<h3>Introduction</h3>
Besides its use in analytical GC, HPLC and CE, the Clarity chromatography software is well suited also for control of preparative chromatography systems. Using the FCGP (General Purpose Fraction Collector) control module, many different fraction collectors could be controlled by the simple Next and Collect/Waste commands generated by the module and transferred to the devices either through the digital Outputs/Inputs or by suitable communication line (RS232, LAN, GSIOC). Not only dedicated fraction collectors, but also multi-position valves could be controlled. The fraction collection parameters (including time windows and signal level or slope triggered collection) are defined within the Clarity FC-GP method setup. 
Two examples of automated systems used for isolation and purification of antibodies, based on common instrumentation and controlled by Clarity chromatography software are presented.
<h3>Automated Immunoaffinity Chromatography</h3>
This instrument setup is designed to isolate specific antibodies from clarified serum. The serum is obtained from an animal immunized with the antigen which we want to generate antibodies against. The media in the column has the same or a similar antigen covalently bound to it, in order to capture antibodies which are specific to that antigen. 
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Fig_1_Diagram_of_the_immunoaffinity_separation_system_2453e733ba/DataApex-Fig.-1-Diagram-of-the-immunoaffinity-separation-system.jpg" alt="DataApex: Fig. 1 – Diagram of the immunoaffinity separation system"/>
The instrument is configured around our existing lab infrastructure (benches, racks, shelves, rods for mounting columns, etc.). A 6 position selector valve allows selection of serum, a wash buffer, an elution buffer, or a column cleaning buffer. The unused positions are plugged so that they can be selected to put the instrument into a standby state which prevents any siphoning of the mobile phases due to gravity. 
The output of the selector valve leads to the pump. Immediately after the pump is a backpressure regulator to ensure proper seating of the check valves and a second one, serving as a pressure relief valve, as the pump does not feature pressure monitoring.
The tubing is then plumbed into a 6 port, 2 position valve, used to allow the direction of flow through the column to be reversed (see plumbing diagram). This allows strongly retained antibodies at the top of the column to be eluted quickly, with minimal exposure to the harsh elution buffer. After flowing through the column, the mobile phase returns to the valve and is directed through pH and UV detectors to a second 6 position selector valve, where the output can be directed to reservoirs for waste, eluted material, or material to be reloaded for further processing. 
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Fig_2_Example_of_the_elution_cycle_in_immunoaffinity_separation_09c29ecf9a/DataApex-Fig.-2-Example-of-the-elution-cycle-in-immunoaffinity-separation.jpg" alt="DataApex: Fig. 2 - Example of the elution cycle in immunoaffinity separation"/>
Currently we have 13 instruments in service that match this general description. Each instrument takes up roughly 50 cm x 50 cm of bench space, making use of shelving above the bench to hold large reservoirs. The “prototype” for this instrument design was assembled primarily from components we had in our lab that were not in use.
The full version of Clarity with the LC module is used on all instruments in order to allow for expansion. Most of the stations already have the maximum number of 4 instruments installed. Serial communication ports for the valves and pumps are provided by a DataApex Multicom device. All valves are mounted on Valco Microelectric Actuators with RS-232 communication. Analog signals from the pH probe and UV absorbance detector are acquired using either an INT9 A/D PCI card, a 4 channel Colibrick device, or a 2 channel UPAD, depending on the instrument. The PCs used are from various manufacturers, or are built to specifications in house.
<h5>Table 1- Immunoafinity System Components</h5>
<h5>No. / Name / Description</h5>
<ol>
<li>Reservoirs / Sample, Wash, Eluent, Column Cleaning</li>
<li>Selection valve / 6 position selector valve, (Valco, C25-6186EMH)</li>
<li>Pump / SSI/LabAlliance Series 1 Pump (Chromtech, P-040), with 40 ml/min heads</li>
<li>Backpressure regulator / 40 psi, to provide backpressure for pump valves</li>
<li>Backpressure regulator / 100 psi, connected by a tee, serving as pressure relief valve</li>
<li>Switching valve / 6 port, 2 position valve (Valco C22-6186EH)</li>
<li>Column / 5 cm diameter x 5 cm length</li>
<li>pH detector / Flow cell (Sensorex, FC45C) with Flat pH electrode (Sensorex, S450CD)</li>
<li>UV detector / UV absorbance detector (Bio-Rad, EM-1)</li>
<li>Selection valve / 6 position selector valve, (Valco, C25-6186EMH)</li>
<li>Reservoirs / Waste, Pure Product, Impure Product for reloading</li>
</ol>
1/8” ID Dupont PFA tubing is used throughout for connections
