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<p><strong>NIST26 introduces integrated chromatogram processing, deconvolution, and library searching for EI GC-MS and LC-MS/MS data, but the workflow begins with one essential requirement: chromatographic data must be available in the mzML format. In his presentation </strong><a target="_blank" rel="noopener noreferrer" href="https://labrulez.com/pdf/Conversion_to_mz_ML_63e134bb34.pdf"><i><strong>Conversion to mzML Format for NIST26 Chromatogram Processing</strong></i></a><strong>, James Little of Mass Spec Interpretation Services explains how vendor data can be converted to mzML using either instrument-vendor software or the freely available MSConvert tool from ProteoWizard, and highlights several settings that are critical for successful processing in NIST26.</strong></p><h4><span><strong>NIST26 Chromatogram processing requires mzML</strong></span></h4><p>For the chromatogram-processing workflow described in the presentation, <strong>mzML is the accepted input format</strong>. Proprietary LC-MS or GC-MS data therefore need to be converted before they can be loaded into the NIST26 chromatogram-processing environment.</p><p>There are two principal ways to obtain an mzML file:</p><ul><li>conversion using software supplied by the instrument manufacturer,</li><li>conversion using <strong>MSConvert</strong>, which is included in the free <strong>ProteoWizard</strong> software package.</li></ul><p>Using an open format such as mzML also provides a practical way to move mass spectrometry data between different software environments without relying exclusively on proprietary vendor formats.</p><h4><span><strong>Using ProteoWizard and MSConvert</strong></span></h4><p>MSConvert is installed as part of the complete ProteoWizard package rather than as a separate application. After installing ProteoWizard, users can access either the graphical MSConvert interface or the command-line version.</p><p>The presentation recommends the stable release for routine work, while noting that newer or nightly builds may sometimes provide improved support for recently introduced vendor formats or additional control over data-processing filters. This can be particularly relevant when handling vendor files in which centroiding behavior or peak picking requires closer attention.</p><p>For most users, the graphical interface provides a straightforward route from proprietary raw data to an mzML file suitable for further NIST26 processing.</p><h4><span><strong>Start by selecting mzML as the output format</strong></span></h4><p>The first step in MSConvert is to select the source file or dataset using the <strong>Browse</strong> function.</p><p>The software supports a broad range of mass spectrometry data formats, and the file-selection window can either be restricted to a particular vendor format or set to display any supported spectral format.</p><p>After selecting the source data, the output format must be set to <strong>mzML</strong>. The screenshots in the presentation show this setting directly in the MSConvert options panel before the conversion is started.</p><p>The user can also select the destination folder and other file-output options before adding the selected dataset to the conversion queue.</p><h4><span><strong>Add the data and start the conversion</strong></span></h4><p>Once the source file and output settings have been selected, the file is added to the conversion list using the <strong>Add</strong> command.</p><p>The conversion itself is then launched with <strong>Start</strong>.</p><p>For simple datasets that are already stored in the correct spectral representation, this may be all that is required. However, James Little emphasizes an additional requirement that is particularly important for NIST26: the data must be <strong>centroided</strong>.</p><h4><span><strong>Centroided data are required</strong></span></h4><p>According to the presentation, <strong>profile-mode data are not acceptable for this NIST26 chromatogram-processing workflow</strong>. The spectra must instead be in centroided, or peak-picked, form.</p><p>Profile spectra contain the full measured shape of each mass spectral signal across the m/z axis. Centroided data reduce these profiles to discrete peaks represented by their characteristic m/z and intensity values.