li><li>"Blocked HW key"</li></ul>Causes:<ul><li>Key not plugged in, damaged USB port, or missing driver.</li></ul>Solution:<ol><li>Reinsert the HW key into a direct USB port (avoid USB hubs).</li><li>If drivers are missing or outdated, reinstall the HW key drivers and restart the PC.</li><li>Contact DataApex support if the key is blocked or invalid.</li></ol><h5>3.3 Visual C++ Redistributable Installation Fails</h5>Error:<ul><li>"Exit code: 1618" during Clarity installation.</li></ul>Cause:<ul><li>Another installation is already running (e.g., Windows Update).</li></ul>Solution:<ul><li>Wait for the current installation to finish, restart the system, and rerun the Clarity installer.</li></ul><h5>3.4 Instrument Communication Failure</h5>Error:<ul><li>"Cannot establish communication with XXX SN xxx!"</li></ul>Possible Causes:<ul><li>Instrument is turned off or disconnected.</li><li>Wrong or missing driver.</li><li>Incorrect COM port or IP address.</li></ul>Solution:<ol><li>Power on the instrument and verify all connections.</li><li>Use Clarity → System Configuration → Devices to verify driver and port settings.</li><li>Restart the driver or reassign the port if needed.</li></ol><h5>3.5 RAW File Creation Errors</h5>Error:<ul><li>"Cannot create RAW file"</li><li>"Cannot create $ch1temp.raw"</li></ul>Cause:<ul><li>Clarity fails to rename the RAW file due to a file conflict or improper termination.</li></ul>Solution:<ul><li>Ensure the previous acquisition was closed properly.</li><li>Clear error dialogs and restart the acquisition.</li></ul><h5>3.6 Project Change Requires Restart</h5>Error:<ul><li>"Changing project requires to restart instrument."</li></ul>Solution:<ul><li>Save your changes and allow the instrument to restart as prompted.</li></ul><h5>3.7 Configuration File Corruption or Version Conflict</h5>Errors:<ul><li>"Configuration file is not valid"</li><li>"Incompatible device driver"</li></ul>Cause:<ul><li>Attempting to load a project or method created in a newer software version.</li></ul>Solution:<ol><li>Use backup files provided by Clarity.</li><li>Reconfigure devices manually if needed.</li><li>Install matching drivers compatible with your current Clarity version.</li></ol><h5>3.8 Method and Table Errors</h5>Common Issues:<ul><li>"Fraction table contains overlapping time intervals"</li><li>"Too many peaks in chromatogram"</li><li>"Method file does not match instrument configuration"</li></ul>Solution:<ul><li>Adjust fraction time intervals to prevent overlaps.</li><li>Tweak peak detection settings (width, threshold).</li><li>Modify or recreate the method to reflect hardware changes.</li></ul><h4>4. General Troubleshooting Workflow</h4><ol><li>Reboot your PC – resolves many temporary issues.</li><li>Check file and folder permissions – especially the Temp and project directories.</li><li>Verify hardware connections – including USB and serial ports.</li><li>Update or reinstall drivers – HW key, devices, or Clarity modules.</li><li>Restore from backups – when configuration or method files are corrupted.</li></ol><h4>5. Analysis and Best Practices</h4><ul><li>70% of reported issues are related to permissions, HW key problems, or outdated drivers.</li><li>Always keep Clarity and related drivers updated from the official source.</li><li>Ensure project and method files are compatible with the Clarity version you are using.</li><li>Use administrative privileges when installing or configuring hardware/software.</li></ul><h4>6. Conclusion</h4>Clarity is a robust chromatography software platform, but like any system, it may encounter operational or configuration errors. This guide outlines practical and verified troubleshooting techniques derived from real-world scenarios shown in the DataApex tutorial video.For persistent or unclear issues, consult the DataApex Support Portal for documentation, driver downloads, and direct contact with technical support.<blockquote><h5>Quick Tips Recap</h5><ul><li>Always start with a reboot and check permissions.</li><li>Reinstall drivers if devices or keys are not recognized.</li><li>Use correct project/method versions matching your Clarity installation.</li></ul></blockquote>

