NIST26 includes integrated processing tools for LC-MS/MS data, but there are situations where working directly from instrument vendor software can be faster and more practical. When only a few peaks need to be evaluated, when mzML conversion is inconvenient, or when nominal-mass data are involved, spectra can be transferred directly into NIST Library Search for identification. This workflow can streamline spectral searching while still providing access to NIST high-resolution and low-resolution libraries, public MS/MS resources, and flexible search settings.<h4>When does direct transfer from vendor software make sense?</h4>NIST26 provides integrated data processing in the Chromatogram tab, including workflows for deconvolution and library searching. In many cases, this is the most comprehensive way to process LC-MS/MS datasets.However, chromatogram-based processing generally requires conversion of the original vendor data into mzML, for example using ProteoWizard/MSConvert. If a chromatogram is relatively simple, deconvolution is unnecessary, and only a small number of peaks need to be investigated, converting and processing the entire file may add unnecessary steps.In these situations, it can be more efficient to select an MS/MS spectrum directly in the original vendor software and send it to NIST Library Search.There are also other cases where direct transfer becomes particularly useful. Some proprietary data formats may not convert cleanly into mzML, while nominal-mass MS/MS data are not supported for MS/MS searching in the NIST26 Chromatogram tab. For this type of data, transferring or importing spectra into Library Search becomes the practical alternative.<h4>Which vendor software can send spectra directly to NIST?</h4>Several major instrument platforms provide direct integration with NIST Library Search.The workflow is available with software from:<ul><li>Agilent, including MassHunter and OpenLab,</li><li>Waters,</li><li>Thermo Fisher Scientific.</li></ul>Wiley KnowItAll can also import spectra into NIST Search and supports numerous vendor data formats through its own software environment.For some other platforms, direct NIST integration may not be available. In those situations, spectra can potentially be exported in text-based formats such as TXT or MSP ASCII and then imported into the Spectrum List in NIST Library Search.Direct transfer is generally more convenient because it avoids intermediate export and import steps.<h4>A practical Agilent example</h4>The workflow can be demonstrated using Agilent software.An analyst first selects the desired MS/MS region, averages the spectrum if necessary, and transfers it into the spectrum display. From there, the spectrum can be sent to NIST using the Search Using NIST MS Program command.Once properly configured, NIST automatically receives the spectrum and initiates the specified search. Before relying on this workflow, however, the import and library search parameters should be checked carefully.<h4>Setting up accurate-mass spectrum import</h4>For high-resolution MS/MS data, the first important step is found under Spectrum Import Options.Accurate-mass spectra should be imported with the appropriate number of decimal places for precursor and product ions, and the Accurate m/z spectrum type must be selected.Preserving mass accuracy is essential because one of the main advantages of HRMS library searching is the ability to distinguish candidates using precise precursor and fragment masses.Once the import settings are correct, the next step is configuring the library-search parameters.<h4>Searching without a precursor ion</h4>Depending on how the spectrum is selected or averaged in the vendor software, precursor information may not always be transferred automatically.NIST26 can still search such a spectrum using HiRes NoPrecursor mode.Alternatively, if the precursor m/z is known, it can be entered manually and the search can then include precursor information.The no-precursor approach can be convenient when quickly screening manually selected MS/MS spectra, particularly when the fragment pattern itself contains enough information to generate useful candidate matches.<h4>Setting mass tolerances</h4>For accurate-mass MS/MS searching, suitable precursor and product-ion tolerances are essential.An example configuration uses:<ul><li>20 ppm for the precursor ion</li><li>40 ppm for product ions</li></ul>These settings can be kept consistent with those used in the NIST26 Chromatogram workflow.Proper tolerance settings help balance search sensitivity with selectivity. If tolerances are too wide, more irrelevant candidates may be returned; if they are too narrow, valid matches can be missed because of normal measurement variation.