</p><p>If the original vendor data are still in profile mode, centroiding can be performed during conversion by adding the <strong>Peak Picking</strong> filter in MSConvert.</p><p>This means that the conversion step can perform two operations at once:</p><p><strong>vendor raw data → centroiding / peak picking → mzML</strong></p><p>The resulting mzML file can then be used as input for NIST26 chromatogram processing.</p><h4><span><strong>Peak Picking must be the first filter</strong></span></h4><p>One of the most important practical details in the presentation is the position of the Peak Picking operation in the MSConvert filter sequence.</p><p>If centroiding is required, <strong>Peak Picking must be the first algorithm or filter in the list</strong>. Placing another processing function before it can interfere with the intended conversion workflow.</p><p>MSConvert allows the user to select the Peak Picking filter, define the relevant MS levels, and add it to the processing sequence before starting conversion. The example shown in the presentation applies vendor-based peak picking to selected MS levels.</p><p>If there is uncertainty about whether the source data are already centroided, the Peak Picking filter can still be included. According to the presentation, applying it to data that are already centroided does not alter the file unnecessarily.</p><p>This provides a useful safeguard when the acquisition mode of an older dataset is uncertain.</p><h4><span><strong>Selecting the appropriate MS levels</strong></span></h4><p>Peak picking does not necessarily have to be applied identically to every spectrum in a dataset. MSConvert allows users to specify the <strong>MS levels</strong> to which the filter should be applied.</p><p>This is especially relevant for LC-MS/MS data, where a file can contain both precursor-level MS spectra and tandem MS spectra.</p><p>The conversion settings should therefore reflect the way the original data were acquired and how those data will subsequently be processed in NIST26.</p><h4><span><strong>Be aware of changes in file size</strong></span></h4><p>The presentation also notes that converted files may become substantially different in size from the original vendor files.</p><p>This is worth considering when working with large LC-MS/MS datasets or processing batches of chromatograms. The size of the resulting mzML file can depend on the original acquisition mode, centroiding, compression settings, the number of MS levels, and other output parameters.</p><p>Storage requirements should therefore be considered before converting large collections of raw data.</p><h4><span><strong>A simple workflow for preparing data for NIST26</strong></span></h4><p>The overall procedure presented by James Little can be summarized as a short sequence:</p><ol><li>Obtain the original vendor LC-MS or GC-MS data.</li><li>Open the data in MSConvert or use the vendor's own conversion software.</li><li>Select <strong>mzML</strong> as the output format.</li><li>Check whether the spectra are centroided.</li><li>If necessary, add <strong>Peak Picking</strong> as the first processing filter.</li><li>Select the appropriate MS levels.</li><li>Add the file to the conversion list.</li><li>Start the conversion.</li><li>Use the resulting mzML file for NIST26 chromatogram processing.</li></ol><p>The procedure itself is straightforward, but the centroiding requirement is important. A file can have the correct <code>.mzML</code> extension and still be unsuitable for the workflow if its spectra remain in profile mode.</p><h4><span><strong>From vendor data to integrated NIST26 processing</strong></span></h4><p>File conversion may appear to be a relatively minor step compared with deconvolution, spectral interpretation, and library searching, but it establishes the foundation for the entire downstream workflow.</p><p>By using mzML as the common input format, NIST26 can process data originating from different instrument platforms through a more consistent workflow. ProteoWizard and MSConvert provide a practical bridge between proprietary mass spectrometry files and this standardized format.</p><p>The key message from the presentation is therefore simple: <strong>convert to mzML, ensure the spectra are centroided, and place Peak Picking first whenever centroiding is required</strong>. Once those conditions are met, the data are ready for the integrated chromatogram-processing and library-searching capabilities available in NIST26.</p>