Troubleshooting Guide: Resolving Issues with Clarity Chromatography Software

<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999">Clarity</a> is a professional chromatography data system (CDS) developed by DataApex. This article provides a technical guide to how Clarity organizes and stores its files. You will learn about each key directory, the types of data stored, best practices for backup and transfer, and file dependencies that must be preserved.<h4>🗂️ Main Folder Structure</h4>Once Clarity is installed, several important folders are created within the installation directory:<h5>1. Bin Folder</h5><ul><li>Contains the Clarity software executable files and essential utilities:<ul><li>IQ (Installation Qualification)</li><li>Launch Manager</li></ul></li><li>No user modification or backup is needed here.</li></ul><h5>2. CFG (Configuration) Folder</h5><ul><li>Stores station configuration and user-specific settings.</li><li>Includes:<ul><li>Device configuration files</li><li>User layout files (.DSK)</li><li>Audit trails</li><li>Diagnostic data</li></ul></li><li>Essential for backup and station transfer.</li></ul><h5>3. DataFiles Folder</h5><ul><li>Stores all chromatographic measurement data.</li><li>Organized by projects—details provided in the next section.</li></ul><h5>4. Documentation Folder</h5><ul><li>Includes data sheets, user manuals, and relevant documents for the installed software version.</li></ul><h5>5. uninstall.exe</h5><ul><li>Used to uninstall Clarity from the system.</li></ul><h4>What Should Be Backed Up?</h4>When backing up or transferring a Clarity installation, it is critical to retain the following:<ul><li>The entire CFG folder – contains configuration, settings, and audit data.</li><li>The DataFiles folder – contains all project data and chromatograms.</li><li>Key files:<ul><li>configuration.cfg – station/device setup</li><li>desktop.dsk – user interface layout</li><li>clarity.psw – password storage</li></ul></li></ul><h4>Understanding the DataFiles Folder Structure</h4>Clarity uses a project-based architecture for storing measurement data. The structure of the DataFiles folder is as follows:Top-Level Contents of DataFiles<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Top_Level_Contents_of_Data_Files_ce779a1797.jpg" alt="DataApex: Table 1 Top-Level Contents of DataFiles" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Top_Level_Contents_of_Data_Files_ce779a1797.jpg 245w," sizes="100vw" width="1600" height="377">Inside a Project FolderEach project folder contains the following:<ul><li>Main project directory:<ul><li>Method files (*.met)</li><li>Sequence files (*.sqt)</li><li>SST files (*.sst)</li></ul></li><li>Subfolders (created by default):<ul><li>Calib – for calibration chromatograms and standards</li><li>Data – for unknown samples and bypass measurements</li></ul></li></ul>Users may create subfolders inside Calib and Data for better organization by date, sample type, etc.⚠️ Important: Do not create subfolders outside of Calib and Data. Improper structure may break internal file links and lead to system errors.<h4>📁 Example Files and Their Functions</h4><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Example_Files_and_Their_Functions_f1924494e5.jpg" alt="DataApex: Table 2 Example Files and Their Functions" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Example_Files_and_Their_Functions_f1924494e5.jpg 245w," sizes="100vw" width="1600" height="639"><h4>Best Practices</h4><ul><li>Regularly back up both CFG and DataFiles folders.</li><li>When transferring Clarity to a new PC:<ol><li>Install Clarity as usual.</li><li>Copy over the CFG and DataFiles folders.</li></ol></li><li>Avoid moving or editing files manually outside of permitted folders (Calib, Data).</li></ul><h4>Conclusion</h4>Proper file management in Clarity ensures a stable and reliable workflow. By following the recommended folder structure and backup strategy, users can safeguard their analytical data, simplify system migration, and avoid common issues.