Multiple isolation cycles are needed to process the starting material quantity. The sequence table is thus used to control the instrument. Separate methods are written for the loading, washing, elution, and cleaning phases of the process. These methods are then repeated in the sequence to create cycles, which can be performed automatically until the desired amount of material has been processed. Sequences can also be run overnight, with the primary limitation being the size of the mobile phase and collection reservoirs. 
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Fig_3_Example_of_sequence_table_for_immunoaffinity_separation_58a994a3fe/DataApex-Fig.-3-Example-of-sequence-table-for-immunoaffinity-separation.jpg" alt="DataApex: Fig. 3 - Example of sequence table for immunoaffinity separation"/>
<h3>Preparative size exclusion chromatography with stacked injections using Clarity</h3>
This instrument setup is designed to facilitate removal of aggregates and other high molecular weight species from antibodies. Generally, the harshness of the elution buffer used in the affinity step leads to some degree of aggregation in the isolated antibodies.
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Fig_4_Diagram_of_the_Stacked_Injection_SEC_system_a7622a7986/DataApex-Fig.-4-Diagram-of-the-Stacked-Injection-SEC-system.jpg" alt="DataApex: Fig. 4 - Diagram of the Stacked Injection SEC system"/>
A 6 position selector valve is used to switch between a sample reservoir and a running buffer reservoir. This is connected to a pump, with backpressure regulator configured as a blow-off valve in order to protect the column from excessive pressure in the event of a clog. The outlet of the column is connected to a UV absorbance detector. Fractions are collected using a fraction collector. 
<h5>Table 2 - Size Exclusion System Components</h5>
<h5>No. / Name / Description</h5>
<ol>
<li>Reservoirs / Sample, Eluent, Column Cleaning</li>
<li>Selection valve / 6 position selector valve, (Valco, C25-6186EMH)</li>
<li>Pump / SSI/LabAlliance Series 1 Pump (Chromtech, P-040), with 40 ml/min heads</li>
<li>Backpressure regulator/ 40 psi, to provide backpressure for pump valves</li>
<li>Backpressure regulator / 100 psi, connected by a tee, serving as pressure relief valve</li>
<li>Column / 5 cm x 100 cm (GE, XK-50/100) column packed with Superdex 200 Prep Grade.</li>
<li>UV detector / UV absorbance detector (Bio-Rad, EM-1)</li>
<li>Fraction collector / Isco Foxy 200 fraction collector</li>
</ol>
1/8” ID Dupont PFA tubing is used throughout for connections.
Again, multiple injections are needed to load all the sample to be processed. In order to reduce the time required to process large samples, a stacked injection technique is used. As a run begins, the solvent selection valve loads the first portion of the sample from the sample reservoir then switches back to the running buffer.
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Fig_5_Example_of_Stacked_Injection_Method_Event_Table_687cda6e11/DataApex-Fig.-5-Example-of-Stacked-Injection-Method-Event-Table.jpg" alt="DataApex: Fig. 5 - Example of Stacked Injection Method Event Table"/>
After the first portion has migrated some distance down the column, the valve switches to the sample reservoir loading a second portion. After the second portion has migrated down the column a third can be loaded, and so on. If the characteristics of the sample are known, spacing between samples can be reduced significantly versus loading one sample and waiting for it to elute completely. In one example, a single sample takes 165 minutes to elute completely, however 8 samples can be processed in 790 minutes, saving almost 9 hours by using stacked injections. Multi-gram quantities of material can be processed per day using this technique. 
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Fig_6_Example_of_stacked_injection_SEC_separation_019f37638a/DataApex-Fig.-6-Example-of-stacked-injection-SEC-separation.jpg" alt="DataApex: Fig. 6 - Example of stacked injection SEC separation"/>
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Fig_7_Detail_of_stacked_injection_SEC_separation_cycle_bc1be53e3f/DataApex-Fig.-7-Detail-of-stacked-injection-SEC-separation-cycle.jpg" alt="DataApex: Fig. 7 - Detail of stacked injection SEC separation cycle"/>
<h3>Conclusion</h3>
We have demonstrated the use of Clarity in purification of antibodies using two specific setups, the automated immunoaffinity chromatography and preparative size exclusion chromatography with stacked injections.
Similar setups can be used with large range of fraction collectors and multi-position valves. The description can also help with setting up systems for other preparative applications.
<h3>Featured Clarity products</h3>
In both applications the same Clarity Chromatography Software system has been used:
<h5>Table 3 - Clarity Software Components (Item - p/n)</h5>
<ul>
<li>Clarity Single Instrument - C50</li>
<li>LC Control Module - A24</li>
<li>AD Converters- e.g. Colibrick 4 ch - U34</li>
<li>Add on instruments (optional – to control more systems from 1 station) - C55</li>
</ul>