Conversion to mzML Format for NIST26 Chromatogram Processing

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Thermo Scientific™ Dionex™ Easion™ Ion Chromatography System

Compact IC system with built-in suppressor, heated conductivity detection, and automated sample handling—ideal for routine anion and cation analysis in water and environmental labs.

<h4><strong>Compact, intuitive IC system for routine anion and cation analysis</strong></h4><p><strong>The Dionex Easion IC system is a small yet powerful ion chromatography solution designed for routine water and environmental analysis. With its compact footprint, easy setup, and intuitive Chromeleon™ CDS control, the system enables fast, reliable quantification of both anions and cations—even for inexperienced users. Built-in chemical suppression, minimal maintenance, and preconfigured analysis kits make it ideal for any lab performing standard IC workflows.</strong></p><h3><strong>Key Features and Benefits</strong></h3><h4>🧪 <strong>Simple, Complete System</strong></h4><ul><li>Fully integrated setup includes suppressor, columns, eluent and regenerant concentrates</li><li>Ready to operate in under <strong>90 minutes</strong>—no extra pumps or accessories needed</li><li>Compatible with 2, 3, and 4 mm anion and cation columns</li></ul><h4>📏 <strong>Reliable, Reproducible Performance</strong></h4><ul><li><strong>Heated bipolar conductivity cell</strong> ensures signal stability and low noise</li><li>Chemical suppression with <strong>Dionex CRS 500</strong> suppressor—no regeneration steps needed</li><li>Fixed-loop valve for <strong>manual or automated injections</strong></li><li>Flow range: 0.01–5.00 mL/min; pressure up to 5000 psi</li></ul><h4>💡 <strong>Smart and Compact Design</strong></h4><ul><li>All-PEEK flow path—metal-free and chemically inert</li><li>Simple eluent preparation with concentrates and high-purity water</li><li>Bench-friendly size (33 × 24 × 40 cm, 10 kg) with minimal maintenance</li></ul><h4>🔁 <strong>Automation Ready</strong></h4><ul><li>Supports <strong>Dionex AS-DV, AS-AP, and AS-HV autosamplers</strong></li><li>Built-in sample filtration (with AS-DV) and dilution workflows</li><li>Autosampler-based inline filtration and degassing options available</li></ul><h4>🧠 <strong>Controlled by</strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/76"><strong> Chromeleon™ CDS</strong></a></h4><ul><li>Intuitive system setup with ProcedureWizards™ and application templates</li><li>Built-in calibration memory and audit trail</li><li>Virtual column simulator and multi-vendor instrument integration</li></ul><h3><strong>Applications</strong></h3><ul><li><strong>Drinking water</strong> and <strong>wastewater</strong> monitoring</li><li><strong>Inorganic ion analysis</strong> (F⁻, Cl⁻, NO₃⁻, PO₄³⁻, SO₄²⁻, etc.)</li><li><strong>Routine ammonium and cation detection</strong> (Li⁺, Na⁺, NH₄⁺, Ca²⁺...)</li><li><strong>Educational and QA/QC laboratories</strong></li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Dionex_Easion_System_news_1f1d3e6c64/Thermo-Dionex-Easion-System-news.jpg" alt="Thermo Scientific™ Dionex™ Easion™ Ion Chromatography System" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Dionex_Easion_System_news_1f1d3e6c64/thumbnail_Thermo-Dionex-Easion-System-news.jpg 215w," sizes="100vw" width="1103" height="800"></p>

Waters Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry

The Xevo® G2-XS QTof combines StepWaveTM ion optics with the XS Collision Cell, providing a significant increase in sensitivity with no reduction in selectivity.