Clarity File Storage and Organization: A Complete Guide

🎤 Presenter: Ivo Novotny (LabRulez, Prague, Czech Republic)💾 <a target="_blank" rel="noopener noreferrer" href="https://gcms.cz/paper/28892">PDF presentation</a><blockquote>💡 Book in your calendar: <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/events/787">17th Multidimensional Chromatography Workshop (MDCW)</a> 13 - 15. January 2026</blockquote><h3>Abstract</h3>LabRulez portals [1] are a unique global concept focused on quick, simple and effective access to information, especially in the field of analytical chemistry. State-of-the-art IT technologies thus enable visitors to search, filter, and find information in one place, which would otherwise be time-consuming and sometimes impossible to find.Information from GC×GC and 2DLC area are heavily represented mainly on the LabRuleuGCMS and LabRulezLCMS [2] portals, providing visitors with an unique source of news, applications, instrumentation and consumables overview and e.g. expert webinars or career section focused on analytical chemistry jobs. Together we will see how to work with and search this information.Stop looking and start finding. Fast, efficient and in one place. Anyone can create a profile on the LabRulez analytical portals in ENG language. Whether you are an individual, a research group, a university or a company. Build your brand and share information in the community of (not only) analytical chemists.[1] <a target="_blank" rel="noopener noreferrer" href="https://labrulez.com">https://labrulez.com</a> [2] <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com">https://gcms.labrulez.com</a>, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com">https://lcms.labrulez.com</a><h3>Video transcription</h3><h4>Introduction</h4>In a presentation at the MDCW conference, Ivo Novotný, CEO of LabRulez, introduced a global digital platform revolutionizing how scientists access and share analytical chemistry information. Designed to support researchers, universities, manufacturers, and laboratories, the LabRulez portals bring together content from across the scientific community in one centralized, searchable space.<h4>What Is LabRulez?</h4>LabRulez is a network of specialized portals that enables fast, targeted access to scientific information in analytical chemistry. The platforms integrate the latest web technologies to help users search, filter, and access data that would otherwise be difficult—or impossible—to find efficiently.<blockquote><h5>Core mission:</h5>Help analytical chemists find the right information quickly, and help institutions share their knowledge with the world.</blockquote><h5>Reach and Impact</h5><ul><li>Over 20 million Google search impressions annually</li><li>1+ million documents opened from the library</li><li>Nearly 1 million page views yearly</li><li>Extensive reach across social networks and scientific communities</li></ul><h4>The LabRulez Portal Ecosystem</h4>There are currently three main LabRulez portals:<ul><li><a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/">LabRulez GCMS</a> – Focused on gas-phase analytical techniques</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/">LabRulez LCMS</a> – Covers liquid-phase chromatography and mass spectrometry</li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/">LabRulez ICPMS</a> – The newest portal, dedicated to spectroscopy and elemental analysis</li></ul><h4>Key Functionalities and Benefits</h4><h5>User Profiles</h5><ul><li>Any company, research group, or individual can create a profile</li><li>Profiles serve as centralized hubs with:<ul><li>Contact info</li><li>Publications</li><li>Application notes</li><li>Webinars</li><li>Linked content across the portal</li></ul></li></ul><h5>Advanced Searchable Library</h5><ul><li>A non-scientific library with powerful filters</li><li>Find PDFs, posters, and presentations from events like MDCW</li><li>Filter by technique (e.g. GC×GC, 2DLC), manufacturer, content type, etc.</li><li>Hundreds of GC×GC and 2DLC-related documents freely accessible</li></ul><h5>News Section</h5><ul><li>Share company updates, research group news, or announcements</li><li>All conference content (past and present) is available online</li></ul><h5>Webinar Database</h5><ul><li>Largest analytical chemistry webinar database globally</li><li>Over 4,000 webinars</li><li>80+ specifically on GC×GC</li><li>Filterable by technique, application, speaker, etc.</li><li>Free and open access</li></ul><h5>Product Section (Marketplace)</h5><ul><li>Amazon-style overview of techniques, instruments, services, and manufacturers</li><li>Currently launching the commercial product portal in English</li><li>Built on success of the Czech-language version</li><li>Designed to support discoverability of products and services in analytical labs</li></ul><h5>Job Portal</h5><ul><li>Unique job search by:<ul><li>Technique</li><li>Country/Region</li><li>Employer type</li></ul></li><li>Supports global mobility and career development in analytical chemistry</li></ul><h4>What’s Next? LabRulez Roadmap</h4><ol><li>Virtual Academic Training Center<ul><li>A curated “Wikipedia” for analytical chemistry—high-quality, structured educational content</li></ul></li><li>Refurbished Equipment Marketplace<ul><li>A scientific eBay-style platform for buying and selling used instruments</li><li>Consumables section in development</li></ul></li><li>AI Integration<ul><li>Plans to leverage artificial intelligence for personalized data discovery</li></ul></li><li>Global Expansion<ul><li>From Czech Republic to global portals</li><li>Upcoming launches: Germany, Italy, France, and more</li></ul></li></ol><h4>Conclusion</h4>LabRulez is not just a portal—it’s an evolving ecosystem that brings together researchers, instrument manufacturers, and labs into one vibrant community. Whether you're searching for application notes, scientific webinars, conference posters, or a new job in analytical chemistry, LabRulez helps you stop looking and start finding.<blockquote>🔗 <a target="_blank" rel="noopener noreferrer" href="https://labrulez.com">Explore LabRulez</a> 🔗<a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com">GCMS Portal</a> 🔗<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com">LCMS Portal</a></blockquote><blockquote> This text has been automatically transcribed from a video presentation using AI technology. It may contain inaccuracies and is not guaranteed to be 100% correct.</blockquote>