Automated SW solution for preparative HPLC

Invitation to ISC 2024 - Early Bird Registration Ending Soon! 

<h4>Here's what Clarity 10.0 offers:</h4>For a comprehensive function overview, please refer to the full details on our website. Also, check our Upgrade policy.&nbsp;<ul style="margin-top:0px;"><li>Dual Chromatogram Mode: two samples can be measured during one analysis using dual tower or dual loop samplers.</li><li>Extended GLP options for regulated environments.</li><li>Many improvements for Clarity Extensions: MS, PDA, DHA, NGA.</li><li>Updated and new control modules.</li></ul>For a comprehensive function overview, please refer to <a target="_blank" rel="noopener noreferrer" href="https://www.dataapex.com/news/140846/clarity-10-released">the full details on our website</a>. Also, check our <a target="_blank" rel="noopener noreferrer" href="https://www.dataapex.com/product/upgrade">Upgrade policy</a>.Upgrade now and experience Clarity 10.0!<blockquote><a target="_blank" rel="noopener noreferrer" href="https://www.dataapex.com/product/clarity-demo">GET FREE DEMO</a><ul><li>Check the <a target="_blank" rel="noopener noreferrer" href="https://www.dataapex.com/version_history?product=1&amp;version=10.0">What is new</a>.</li><li>Read the <a target="_blank" rel="noopener noreferrer" href="https://www.dataapex.com/downloads/140899/view">Clarity (Lite) 10 vs. 9.0</a> guide.</li></ul></blockquote>&nbsp;Thank you for your trust in our products,Your DataApex team<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Dataapex_Clarity_10_released_91e9897b7d.jpg" alt="Dataapex: Clarity 10 chromatography software released" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Dataapex_Clarity_10_released_91e9897b7d.jpg 227w," sizes="100vw" width="800" height="550"><h3><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999">DataApex Clarity Chromatography Software</a></h3>Clarity is a chromatography data software for data acquisition, processing, and instrument control in regulated environment. Clarity is a flexible solution for devices from different vendors, supporting different applications.Optional control modules provide integrated control of selected instruments such as GCs, LCs, pumps, detectors, autosamplers, etc. Extensions provide functions for specific separation techniques or calculations such as PDA, GPC analysis, Mass spectrometry, or SST. Clarity can run in English, French, German, Russian, Spanish, and Chinese language. Support technicians and developers are close to their users and ready to provide extensive Support from DataApex.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Clarity_Chromatograficky_Software_3_4adabdd9a6/DataApex-Clarity-Chromatograficky-Software-3.png" alt="DataApex: Clarity Chromatography Software" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Clarity_Chromatograficky_Software_3_4adabdd9a6/thumbnail_DataApex-Clarity-Chromatograficky-Software-3.png 230w," sizes="100vw" width="1862" height="1265">