<h4><strong>eXtreme Sensitivity, eXtraordinary Selectivity, eXceptional Solutions</strong></h4><div><p><strong>For the scientist who needs to identify, quantify and confirm the broadest range of compounds in the most complex and challenging samples.</strong></p><ul><li>Maximum robustness with no compromise in performance</li><li>Class-leading real-world quantitative sensitivity</li><li>Highest quality, most comprehensive qualitative information</li><li>Flexibility to adapt to changing needs</li><li>Accessible to experts and non-experts alike</li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_1_b9f8dd32be/Waters-Xevo-G2-XS-QTof-Quadrupole-Time-of-Flight-Mass-Spectrometry-1.jpg" alt="Waters Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_1_b9f8dd32be/thumbnail_Waters-Xevo-G2-XS-QTof-Quadrupole-Time-of-Flight-Mass-Spectrometry-1.jpg 173w," sizes="100vw" width="1099" height="991"></p><h3><strong>Overview</strong></h3><div><h4><strong>Maximum robustness with no compromise in performance</strong></h4><p>The trend for increasing complexity of both samples and studies can result in difficulty obtaining high quality data for every component of interest while maintaining optimum performance throughout the analysis.</p><p>The <strong>Xevo® G2-XS QTof</strong> combines <strong>StepWave<sup>TM</sup> ion optics</strong> with the <strong>XS Collision Cell</strong>, providing a significant increase in sensitivity with no reduction in selectivity.&nbsp; During long analyses, critical hardware components stay clean for longer, so results are more reproducible and the laboratory stays productive.</p><p>Meaningful information is obtained for a greater number of components across a larger population of samples than ever before, giving a more complete picture for improved understanding and more confident decision making.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_437f84bacd.jpg" alt="Waters Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry: Maximum robustness with no compromise in performance." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_437f84bacd.jpg 224w," sizes="100vw" width="900" height="628"></p><div><h4><strong>Class-leading real-world quantitative sensitivity</strong></h4><p>In targeted quantitative analysis, the greatest challenge is to detect and quantify components of interest down to the lowest possible levels, often in the presence of interferences from complex matrix.&nbsp; Large variation in the concentrations of different components further adds to this challenge.</p><p>The <strong>Xevo G2-XS QTof</strong> combines sensitivity and selectivity with the mass accuracy, dynamic range and speed provided by <strong>QuanTofTM technology</strong> and the enhanced quantitative capability of <strong>Tof-MRM data acquisition</strong>.&nbsp; The end result is class-leading quantitative performance in real everyday laboratory conditions, demonstrated by limits of detection and quantification superior to anything achieved before with high resolution MS.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_2_d805c7aa49.jpg" alt="Waters Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry: Class-leading real-world quantitative sensitivity." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_2_d805c7aa49.jpg 245w," sizes="100vw" width="900" height="312"></p><div><h4><strong>Highest quality, most comprehensive qualitative information</strong></h4><p>In addition to accurate quantitative profiles, complete understanding of a sample requires detailed and comprehensive qualitative information.</p><p><strong>MS<sup>E</sup></strong> is a simple but powerful approach that delivers accurate mass precursor and fragment ion data for every detectable component, whether chromatographically resolved or not.&nbsp; This represents the ultimate in qualitative information, and because the approach is un-targeted, the data can be interrogated again later as scientific questions evolve.</p><p><strong>FastDDA</strong> is an automated, targeted data acquisition method that provides rapid, intelligent accurate mass MS/MS capability for confirmation of known compounds or characterization of unknowns, for situations where only true MS/MS data will suffice.</p><h4><strong>Flexibility to adapt to changing needs</strong></h4><div><p>The growing emphasis on efficiency and productivity in the laboratory demands analytical systems that are not only robust and reliable, but that also have the flexibility to accomplish a wide variety of tasks today, with future-proofing for the innovations of tomorrow.&nbsp;</p><p><strong>Waters’ Universal Ion Source Architecture</strong> enables the use of a single analytical platform for many different applications and molecule types, as well as providing the option to add new functionality as requirements and priorities change.&nbsp; All source options are designed to be quickly interchangeable and ready to use within minutes, maximizing versatility and minimizing downtime.</p><div><h3><strong>Accessible to experts and non-experts alike</strong></h3><p>Traditionally the ability to achieve and maintain optimum performance from such a powerful analytical system would require a level of knowledge and experience held only by expert users.</p><p>The <strong>Xevo G2-XS QTof</strong> features <strong>IntelliStartTM technology</strong>, an intuitive user interface that automates routine tasks and ensures reproducible data of the highest quality, ensuring the full capability of the system is accessible to all.</p><p><strong>IntelliStart enables essential functions to be carried out automatically:</strong></p><ul><li>MS resolution and calibration checks</li><li>Simple setup of diverse experiments</li><li>Scheduled LC-MS system checks</li><li>Continuous system monitoring</li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_3_279cf35277.jpg" alt="Waters Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry: Accessible to experts and non-experts alike." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Waters_Xevo_G2_XS_Q_Tof_Quadrupole_Time_of_Flight_Mass_Spectrometry_3_279cf35277.jpg 136w," sizes="100vw" width="900" height="1038"></p></div></div></div></div></div></div>

Thermo Scientific™ Dionex™ ICS-4000 Capillary HPIC™ System

Capillary HPIC system for high-resolution, reagent-free ion chromatography with 24/7 readiness, ultra-low eluent use, and versatile detection in a compact format.

