At the recent Thermo Fisher Scientific sponsored workshop at the MSACL 2025 conference in Montreal, Canada, Dr. Patrick Vanderboom from Mayo Clinic shared groundbreaking research into the use of extracellular vesicles (EVs) as potential biomarkers for neurodegenerative diseases such as ALS (Amyotrophic Lateral Sclerosis). His team’s work highlights not only the biological promise of EV-based biomarkers, but also the power of complementary mass spectrometry strategies, leveraging deep discovery on the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/836">Thermo Scientific Orbitrap Astral mass spectrometer</a> and highly sensitive, multiplexed targeted validation on the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1149">Thermo Scientific Stellar mass spectrometer</a>.&nbsp;Together, these approaches are redefining what is achievable in both discovery and validation proteomics.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Breaking_Sensitivity_Barriers_How_MS_is_Transforming_Biomarker_Discovery_for_ALS_and_Beyond_75c7fe8571.jpg" alt="Photo: Thermo Fisher Scientific: Breaking Sensitivity Barriers: How MS³ is Transforming Biomarker Discovery for ALS and Beyond" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Breaking_Sensitivity_Barriers_How_MS_is_Transforming_Biomarker_Discovery_for_ALS_and_Beyond_75c7fe8571.jpg 245w," sizes="100vw" width="1024" height="512"><h3>The challenge of sensitivity in biomarker discovery</h3>Detecting disease-relevant proteins from complex, low-abundance samples like cerebrospinal fluid (CSF) or plasma remains a formidable analytical challenge. Even with advanced LC-MS workflows, background noise and insufficient detection sensitivity can obscure critical peptide signals, limiting biomarker validation and reproducibility.Dr. Vanderboom’s team confronted this head-on while developing workflows to identify EV-based ALS-specific markers. Early targeted assays using traditional MS² approaches revealed promising candidates but struggled with low signal intensity and limited reproducibility, clear signs of hitting the sensitivity ceiling.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Breaking_Sensitivity_Barriers_How_MS_is_Transforming_Biomarker_Discovery_for_ALS_and_Beyond_2_6be7e53a18.jpg" alt="Thermo Fisher Scientific - Breaking Sensitivity Barriers - How MS³ is Transforming Biomarker Discovery for ALS and Beyond 2.jpg" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Breaking_Sensitivity_Barriers_How_MS_is_Transforming_Biomarker_Discovery_for_ALS_and_Beyond_2_6be7e53a18.jpg 208w," sizes="100vw" width="800" height="600"><h3>The MS³ advantage</h3>To overcome these challenges, the Mayo team (pictured above) explored targeted validation on the Stellar MS. Stellar displayed an increase in sensitivity while achieving a fast cycle time, allowing for more points across the peak and increased reproducibility. Several peptides suffered from interfering signal. For these targets, the team explored MS³ (multi-stage fragmentation). By introducing an additional fragmentation and isolation stage, MS³ effectively reduces background interference, producing cleaner spectra and allowing for lower limits of detection.In Vanderboom’s words:“You can see there’s quite a bit of noise in the background, but if you look at that same peptide when we acquired it with MS³, it just cleans up the background. It’s almost like high resolution.”The result? Peptides that were previously undetectable became measurable, enabling discrimination between ALS cases and controls with improved confidence and reproducibility.<h3>From discovery to clinical potential</h3>EVs are a promising new source of biomarkers, but several challenges have limited progress. By leveraging the Obitrap Astral for deep, unbiased discovery using fast DIA with narrow isolation windows, the team identified nearly 6,000 proteins from small EVs in CSF, an unprecedented level of coverage. This expansion in detectable proteome depth represents a critical step toward finding reliable biomarkers that can distinguish ALS from similar neurological conditions.Although state of the art discovery workflows allow for unprecedented depth, confirming targets identified on this platform can be difficult. This is where Stellar comes in. The ability to run highly multiplexed assays with extreme sensitivity, fast LC gradients, and MS³-enabled selectivity allows investigators to fully capitalize on even the most challenging candidate biomarkers.