The LabRulez portals: a unique source of information not only in the field of GCxGC and 2DLC (Ivo Novotný, MDCW 2025)

Manual population of sequence and calibration tables can be a time-consuming task in chromatography data systems. <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999">Clarity software</a> from DataApex offers two powerful tools—Fill Down and Fill Series—to streamline this process and reduce repetitive typing. This article provides a structured and technical explanation of how to use these features effectively within Clarity, enabling users to improve their workflow efficiency during method setup and sample analysis.<h4>Tools and Environment</h4><ul><li>Software: Clarity Chromatography Data System</li><li>Modules Covered: Sequence Table, Calibration Table</li><li>User Access: Requires access to sequence or calibration tables within Clarity</li><li>Navigation: Edit menu or right-click (local menu) access to commands</li></ul><h4>Overview of Table Filling Commands</h4>Clarity provides two primary functions for populating table columns:<ul><li>Fill Down: Replicates the content of a single cell downward through the column.</li><li>Fill Series: Fills a range of selected cells with a numeric or text pattern, typically incremented values.</li></ul>These commands can be invoked from:<ul><li>The Edit menu in the main application window.</li><li>The local (right-click) menu within a specific table.</li></ul><h4>Step-by-Step Procedure</h4><h5>1. Using Fill Down</h5>This function is used to copy the contents of the currently selected cell to all cells below it in the same column.Instructions:<ol><li>Open the sequence or calibration table in Clarity.</li><li>Select the cell containing the value to be copied.</li><li>Navigate to Edit &gt; Fill Down or right-click and select Fill Down.</li><li>All cells below the selected cell in the same column are populated with the same content.</li></ol>Use Case Example: If "Unknown 1" is typed in a single row, Fill Down can replicate "Unknown 1" across all subsequent rows of that column.<h5>2. Using Fill Series</h5>Fill Series is used when a user needs to populate a sequence of incrementally numbered or structured entries.Instructions:<ol><li>Select the range of cells in a column you wish to populate.</li><li>Right-click the selection and choose Fill Series from the local menu.</li><li>A dialog window titled Fill Series appears.</li><li>Enter the desired increment value (e.g., 2).</li><li>Click OK to apply the series.</li></ol>Example Scenario:<ul><li>If you start with “Unknown 1” and apply an increment of 2, the resulting entries will be:<ul><li>Unknown 1</li><li>Unknown 3</li><li>Unknown 5</li></ul></li></ul>The increment applies to the numeric component of the entry while maintaining the text prefix.<h4>Functional Notes and Best Practices</h4><ul><li>Partial Column Filling: Both Fill Down and Fill Series work on selected cells only, allowing partial updates without overwriting the entire column.</li><li>Reversible Actions: All filling operations can be undone using the standard Undo feature if applied incorrectly.</li><li>Numeric Incrementation: Fill Series interprets trailing numbers in strings and adjusts only the numeric portion.</li><li>Flexibility: The Fill Series dialog also includes a switchable option to use Fill Down as an alternative, depending on user need.</li></ul><h4>Benefits of Using Fill Functions</h4><ul><li>Time Efficiency: Reduces manual typing, especially for large sequences.</li><li>Error Reduction: Minimizes input errors from repetitive data entry.</li><li>Standardization: Ensures consistent naming conventions across rows.</li></ul><h4>Conclusion</h4>The Fill Down and Fill Series features in Clarity provide powerful, user-friendly tools for populating sequence and calibration tables quickly and accurately. By leveraging these commands, laboratory professionals can improve workflow efficiency, reduce errors, and maintain consistent data entry standards across analytical sequences.