Clarity 10 chromatography software released

<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1001">The PDA Extension</a> is an optional Extension that is used for processing data that has been acquired from selected photo diode array detectors. Spectral data, together with chromatograms, add a third dimension to analytical data analysis. This extension expands the capability of Clarity by providing interactive spectral analysis, peak purity analysis and compound identification that is based on a spectral library search. PDA data can be displayed in a set of optional views including 3D rendering.All data is saved in a single file; a chromatogram at any wavelength or even only a spectrum can simply be recalled for review after an analysis. UV-VIS spectra, acquired using a PDA detector, may be interactively selected from a chromatogram signal for visual inspection and comparison. The spectra may also be used for peak purity determinations, wavelength optimization and component identification through spectral libraries.<ul><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?manufacturerItems=58&amp;search=pda+extension">The PDA Extension</a> is an optional, fully integrated addition to <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999">Clarity software</a>.&nbsp;</li><li>It can be ordered as a part of new software or as an extension to existing software.</li><li>The LC-PDA mode is selectable for any LC Instrument within a station.&nbsp;</li><li>The PDA Extension is also compatible with Clarity Offline software.</li></ul><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_PDA_Extension_776dbd48dd.jpg" alt="DataApex - PDA Extension" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_PDA_Extension_776dbd48dd.jpg 245w," sizes="100vw" width="1206" height="534"><h4>Features</h4><ul><li>PDA Data: All data is saved in a single file; a chromatogram at any wavelength or a spectrum only can be simply recalled after an analysis for review. UV-VIS spectra, acquired using a PDA detector, may be interactively selected from a chromatogram signal for visual inspection and comparison. The spectra may also be used for peak purity determinations, wavelength optimization and component identification through spectral libraries.</li><li>PDA View: The PDA view is customizable; up to four views can be displayed at one time (possible views: Isoplot, Chromatogram, Spectra, 3D Display, Peak Purity, Peak Purity Spectra, Library Spectra Search and Spectral Library). The user can easily extract chromatographic signals from PDA data to determine the optimal detection wavelength for each peak.</li><li>PDA Method: The Clarity PDA method includes an option for Spectral Library Search and Peak Purity analysis.</li><li>Peak Purity: This analysis helps to discover hidden impurities. Purity is calculated from 5 or all spectra within the peak. The similarity curve is displayed in the PDA window. Peak Purity analysis can be optimized by setting custom preferences relating to the purity threshold, wavelength restriction and absorbance threshold.</li><li>Spectral Library: The Clarity software compares the peak spectra with the spectra of an unlimited number of spectral libraries. Spectra stored in a Spectral Library include retention times and analysis parameters. The Spectral Library Search can perform automatic identification of integrated/calibrated components (peaks). The library search may be constrained by the RT Window and by Wavelength Range. A Background Correction option is also available.</li><li>Import/Export Data: Spectral data can be imported/exported in ASCII text formats to or from the Clarity software.</li><li>Reports: Users can easily include PDA options such as data 3D Display, Isoplot, Spectra, Peak Purity and Library Search results in reports using the intuitive Report Setup dialog.</li><li>Instrument Control: Control modules (p/n A24) for Agilent, Shimadzu, Knauer and Duratec DADs are available (as of May 2007). Additional control modules for other PDA detectors can be developed upon request.</li></ul><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_The_PDA_Window_displays_four_views_organized_in_splitters_8c614fb6f0.jpg" alt="DataApex: The PDA Window displays four views organized in splitters. Currently displayed in the example are: Isoplot, Chromatogram, Spectral, 3D Display The user can additionaly select also Peak Purity, Peak Purity Spectra, Library Spectra Search and Spectral Library." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_The_PDA_Window_displays_four_views_organized_in_splitters_8c614fb6f0.jpg 191w," sizes="100vw" width="1098" height="896"><h4>Specification</h4><ul><li>Part No.: A29</li><li>Related Products:&nbsp;<ul><li>Clarity (p/n C50) - required</li><li>Clarity offline (p/n C59)</li><li>LC Control (p/n A24) - see the list of available PDA detectors at www.dataapex.com</li></ul></li></ul>