<h4>Combining multiple spectral libraries</h4>One of the strengths of NIST Search is the ability to search multiple libraries simultaneously.A typical configuration can include the NIST high-resolution MS/MS library together with the NIST low-resolution tandem library.The NIST low-resolution library can participate in accurate-mass workflows because it contains the required indexing information. This is important because not every custom or older low-resolution library will necessarily be compatible with the same type of high-resolution search.Additional public resources can also be included, such as:<ul><li>MS-DIAL positive-mode libraries</li><li>MS-DIAL negative-mode libraries</li><li>MoNA LC-MS/MS</li></ul>Combining commercial and public libraries can substantially broaden spectral coverage. In the demonstrated workflow, several million spectra could be searched in a single configuration.For laboratories dealing with unusual metabolites, impurities, environmental contaminants, or compounds outside mainstream commercial libraries, this expanded search space can be particularly valuable.<h4>Structure searches require separate library selection</h4>MS/MS searching and structure searching do not necessarily use the same library selections.If structural searching is required, the appropriate structure-containing libraries must also be loaded in the corresponding Library Search settings.This distinction is easy to overlook when first configuring NIST26. A library may contain useful spectra but no associated structures, or the structure database may need to be explicitly selected before substructure or related structural searches can be performed.<h4>Automating the search</h4>Once the library and tolerance settings have been defined, Automatic Search can be enabled.This allows the spectrum transferred from vendor software to trigger a search immediately rather than requiring the user to launch it manually each time.For repeated workflows involving many manually selected peaks, this small automation can save considerable time.After the configuration has been optimized, it is useful to save it as a dedicated setup—for example, a configuration specifically designed for vendor-imported spectra.<h4>Understanding the result table</h4>NIST search results are typically ranked by score, but additional parameters can also help interpret the matches.Fields can include:<ul><li>score,</li><li>reverse score,</li><li>partial spectrum search score,</li><li>dot product,</li><li>molecular weight,</li><li>other user-selected parameters.</li></ul>The search result display can be customized by right-clicking the column headers and adding or removing fields.Although the standard score will usually remain the primary ranking criterion, alternative metrics can be useful when evaluating spectra with missing fragments, additional peaks, partial spectral overlap, or related structures.<h4>Why it can be useful to keep duplicate matches visible</h4>NIST includes a Best Matching Only option that reduces duplicate or repeated entries in the displayed results.When enabled, the software may reduce a list containing several library records of the same compound to the best representative match.This makes the result list easier to review, but it can also hide useful information.For initial evaluation, it is often preferable to leave this option disabled so that all matching spectra remain visible. Multiple spectra of the same compound may come from different collision energies, instruments, ion forms, or libraries, and reviewing these variations can provide useful confirmation.Filters can always be applied later once the analyst understands the full result set.<h4>Visual comparison of unknown and library spectra</h4>NIST Library Search provides several complementary views of each candidate.The experimentally acquired unknown spectrum is displayed together with the selected library spectrum, while a head-to-head spectral comparison provides an immediate visual representation of matching and non-matching ions.This is important because library-search scores should not be treated as a fully automated identification decision.A strong match should still be examined visually, especially when dealing with complex spectra, low-abundance fragments, co-isolated ions, or compounds with closely related structural analogues.The combination of numerical scoring and visual inspection provides a stronger basis for interpretation.<h4>An important issue with the Intensity Threshold setting</h4>One practical software issue deserves particular attention when importing high-resolution spectra.The Spectrum Import Options window includes an Intensity Threshold function that can remove low-intensity signals and reduce spectral noise.In principle, this would be useful. However, when an intensity threshold is applied, imported high-resolution spectra may lose their decimal mass information and be transferred as nominal-mass spectra instead.An accurate-mass peak such as 176.0815 could therefore appear simply as m/z 176.For HRMS users, this effectively removes one of the most important dimensions of the data and can compromise accurate-mass searching.Until this behavior is corrected, the safer approach is to avoid using the Intensity Threshold option during high-resolution spectrum import and perform any necessary filtering elsewhere.