Efficient Table Population in Clarity Software: Using Fill Down and Fill Series Functions

<h3>1. Introduction</h3>This tutorial video demonstrates how to use a template sequence within the<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999"> Clarity chromatography software</a>. It focuses on automating parameters that frequently repeat when building analysis sequences, thereby increasing efficiency and reducing data entry errors.<h3>2. Tools and Prerequisites</h3><ul><li>Software: DataApex Clarity chromatography software with sequence functionality enabled.</li><li>Template Sequence: A preconfigured sequence file to prefill recurring parameters.</li><li>User Context: Recommended for users who frequently run similar batches of analyses.</li></ul><h3>3. Objective</h3>The goal is to automatically prefill repeating sequence parameters (e.g. run names, sample types, injection volumes) via a template, rather than entering them manually each time. Especially valuable in high-throughput or standardized lab workflows.<h3>4. Step‑by‑Step Procedure</h3><h4>4.1 Prepare a Base Sequence</h4><ul><li>Open Clarity and create a sequence that includes all desired fields populated with default or typical values.</li><li>Ensure metadata and method parameters reflect your most common use case.</li></ul><h4>4.2 Save as Template</h4><ul><li>Save or export this sequence layout as a template sequence file.</li><li>This file captures both column definitions and parameter defaults.</li></ul><h4>4.3 Apply Template to New Sequences</h4><ul><li>When creating a new analysis sequence:<ul><li>Select the saved template.</li><li>The sequence grid populates automatically with prefilled entries.</li><li>Only fill in sample‑specific information (e.g. new sample IDs, actual run dates).</li></ul></li></ul><h4>4.4 Review and Adjust</h4><ul><li>Confirm all parameters such as run parameters, autosampler settings, and sample descriptors.</li><li>Optional: Edit fields manually if slight variations are needed for certain runs.</li></ul><h3>5. Key Benefits and Discussion</h3><h4>5.1 Time Savings</h4><ul><li>Reduces repetitive manual input across sequences.</li><li>Ideal for laboratories that frequently use standardized analysis protocols.</li></ul><h4>5.2 Error Minimization</h4><ul><li>Ensures consistency in method definitions and reduces typos or omissions.</li><li>Helps maintain compliance and traceability.</li></ul><h4>5.3 Workflow Scalability</h4><ul><li>Template sequences facilitate batch processing across multiple users or instruments.</li><li>Enables fast replication of standardized methods.</li></ul><h3>6. Best Practices</h3><h4>6.1 Keep Templates Updated</h4><ul><li>Periodically review and update your template as protocols evolve.</li><li>Ensure columns reflect current metadata needs (e.g. updated identifiers, flags).</li></ul><h4>6.2 Version Control and Naming</h4><ul><li>Use a naming convention (e.g. Template_Common_Run_v1) to track revisions.</li><li>Store older versions to support reproducibility or audit trails.</li></ul><h4>6.3 Validation and Training</h4><ul><li>Validate a template with a test run before full deployment.</li><li>Train users on selecting and applying templates consistently.</li></ul><h3>7. Example Use Case</h3><ul><li>Scenario: A chromatography lab runs a daily series of QC samples with identical method settings but different sample IDs.</li><li>Template Setup: The method, flow rate, detector settings, and injection volume are prefilled.</li><li>Execution: When generating a new sequence, the operator only enters sample identifiers and run date; the rest is inherited automatically.</li></ul><h3>8. Conclusion</h3>The Clarity template sequence feature significantly streamlines lab workflows by automating recurring sequence parameters, ensuring standardization, efficiency, and reduced error rates. Its use is particularly beneficial in environments with repetitive analytical tasks. Periodic template review and adherence to versioning best practices help maintain accuracy and usability over time.<h3>9. Summary of Benefits</h3><h4>Benefit&nbsp;&nbsp;/&nbsp;&nbsp;Description</h4><ul><li>Efficiency: Faster creation of analysis sequences</li><li>Consistency: Uniform formatting and method application</li><li>Error Reduction: Minimizes manual data entry and associated mistakes</li><li>Scalability: Facilitates broader use across teams and instruments</li></ul>By adopting template sequences in Clarity, laboratories can simplify recurring tasks, maintain uniformity in methods, and optimize throughput.