<h4><strong>Always on, always ready — high-resolution capillary IC in a compact platform</strong></h4><p>The <strong>Dionex ICS-4000</strong> is the world’s first <strong>dedicated capillary high-pressure reagent-free ion chromatography (HPIC) system</strong>. Designed for high-resolution, low-flow separations, it delivers exceptional chromatographic performance, fast analysis times, and 24/7 on-demand readiness. With integrated control, capillary-optimized detectors, and minimal eluent consumption, it offers a new standard for reliable, low-maintenance ion chromatography.</p><h3><strong>Key Features and Benefits</strong></h3><h4>🧪 <strong>Capillary HPIC Performance</strong></h4><ul><li>Supports <strong>high-pressure separations</strong> with 4 µm columns</li><li><strong>Fast, high-resolution gradients</strong> in minutes</li><li>Continuous operation with <strong>no equilibration needed</strong></li></ul><h4>♻️ <strong>Reagent-Free Simplicity</strong></h4><ul><li><strong>Eluent generation</strong> from deionized water via EGC cartridge</li><li>Just <strong>15 mL of water/day</strong> for continuous operation</li><li>Eluent cartridges last up to <strong>18 months</strong></li></ul><h4>🧠 <strong>Integrated Smart Design</strong></h4><ul><li>Fully integrated system in <strong>compact footprint</strong></li><li><strong>Tilt-up lid</strong>, color-coded connections, and pre-cut tubing</li><li><strong>Vacuum degassing</strong>, seal wash (option), and inline shut-off valves</li></ul><h4>🧲 <strong>Versatile Detection Options</strong></h4><ul><li><strong>Conductivity Detector (CD)</strong> – with self-regenerating suppressor</li><li><strong>Electrochemical Detector (ED)</strong> – ideal for cyanide, amines, carbohydrates</li><li><strong>QD Charge Detector</strong> – signal proportional to ion charge and concentration</li></ul><h4>🔁 <strong>Flexible Column Chemistry</strong></h4><ul><li>Compatible with <strong>over 20 capillary columns</strong></li><li>Suitable for a wide range of inorganic and organic ions, sugars, acids, amines</li></ul><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Dionex_ICS_4000_Iontovy_Chromatograf_2_64107dbdca/Thermo-Dionex-ICS-4000-Iontovy-Chromatograf-2.jpg" alt="Thermo Scientific™ Dionex™ ICS-4000 Capillary HPIC™ System" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Dionex_ICS_4000_Iontovy_Chromatograf_2_64107dbdca/thumbnail_Thermo-Dionex-ICS-4000-Iontovy-Chromatograf-2.jpg 156w," sizes="100vw" width="650" height="650"></p><h3><strong>Automation and Sample Handling</strong></h3><ul><li>Compatible with <strong>Dionex AS-DV</strong> and <strong>AS-AP</strong> autosamplers</li><li>Advanced prep (dilution, derivatization, matrix removal)</li><li>Supports <strong>vials, well plates</strong>, and &lt;30 s injection cycles</li><li>Optional <strong>Sample Conductivity &amp; pH Accessory</strong> with conditional logic</li></ul><h3><strong>Software Integration</strong></h3><ul><li>Controlled by <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/76"><strong>Chromeleon™ Chromatography Data System (CDS)</strong></a></li><li>eWorkflows™ simplify analysis from injection to report</li><li>Interactive charts and MiniPlots for intuitive data interpretation</li></ul><h3><strong>Ideal for Applications in</strong></h3><ul><li>Food and beverage (e.g., sugars, organic acids, preservatives)</li><li>Environmental (e.g., drinking water, wastewater)</li><li>Pharmaceutical (e.g., excipients, counterions)</li><li>Educational and routine analytical labs</li></ul>

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