<h4>A related display issue in the Chromatogram window</h4>A second software behavior concerns how Spectrum Import Options are reflected in the Chromatogram tab.If the decimal precision is set to zero for importing low-resolution spectra, the head-to-head spectral display may subsequently show masses truncated according to those settings.Importantly, this is a display issue only.It does not change the accurate-mass deconvolution results or the library-search table. The underlying processed data remain unaffected; only the visual comparison at the top of the Chromatogram window reflects the altered import settings.Understanding this distinction can prevent users from mistakenly assuming that accurate-mass data have been lost from the processed results.<h4>When direct vendor-to-NIST searching is most useful</h4>Direct transfer from vendor software is not intended to replace the complete NIST26 Chromatogram workflow.Instead, it provides a complementary route for situations where full chromatographic processing is unnecessary or unavailable.It can be particularly effective when:<ul><li>only a few peaks need identification,</li><li>deconvolution is not required,</li><li>mzML conversion adds unnecessary processing,</li><li>vendor files cannot be converted reliably,</li><li>nominal-mass MS/MS spectra need to be searched,</li><li>spectra have already been reviewed and selected in the vendor environment.</li></ul>For these cases, direct spectrum transfer offers a fast route from the original MS/MS data to spectral library identification.<h4>Connecting vendor software with broader NIST26 capabilities</h4>The workflow also illustrates a broader advantage of NIST26: analysts do not have to choose between the instrument vendor's software and an independent spectral-search environment.Vendor software can remain the primary platform for inspecting chromatograms and selecting spectra, while NIST provides access to large commercial libraries, public MS/MS databases, flexible scoring, spectral comparison, and additional interpretation tools.Used together, these environments can provide a practical workflow for both rapid routine searching and more detailed unknown identification.The key is careful configuration. Accurate-mass import settings, mass tolerances, library selection, search mode, and result-display options all influence how effectively the workflow performs.Once these parameters are properly established and saved, sending a spectrum from the vendor software to NIST26 can become a rapid and repeatable part of everyday LC-MS/MS data interpretation.

Sending MS/MS (Tandem) Spectra to NIST26 Search

UCTP-REFINE Lab is a research group at the University of Chemistry and Technology Prague focused on sustainable waste valorization, chemical recycling, and the production of alternative feedstocks for chemicals and fuels. The team combines chemical engineering, catalysis, and advanced analytical chemistry to study the thermal and catalytic conversion of complex waste streams, particularly plastics, tires, and biomass, including pyrolysis and upgrading of resulting oils. A strong emphasis is placed on comprehensive characterization of feedstocks, intermediates, and products to link composition and process conditions with product quality and support the development of circular, resource-efficient technologies.<h3>PhD position Chemometric processing of GC×GC data from alternative fuels and oils produced via thermochemical conversion of biomass and plastics</h3><h4>Expected experience:</h4><ul><li>Master's degree in chemistry or chemical engineering</li><li>Strong background in analytical chemistry and chemistry in general; a background in chemical engineering is beneficial</li><li>Experience with chromatography is mandatory.</li><li>Experience with chemometric data processing (e.g. in Python) and GC×GC is not required but is beneficial.</li><li>Top-level English, both spoken and written, ideally proven by a certificate.</li></ul><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/refine_lab_equipment_33ff27095e.jpg" alt="UCTP-REFINE-lab: Process Gas Chromatograph with Electrolyzer" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_refine_lab_equipment_33ff27095e.jpg 208w," sizes="100vw" width="500" height="375"><h4>Expected work:</h4><ul><li>Close collaboration with all involved colleagues and relevant partners from the project consortium.</li><li>GC×GC analysis of complex samples utilizing FID, MS and NCD detectors.</li><li>The focus will be on alternative fuels and oils from thermochemical depolymerisation of biomass and plastics, as well as the samples after hydrotreating.</li><li>Advanced GC×GC data processing using chemometrics for prediction model development.</li><li>Participation also in sample production.</li><li>Contribution to project reports, publications, and conference presentations.</li></ul><h4>What we offer:</h4><ul><li>A young but fast-growing Team with strong international collaborations with academia and industry.</li><li>Top-level facilities and expertise in hydrotreating and liquid product analysis.</li><li>Work on a prospective topic in close collaboration with top EU companies as part of a demonstration EU project.</li><li>Competitive income, which level depends entirely on your activity and productivity.</li></ul>Questions? Feel free to contact our students Adham (yaghia@vscht.cz) or Vít (vyskocit@vscht.cz).<ul><li>Preferred start: early 2027</li><li>Application deadline: 30th October 2026</li><li>Funding: Fully funded PhD position as part of an upcoming HE project.</li></ul>If you are interested and meet the criteria, apply through the application form below.<blockquote><a target="_blank" rel="noopener noreferrer" href="https://www.uctp-refine-lab.com/joining-our-team-form-gcxgc">Apply through this form</a></blockquote>