How to use template sequence effectively 

<h3>Introduction</h3>In chromatographic data analysis, efficient handling of measured chromatograms is crucial for productivity and accuracy. This technical guide provides a step-by-step explanation of how to open and manage chromatograms that were measured as part of a sequence using <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999">Clarity Chromatography Software</a>. The procedures outlined are based on a demonstration video from DataApex’s official YouTube channel and are tailored for users seeking a streamlined analytical workflow.<h3>Tools and Software</h3><ul><li>Software: Clarity Chromatography Software by DataApex</li><li>System Requirements: PC with sufficient RAM to handle multiple chromatograms in memory</li><li>Prerequisites:<ul><li>A completed measurement sequence</li><li>Access to the Sequence and Chromatogram windows in the software</li></ul></li></ul><h3>Method 1: Opening Chromatograms from the Sequence Window</h3><h4>Step 1: Navigate to the Sequence Window</h4><ul><li>Open the Sequence window within Clarity.</li><li>Load a previously measured sequence.</li></ul><h4>Step 2: Expand the Status Cell</h4><ul><li>Locate the status cell in a row corresponding to a finished measurement.</li><li>If the row produced chromatograms, the status cell is expandable.</li><li>Click on the arrow icon in the status cell to reveal a local menu.</li></ul><h4>Step 3: Select Chromatograms to Open</h4><ul><li>In the local menu, select one or more chromatograms you wish to open from that row.</li><li>The chromatograms will open in overlay mode.</li></ul><h4>Note on Overlay Mode</h4><ul><li>Overlay mode is automatically enabled when multiple chromatograms are opened using this method.</li><li>By default, a maximum of 20 chromatograms can be opened in overlay mode.</li><li>If more chromatograms are selected, the earliest one opened will be automatically closed.</li></ul><h4>Optional: Adjust the Overlay Limit</h4>To change the default overlay limit:<ol><li>Go to the Instrument window menu.</li><li>Navigate to: <code>Setting</code> &gt; <code>User Options</code></li><li>In the General tab, locate the Limit section.</li><li>Adjust the maximum number of chromatograms allowed in overlay mode.</li></ol><blockquote>⚠️ Recommendation: Set a reasonable limit based on your system’s memory capacity. Opening too many chromatograms simultaneously can lead to performance issues.</blockquote><h3>Method 2: Opening All Chromatograms from the Chromatogram Window</h3><h4>Step 1: Navigate to the Chromatogram Window</h4><ul><li>Ensure that no chromatograms are currently open, or manually close them if needed.</li></ul><h4>Step 2: Use the File Menu</h4><ul><li>Go to the File menu.</li><li>Select Open Chromatograms from Sequence to invoke the file selection dialog.</li></ul><h4>Step 3: Select and Confirm</h4><ul><li>Choose the desired measured sequence from the dialog box.</li><li>Confirm the selection.</li></ul>All chromatograms associated with the selected sequence will now open simultaneously in the chromatogram window.<h3>Conclusion</h3>Clarity Chromatography Software offers flexible options for opening chromatograms measured in a sequence. Whether accessed from the Sequence window for selective viewing or from the Chromatogram window for batch loading, both approaches enhance the user’s ability to review data efficiently. By adjusting overlay settings to match system capabilities, users can tailor the experience to their specific workflow needs.<blockquote>For further video tutorials and advanced tips, visit the <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/@DataapexPrague">DataApex YouTube Channel</a>.</blockquote>