<h3>Conclusion</h3>The incorporation of MS³ workflows on Stellar marks a pivotal evolution in targeted proteomics. As Dr. Vanderboom’s work demonstrates, increasing selectivity while maintaining extreme sensitivity doesn’t just enhance data — it opens new analytical frontiers for diseases where early detection is vital. By combining robust EV isolation with advanced MS³ enabled methods, researchers are now poised to illuminate the molecular signatures of neurodegeneration with unprecedented clarity.Watch the full workshop recording: <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=lweW3JRr0Ow">Extracellular Vesicle Biomarkers for Neurodegenerative Disease</a><h3>Resources</h3><ul><li>Related blogs in this series → <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/7480">Accelerating Biomarker Discovery and Validation: From Discovery to Clinical Utility – AnalyteGuru</a></li><li>Other on-demand webinars featuring Stellar → <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/4735">Next-generation workflows for small molecule quantitation using the Thermo Scientific Stellar mass spectrometer</a></li><li>Promotions → <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/mass-spectrometer-price-affordability-programs.html">Mass Spectrometer Affordability Programs | Thermo Fisher Scientific – US</a></li><li>Follow along <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/about-us/events/industrial/msacl-us.html">MSACL 2025</a> for more information on Thermo Fisher Scientific participation in MSACL 2026</li><li>Interested in speaking opportunities at future events? Contact <a href="mailto:ema.ruzic@thermofisher.com">Ema Ruzic</a></li></ul><blockquote>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#Stellar #MayoClinic #Biomarkers #MassSpectrometry</blockquote>

Breaking Sensitivity Barriers: How MS³ is Transforming Biomarker Discovery for ALS and Beyond

The <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2462">new NIST26 release expands LC-MS/MS data</a> processing with integrated chromatogram analysis and MS/MS library searching. Within the Chromatogram Window, users can load LC-MS/MS data, configure processing parameters, search spectral libraries, filter results, review identified components, and export selected results for further evaluation.This practical guide is based on James Little’s Processing MS/MS Data in NIST26 Chromatogram Window material from Mass Spec Interpretation Services. It walks through the fundamental workflow for processing MS/MS data in the NIST26 Chromatogram Window, from selecting the appropriate processing mode and input file to library searching, reviewing candidate identifications, and exporting results.<blockquote>👉<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/Processing_MSMS_Data_in_Chromatogram_Window_NIST_26_09aa3c2996.pdf">Download PDF handout here</a></blockquote><h3>Before You Begin: Navigating the Chromatogram Window</h3>The workflow assumes that users are already familiar with configuring and navigating the NIST26 Chromatogram Window. For new users, the author recommends first reviewing the separate material dedicated to configuring and navigating this environment.NIST26 also provides extensive integrated help. Pressing F1 while working in the Chromatogram Window opens documentation and practical tips for processing tandem MS data. The presentation emphasizes that this help resource contains useful information for understanding individual functions and settings.<h4>1. Set Processing to Tandem Mode</h4>If both EI and tandem NIST software are installed, the first useful step is to specify the type of spectra being processed.<blockquote>In the Chromatogram Window, select: File → Select Spectrum Type → Tandem</blockquote>Selecting Tandem mode simplifies menu navigation and ensures that functions relevant to MS/MS data processing are readily available.<h4>2. Prepare Your Data in mzML Format</h4>For the workflow described in the presentation, NIST26 processes mzML files. Data stored in proprietary instrument formats therefore need to be converted before processing.The presentation recommends using ProteoWizard/msconvert for file conversion.<blockquote>Once the mzML file is available, processing can be started through: File → Analyze MS/MS Input File</blockquote>Select the appropriate mzML file and configure the required processing parameters.