Clarity software - PDA (Photodiode Array) Extension

News from LabRulezLCMS Library - Week 16, 2025

News from LabRulezLCMS Library - Week 17, 2025

<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

Clarity 10.1 expands calibration capabilities to help you work more confidently and efficiently. From clearer guidance and better warnings to flexible internal standard evaluation, this update streamlines calibration development, improves traceability, and supports compliance where it matters most.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Clarity_10_1_397aba9bab.jpg" alt="DataApex: Clarity 10.1 released" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Clarity_10_1_397aba9bab.jpg 143w," sizes="100vw" width="849" height="925"><h4><a target="_blank" rel="noopener noreferrer" href="https://lcms.cz/labrulez-bucket-strapi-h3hsga3/P063_Clarity_10_1_New_Features_283323fcd2.pdf">Clarity 10.1 highlights</a></h4><ul><li>ISTD from a different signal</li><li>Determination Coefficient (R2)</li><li>Enhanced calibration warnings and blank handling</li><li>Electronic Signature improvements</li><li>New and updated control modules</li></ul><h5>Internal standard from another signal</h5>Clarity 10.1 introduces support for evaluating results using an internal standard from a different signal within the same chromatogram. This is especially useful for workflows like ICP-MS, where some signals may lack an ISTD peak.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Internal_standard_from_another_signal_2f2ac068f8.jpg" alt="DataApex: Internal standard from another signal" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Internal_standard_from_another_signal_2f2ac068f8.jpg 228w," sizes="100vw" width="380" height="260"><h5>Determination Coefficient (R²)</h5>Clarity now displays the Determination Coefficient (R²) alongside the Correlation Coefficient in each compound's calibration curve tab.Determination Coefficient (R²) gives you a more accurate view of how well your calibration model fits the data - especially valuable during method development and validation.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Data_Apex_Determination_Coefficient_57673d0ac3.jpg" alt="DataApex: Determination Coefficient" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Data_Apex_Determination_Coefficient_57673d0ac3.jpg 228w," sizes="100vw" width="380" height="260"><h5>Enhanced calibration warnings and blank handling</h5>Clarity 10.1 helps you catch issues earlier and set up calibration with greater confidence. Warnings are now more visible and more specific - appearing above both the Results Table and the Calibration Summary Table. When multiple issues occur, an ellipsis appears with full details available on hover.Blank handling has also been clarified: blanks are included only when Ignore Origin is selected. If the origin is used, blanks are excluded, and Clarity now clearly warns and visually shows when a blank is ignored.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Dataapex_Enhanced_calibration_warnings_and_blank_handling_e9fe7fa31e.jpg" alt="Dataapex: Enhanced calibration warnings and blank handling" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Dataapex_Enhanced_calibration_warnings_and_blank_handling_e9fe7fa31e.jpg 228w," sizes="100vw" width="380" height="260"><h5>Signature improvements</h5>Clarity 10.1 improves how signatures are handled, making it easier to understand what is and isn't signed. Chromatograms opened with a linked calibration are always marked Not Signed. Once signed, the mode switches to Stored Calibration, so you always see the final, signed result. Even historical versions now reliably show their signature state and details.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Dataapex_Signature_improvements_a2bebe7875.jpg" alt="Dataapex: Signature improvements" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Dataapex_Signature_improvements_a2bebe7875.jpg 228w," sizes="100vw" width="380" height="260"><blockquote>Explore the complete list of all changes, fixes, and additions in version 10.1.<a target="_blank" rel="noopener noreferrer" href="https://www.dataapex.com/version_history?product=1">See the complete changelog</a></blockquote>

Clarity Chromatography Software 10.1 released!

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 

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