PhD position Chemometric processing of GC×GC data from alternative fuels and oils

The integrity of sport depends on the ability to detect prohibited substances accurately, reliably and with confidence. However, as doping strategies become increasingly sophisticated, the analytical demands placed on anti-doping laboratories continue to evolve.Today’s laboratories must do more than test for a static list of known compounds. They need broad analytical strategies capable of addressing hundreds of substances across multiple chemical classes, identifying emerging threats and supporting defensible confirmation and reporting of adverse analytical findings. For more than 25 years, Thermo Fisher Scientific has worked globally with World Anti-Doping Agency (WADA)-accredited laboratories to advance the analytical science supporting modern anti-doping programs.<h3>Anti-doping testing is a moving target</h3>The World Anti-Doping Agency publishes an annually updated Prohibited List that provides a global framework for testing programs. Yet the list is non-exhaustive, meaning laboratories may also need to detect structurally related compounds and substances across several categories, with similar chemical structure and biological activity. That creates a significant analytical challenge. Anti-doping laboratories must be prepared to monitor a broad range of compounds while maintaining the sensitivity, specificity, and confidence required for both initial testing and confirmation. At the same time, the landscape continues to change. Emerging substances, rapidly expanding doping strategies and new approaches to sample collection and analysis are creating multiple considerations for anti-doping laboratories to consider. Dried blood spots (DBS), for example, have gained attention as a complementary approach to traditional urine and venous blood collection supporting applications such as detecting steroid esters and monitoring peptides. High-resolution mass spectrometry is also enabling laboratories to consider both targeted analysis and retrospective interrogation of previously acquired data as scientific knowledge and regulations evolve.<h3>From screening to confident confirmation</h3>No single analytical technique can address every anti-doping challenge.With respect to chemical analysis of toxicologically relevant compounds, modern doping control laboratories employ complementary technologies—including liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS) and isotope ratio mass spectrometry (IRMS)—depending on the compounds and analytical questions involved.For initial testing, laboratories may need to efficiently screen biological samples for numerous prohibited substances spanning categories such as steroids, stimulants, metabolic modulators, diuretics, narcotics, cannabinoids and peptides.When &nbsp;an initial Testing Procedure produces a result requiring confirmation, laboratories need analytical approaches capable of supporting confident confirmation.This combination of broad screening and targeted confirmation has made mass spectrometry central to modern anti-doping science.<h3>Expanding possibilities with LC-MS</h3>High-resolution accurate-mass mass spectrometry can provide precise mass measurements while supporting comprehensive screening of known and suspected substances, while preserving information-rich data that can support investigation of emerging or previously untargeted compounds.An important advantage of high-resolution mass spectrometry is the ability to revisit previously acquired data. As new substances, metabolites or other analytical targets are identified, laboratories can potentially re-process previously acquired full scan data (and any corresponding MSn experiment) without reanalyzing the original sample. This strategy is currently used by laboratories to support global re-testing programs.&nbsp; Triple quadrupole <a target="_blank" rel="noopener noreferrer" href="https://labrulez.com/en-us/lcms/products?category=20&amp;manufacturerItems=3">LC-MS</a> can complement these workflows by supporting sensitive, targeted quantitation and confirmation of prohibited substances.Together, these approaches provide laboratories the flexibility needed to address today’s testing requirements while giving laboratories greater flexibility to respond to emerging analytical challenges.