<h4>3. Set the Mass Tolerance</h4>Mass tolerance is one of the important parameters used during data processing and spectral matching.The presentation identifies:<ul><li>20 ppm</li><li>40 ppm</li></ul>as reasonable tolerance values.The appropriate setting should ultimately reflect the characteristics of the dataset and instrumentation. These values should therefore be regarded as practical starting points for the demonstrated workflow rather than universal settings for every LC-MS/MS analysis.<h4>4. Select Libraries for Searching</h4>One of the useful features of NIST26 is the ability to search multiple libraries simultaneously.For the type of analysis demonstrated, James Little identifies hr_msms_nist as the preferred library. Depending on the application, users can also work with APCI and low-resolution libraries or free crowd-sourced libraries.Searching several relevant libraries can broaden the identification space, particularly when investigating complex LC-MS/MS datasets.<h4>5. Examine the Initial Results</h4>After processing is complete, the results are displayed directly within the Chromatogram Window. The workspace combines several types of information, including:<ul><li>the chromatogram</li><li>a list of detected components and search results</li><li>information about library hits</li><li>comparison of experimental and library spectra</li><li>proposed compound identity and structural information</li></ul>This layout makes it possible to move quickly from a chromatographic feature to its potential identification and visually evaluate the quality of the spectral match.Abundance can also be displayed using either a linear or logarithmic scale. A logarithmic view can be particularly helpful when the chromatogram contains both highly abundant signals and much weaker components. Pages 6 and 7 of the presentation illustrate the difference between these two views.<h4>6. Save Your Configuration</h4>Once the desired program parameters have been established across the relevant windows, including the Chromatogram Window, it is useful to save the configuration.NIST allows configurations to be saved and restored as *.ini files.This can be particularly valuable when a laboratory uses different processing configurations for different datasets, libraries, or analytical workflows. Instead of manually recreating the settings each time, users can restore a previously saved configuration.According to the presentation, the Save Configuration option is available from the menu in the Lib Search tab.<h5>7. Filter the Results</h5>Initial processing can generate a large number of potential identifications. NIST26 therefore provides several options for filtering and simplifying the results.Functions available from the upper area of the Chromatogram Window include:<ul><li>Best Hits</li><li>Only IDs</li><li>Bkgd</li><li>Filter Scores</li></ul>Changing these filters affects the displayed hit list and the identifications shown in the chromatogram. This allows users to progressively narrow the results and concentrate on components that are most relevant to the analytical task.<h5>Be Careful with the Background Filter</h5>The presentation specifically highlights the Bkgd setting.According to the material, NIST suggests a background setting of approximately 75%, and this is normally useful. However, the author observed a few instances in which applying the background filter removed major peaks despite their good library search scores.These peaks had an XIC value of 0.If an important candidate disappears after applying background filtering, the settings should therefore be reviewed. For these particular peaks, the presentation notes that Bkgd = Any was required.<h4>8. Use Filter Scores with Care</h4>The Filter Scores function provides another way to remove lower-quality spectra from the displayed results.According to the NIST help information cited in the presentation, filtering is based on five quality factors:<ul><li>background</li><li>purity</li><li>max2min</li><li>signal-to-noise</li><li>isotope analysis</li></ul>The filter can be configured to display only identifications above a specified minimum score.The procedure presented is:<ol><li>Turn on Filter Scores above the chromatogram.</li><li>Enter the desired minimum score.</li><li>Select Fixed in the corresponding selection box.</li><li>Only identifications above the specified score will remain visible.</li></ol>The presentation gives 900 as an example setting for obtaining a clear view of the TIC.The author also notes that the practical interpretation of this feature is not necessarily straightforward and recommends experimenting with it to determine whether it is useful for a particular workflow.