 How to open chromatograms from a sequence 

<h3>Introduction</h3>The <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999">Clarity Chromatography Software</a> provides advanced tools for managing chromatographic sequences. Correct configuration of sequence options is crucial, as it defines how the sequence table operates, how runs are executed, and how results are stored. This article provides a step-by-step guide to setting up sequence options, based on an instructional video demonstration.<h3>Accessing the Sequence Options Dialog</h3><ol><li>Open the Sequence Window.</li><li>Select the Options icon from the toolbar, or choose the Options item from the Sequence menu.</li><li>The Sequence Options dialog will appear, containing several configurable sections.</li></ol><h3>Sequence Description</h3>At the top of the dialog, you will find a Description field. This is a free-text area where you can enter notes or identifiers for the sequence. Although optional, it is useful for documenting specific experiment details.<h3>Sequence Mode</h3>This section controls how Clarity handles the start of a sequence:<ul><li>Passive Mode<ul><li>Clarity waits for an external start signal (e.g., from a connected device).</li><li>Commonly used for manual injections or with uncontrolled autosamplers.</li><li>The run begins when triggered by an external event, such as turning a manual injection valve.</li></ul></li><li>Active Mode (default option)<ul><li>Clarity manages the entire process.</li><li>It waits for all devices to be ready, then signals the autosampler to inject.</li><li>Once injection is complete, the run starts automatically.</li><li>Suitable for the majority of automated workflows.</li></ul></li></ul>For more detailed instrument-specific settings, refer to Chapter 6 of the Getting Started Manual.<h4>Idle Time in Active Mode</h4>You can configure a delay (idle time) between the end of one run and the start of the next injection. This feature is useful if:<ul><li>Devices require additional stabilization time.</li><li>Too many commands at once could cause communication issues.</li></ul><h3>Sequence Row Selection</h3>This field allows you to specify which rows in the sequence table will be executed.<ul><li>The software automatically sets the corresponding checkboxes in the Run column.</li><li>You may still manually adjust them afterwards.</li></ul><h3>Counter Variable Settings</h3>The counter variable can be configured here to increment automatically during the sequence.<ul><li>The counter can be used for labeling runs or files.</li><li>It increments with every new run in the sequence.</li><li>Depending on configuration, it may or may not reset.</li></ul><h3>File Name Conflict Resolution</h3>When multiple analyses are initiated from one row, file naming conflicts may occur. Two options are available:<ul><li>Automatic (default)<ul><li>Clarity appends a vial or injection variable to the file name, preventing duplication.</li></ul></li><li>Manual<ul><li>The user resolves conflicts manually before saving.</li></ul></li></ul><h3>Calibration and Sequence Usage</h3>This section allows you to define the type of calibration cloning used within the sequence.<ul><li>For a full explanation of calibration settings, refer to the<a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=aX-BwAXb0dI&amp;list=PLSPrHzY76_FRTmmtEUbaaQj2NrrGM3PCC"> Calibration playlist</a> provided by Clarity.</li></ul><h3>After Sequence Is Finished</h3>At the end of the sequence, you can set a shutdown method for devices.<ul><li>For example, powering down pumps or turning off detectors.</li><li>A detailed explanation is available in the related tutorial: “<a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=B2NHqaNf05Q">How to Shut Down Devices After the Sequence Is Finished.</a>”</li></ul><h3>Saving and Applying Settings</h3>Once configuration is complete:<ol><li>Click OK to save the sequence options.</li><li>The parameters will apply immediately to the open sequence file.</li></ol><h3>Example Configuration (from video demonstration)</h3><ul><li>Mode: Active</li><li>Idle Time: 5 minutes</li><li>Rows Executed: Only rows 2 and 4</li><li>Row 4: End vial edited to allow multiple measurements</li><li>File Name Conflicts: Solved automatically by appending the vial variable</li><li>Counter Variable: Starts at 5, increments with each run, never resets</li></ul><h3>Conclusion</h3>Configuring sequence options in Clarity Chromatography Software ensures smooth operation, consistent data handling, and efficient automation. By mastering the settings for sequence mode, idle time, file naming, calibration, and shutdown methods, analysts can tailor workflows to specific laboratory requirements.<blockquote><h4>For further guidance, users are encouraged to consult:</h4><ul><li>Chapter 6 of the Getting Started Manual</li><li><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=aX-BwAXb0dI&amp;list=PLSPrHzY76_FRTmmtEUbaaQj2NrrGM3PCC">Calibration tutorials</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=B2NHqaNf05Q">Device shutdown video guide</a></li></ul></blockquote>

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