<h3>The continuing role of GC-MS/MS</h3>Gas chromatography coupled with triple quadrupole mass spectrometry remains an important technology in anti-doing laboratories, particularly for urinary steroid profiling and the screening and confirmation of anabolic- &nbsp;androgenic steroids and other GC-amenable prohibited substances.GC-MS/MS can support both screening and confirmation while providing the sensitivity, selectivity and dymanic range required for screening and confirmatory analysis.The <a target="_blank" rel="noopener noreferrer" href="https://labrulez.com/en-us/all/products/485">Thermo Scientific TSQ 9610 Triple Quadrupole GC-MS</a> is designed to maximize sample throughput, helping laboratories address the demands of routine testing while maintaining analytical performance across a wide dynamic range. &nbsp;The TSQ 9610 incorporates NeverVent technology, designed to increase instrument uptime by reducing the disruption associated with routine source maintenance.As anti-doping workflows evolve, bridging screening and confirmation together within robust analytical strategies can help laboratories respond efficiently to increasingly complex testing requirements.<h3>When identifying a steroid isn’t enough</h3>In some anti-doping investigations, simply detecting a compound does not provide the complete answer.Testosterone, for example, can be produced naturally by the body or administered externally as an anabolic steroid. In cases where laboratories need to distinguish between endogenous and exogenous sources, isotope ratio mass spectrometry can provide another layer of information.GC-IRMS can help laboratories determine whether selected urinary steroids are consistent with an endogenous or exogenous origin by comparing carbon isotope ratios.The result is an analytical toolkit in which different technologies answer different questions—from broad screening and sensitive confirmation to determining the origin of a compound.<h3>Putting advanced workflows into practice</h3>Technology is only part of the equation. Real-world anti-doping laboratories also need to manage high sample volumes, turnaround expectations and continually changing analytical requirements.At Laboratoire Anti-Dopage Français (LADF), Director Dr. Magnus Ericsson and his team use advanced mass spectrometry workflows to support anti-doping testing.According to Ericsson, integration of <a target="_blank" rel="noopener noreferrer" href="https://labrulez.com/en-us/all/products?category=20&amp;manufacturerItems=3">Thermo Scientific TSQ</a> and <a target="_blank" rel="noopener noreferrer" href="https://labrulez.com/en-us/all/products?category=37&amp;manufacturerItems=3&amp;search=vanquish">Vanquish systems</a> has helped enhance efficiency and turnaround while supporting more than 40,000 sample analyses since 2023.Experiences like these demonstrate how integrated analytical workflows can help laboratories translate advances in mass spectrometry into routine anti-doping operations.<h3>Preparing for what comes next</h3>Anti-doping science has advanced dramatically—from early testing approaches to today’s sophisticated, — mass spectrometry technologies; including but not limited to <a target="_blank" rel="noopener noreferrer" href="https://labrulez.com/en-us/gcms/products?category=20&amp;manufacturerItems=3">GC-MS/MS</a>, <a target="_blank" rel="noopener noreferrer" href="https://labrulez.com/en-us/lcms/products?category=20&amp;manufacturerItems=3">LC-MS/MS</a>, <a target="_blank" rel="noopener noreferrer" href="https://labrulez.com/en-us/all/products?category=22&amp;manufacturerItems=3">high-resolution accurate-mass MS</a> and<a target="_blank" rel="noopener noreferrer" href="https://labrulez.com/en-us/gcms/products?category=351&amp;manufacturerItems=3"> isotope ratio MS</a> workflows.But the science cannot stand still.Emerging compounds, evolving regulations and increasingly sophisticated doping strategies mean laboratories must continually evaluate how they manage and process samples and then screen, identify, quantify and confirm prohibited substances. The goal remains constant: provide accurate, high-quality analytical results that help protect the integrity of competition.Explore the technologies, workflows and expert perspectives shaping the next generation of anti-doping testing in our comprehensive eBook, Upholding the Integrity of Sport.<blockquote><h5><a target="_blank" rel="noopener noreferrer" href="https://documents.thermofisher.com/TFS-Assets/CMD/brochures/eb-004467-cl-cmd-ms-antidoping-eb004467-na-en.pdf">Download the anti-doping eBook</a></h5></blockquote>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#AntiDoping #MassSpectrometry #SportsIntegrity #WADA

Advancing Anti-Doping Science: Analytical Strategies for the Evolving Fight Against Doping

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UCTP-REFINE Lab is a research group at the University of Chemistry and Technology Prague focused on sustainable waste valorization, chemical recycling, and the production of alternative feedstocks for chemicals and fuels. 

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