<h4>9. Sort Results and Create a List of Components of Interest</h4>The results table offers considerable flexibility for organizing potential identifications.Clicking a column header allows the results to be sorted according to the selected parameter. Multiple entries can be selected using Shift or Ctrl together with the left mouse button.Selected entries can then be sent to a smaller list containing only components of interest.The presentation emphasizes that there are many possible approaches to organizing the results. Rather than imposing a single rigid workflow, NIST26 allows users to adapt result selection and review to their specific analytical requirements.<h4>10. Manually Review Candidate Identifications</h4>Automated library searching should not necessarily be treated as the final step in compound identification. Once a list of relevant components has been created, the presentation recommends reviewing the candidates individually.A practical approach is to:<ol><li>Sort the results by RT (retention time).</li><li>Left-click the first hit to highlight it.</li><li>Use the up and down arrow keys to move through the list.</li><li>Carefully inspect the spectral comparison for every candidate.</li><li>Decide whether each identification should be included in the final report.</li></ol>An important tool for this review is the butterfly display in the upper-right portion of the workspace. It provides a visual comparison of the measured and reference spectra.Combining automated search scores with expert examination of the spectral match provides a more considered approach to reviewing proposed identifications.<h4>11. Export Selected Results to Excel</h4>Once the relevant identifications have been reviewed, selected results can easily be transferred into a spreadsheet.Highlight the desired entries, right-click, and choose:Copy Selected Hits to ClipboardThe copied information can then be pasted directly into Microsoft Excel.This provides a convenient way to create a customized results table for further evaluation, documentation, or preparation of an analytical report. The workflow is illustrated on page 13 of the presentation.<h4>12. Perform a More Detailed Review with the XIC Browser</h4>For candidate identifications requiring further investigation, the corresponding spectrum can be sent to the XIC Browser/XIC Analyzer.<blockquote>From the selected result, right-click and choose: Send To → XIC Analyzer</blockquote>This opens a more detailed view of the MS/MS data.The example on page 14 demonstrates how the isotope pattern can support an identification involving two chlorine atoms. The XIC Browser also provides MS1 information underlying the MS2 spectrum, adding another layer of information for evaluating a candidate.As with the main Chromatogram Window, users can press F1 or access Help for more detailed information about the XIC Browser and its functions.<h4>Recommended NIST26 Workflow</h4><blockquote>The overall procedure can be summarized as:mzML data → Tandem mode → mass tolerance settings → MS/MS library selection → data processing → result filtering → selection of relevant components → manual spectral review → XIC review → export of results</blockquote>A key advantage of the NIST26 Chromatogram Window is its flexibility. Users do not have to accept every automatically proposed identification. Instead, results can be filtered, sorted, organized into custom lists, and individually reviewed before being included in the final report.<h3>Conclusion</h3>The NIST26 Chromatogram Window provides a more integrated environment for processing LC-MS/MS data and performing spectral library searches. The workflow presented by James Little begins with mzML data and appropriate Tandem mode configuration, followed by library selection, processing, filtering, and systematic review of candidate identifications.An important principle is not to rely exclusively on automated scores. Filters can help transform a large results set into a manageable list of candidates, but final evaluation should also consider spectral comparisons, chromatographic information, and, where appropriate, additional examination in the XIC Browser.The ability to save processing configurations and export selected results to Excel further supports the development of practical and repeatable workflows for routine LC-MS/MS data processing.

Processing MS/MS Data in NIST26 Chromatogram Window

In September 2026, Prague will become a global meeting point for the chromatography community. From 6 to 10 September 2026, the city will host the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/events/644">35th International Symposium on Chromatography – ISC 2026</a>, one of the leading international events dedicated to chromatography, separation science, and analytical chemistry.Shimadzu is proud to support this prestigious event as a Platinum Sponsor.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Shimadzu_at_ISC_2024_2_e0076c08f2.jpg" alt="Shimadzu: Shimadzu at ISC 2024" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Shimadzu_at_ISC_2024_2_e0076c08f2.jpg 117w," sizes="100vw" width="1500" height="2000">ISC 2026 represents a unique opportunity for scientists, researchers, industry experts, application specialists, and technology providers to meet, exchange knowledge, and discuss the latest developments in chromatography and separation science. The conference will bring together experts from academia, pharmaceutical industry, environmental analysis, food safety, healthcare, life sciences, and many other fields where analytical technologies play an essential role.We would like to warmly invite our customers, partners, colleagues, and the wider scientific community to join us at ISC 2026 in Prague. The conference will offer an inspiring scientific programme, lectures by internationally recognised experts, dedicated sessions on current trends and challenges, an exhibition area, and valuable opportunities for networking with the global chromatography community.Following the successful <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/events/642">ISC 2024 in Liverpool</a>, ISC 2026 will bring this important international symposium to the heart of Europe. We are looking forward to meeting you in Prague and contributing together to a strong and successful edition of ISC.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/1728218963766_9d5394a9da.jpg" alt="Gesa Schad: Shimadzu at ISC 2024 in Liverpool" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_1728218963766_9d5394a9da.jpg 156w," sizes="100vw" width="1280" height="1280">Visit <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/events/1371">Shimadzu at ISC 2026</a> in Prague and be part of one of the key international events in chromatography and separation science.<blockquote>Registration is open on the official conference website: <a target="_blank" rel="noopener noreferrer" href="https://www.isc2026.org">www.isc2026.org</a></blockquote><h3>Shimadzu Vendor Seminar: Three New Reasons to Rethink Your Workflow</h3><ul><li>07 September 2026</li><li>12 PM - &nbsp;13 PM</li></ul>Join us for an engaging seminar introducing three new analytical solutions designed to help laboratories work smarter, respond faster, improve robustness, and achieve greater confidence in their results. As analytical demands continue to grow, laboratories need technologies that not only deliver strong performance, but also enhance efficiency, flexibility, and ease of operation. This seminar will highlight how our latest innovations in IC, UHPLC, and GC-MS/MS can streamline workflows, support complex applications, and create new opportunities for productivity across your laboratory.<h5>Nexera IC – New compact ion chromatography solution for reliable, high-sensitivity anion and cation analysis.</h5><ul><li>Dr. Gesa Schad</li></ul><h5>Nexera X4 – Next-generation UHPLC platform designed for ultra-high performance and robust operation without compromise.</h5><ul><li>Dr. Gesa Schad</li></ul><h5>GCMS-TQ RX Series – Advanced triple quadrupole GC-MS/MS systems engineered for enhanced sensitivity and dependable trace-level analysis.</h5><ul><li>Dr. Waldemar Weber</li></ul><blockquote><a target="_blank" rel="noopener noreferrer" href="https://www.shimadzu.eu/forms/vendor-seminar-registartion_isc2026.html">Register here to attend Shimadzu Vendor Seminar</a></blockquote><h3>Scientific Programme Presentation</h3><ul><li>08 September 2026</li><li>10:30 – 12:00</li><li>Fun 5: Separations with Supercritical and Subcritical Fluids&nbsp;</li></ul><h5>Accelerating Forensic Analysis: A Rapid SFC-MS Workflow for Novel Regioisomeric Fluorofentanyl Derivatives and Related Compounds</h5><ul><li>Dr. Jennifer Field, Shimadzu UK, Milton Keynes, UK</li></ul><h3>Winners of the Shimadzu student sponsorship</h3>We are thrilled to announce the winners of the Shimadzu student sponsorship for free tickets to attend the ISC 2026 conference. We received a great number of high-quality abstracts, showcasing the innovative research being conducted by students all over Europe.We extend our heartfelt congratulations to all the winners and look forward to their contributions at the conference. To those who were not selected this time, we encourage you to continue your excellent work and apply again in the future.And the lucky winners are: &nbsp; &nbsp;<h5>Chromatography supports electrochemistry–mass spectrometry (EC-MS) analysis of olaparib and inavolisib metabolites</h5><ul><li>Fabiola Dontsi Tonleu, University of Münster, Germany&nbsp;</li><li>Abstract ID: ISC-0262 &nbsp; &nbsp;</li></ul><h5>Towards circular wind energy: Sample preparation strategies in combination with GC×GC-TOFMS for the characterization of wind turbine blade recycling products&nbsp;</h5><ul><li>Giulia Giacoppo, University of Ferrara, Italy</li><li>Abstract ID: ISC-0169 &nbsp; &nbsp;</li></ul><h5>Implementing SFC for analysis of antibiotics in manure</h5><ul><li>Michelle Hussock, University of Duisburg-Essen, Germany</li><li>Abstract ID: ISC-0220 &nbsp;</li></ul><h5>Identifying optimal LC-MS conditions for oligonucleotide mapping of mRNA: A multi-criteria assessment of methods</h5><ul><li>Athanasios Tsalmpouris, University of Geneva, Switzerland</li><li>Abstract ID: ISC-0211</li></ul><h5>From weeds to crop protectants: phytochemical profiling and dual biopesticidal activities of Chenopodium ambrosioides and Cleome gynandra &nbsp;</h5><ul><li>Rahim Ullah, University of Helsinki, Finland</li><li>Abstract ID: ISC-0249 &nbsp;</li></ul><h4>Poster Presentations</h4><h5>Optimal column selection for experimental surface polarity measurement using supercritical fluid chromatography</h5><ul><li>Yoshiyuki Watabe, Shimadzu Corporation, Kyoto, Japan</li><li>Session: BIO08 - Sample preparation and automation</li></ul><h5>Characterization of SFC stationary phases for Analysis of Essential Oils</h5><ul><li>Martin Meyer, Shimadzu Europa, Duisburg, Germany</li></ul><h5>High-sensitivity analysis of more than 100 pesticides in food using microflow LC-MS/MS</h5><ul><li>Ramy Abou Naccoul, Shimadzu France, Marne la Vallée, France</li><li>Session: HYP05 - Microfluidic and chip separations in MS</li></ul><h5>Streamlined selection of optimal separation conditions using an automated LC/SFC method development platform</h5><ul><li>Dr. Gesa Schad, Shimadzu Europa, Duisburg, Germany</li><li>Session: FUN05 - Separations with super - and sub-critical fluids</li></ul><h5>Ion Chromatographic Determination of Major Inorganic Ions in Beer for Quality Control and Product Differentiation</h5><ul><li>Dr. Vadim Kraft, Shimadzu Europa, Duisburg, Germany</li><li>Session: FUN08 - Separation modes</li></ul><h5>Efficient SFC Method Development for the Analysis of Essential Oils Using Shimadzu LabSolutions MD</h5><ul><li>Dr. Brigitte Bollig, Shimadzu Europa, Duisburg, Germany</li><li>Session: HYP02 - SFC-MS</li></ul><h5>Assessing the applicability of retention modelling as a tool for oligonucleotide analysis using ion-pair HPLC</h5><ul><li>Richard Hodgson, Shimadzu UK, Milton Keynes, UK</li></ul><h3><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/7477">ISC 2026 Scientific program</a> highlights</h3>The programme runs across three parallel tracks — Fundamentals, Bioanalysis &amp; Omics Applications, and Hyphenation Techniques — covering topics from column technology, chiral and multi-dimensional separations, and AI/machine learning in separation science, to proteomics, green analytical chemistry, and LC/MS data processing.<h4>Why it matters for industry</h4>This year's Industry Program is shaping up particularly well, giving companies a direct space to connect with academia and the next generation of scientists:<ul><li>Industry &amp; Education – bridging academic training with industry needs</li><li>Career Presentation – companies showcase career paths and hiring needs to students and professionals</li><li>AI in Separation Science – real-world use of AI in method development and lab workflows</li><li>Sustainability in Separation Science – translating green chemistry research into industrial practice</li></ul>

Shimadzu to Join ISC 2026 in Prague as Platinum Sponsor

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