<h3 id="h-a-stellar-way-to-overcome-barriers-for-discovery-verification-part-1" data-uw-rm-heading="level" role="heading" aria-level="2"><strong>A stellar way to overcome barriers for discovery verification – Part 1</strong></h3><p><strong>This is the first in a multi-part blog series highlighting the key pillars and impressive benefits of the </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1149"><strong>Stellar mass spectrometer</strong></a><strong>-the first-of-its-kind solution purpose-built for discovery verification. Stay tuned for more blog posts in the series. &nbsp;</strong></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Why_You_Need_a_Verification_class_Mass_Spectrometer_45a584008f.jpg" alt="Thermo Fisher Scientific: Why You Need a Verification-class Mass Spectrometer." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Why_You_Need_a_Verification_class_Mass_Spectrometer_45a584008f.jpg 207w," sizes="100vw" width="1024" height="773"></p><p>If you were a handyman, you wouldn’t dream of using a wrench as a hammer, or a screwdriver as a chisel. You always need the right tool for the job. Same is true for clinical and translational researchers, who depend on having the right solution to maximize their productivity while advancing their research.</p><h3 id="h-the-challenge-a-missing-tool-in-the-discovery-to-validation-workflow"><strong>The challenge: A missing tool in the discovery-to-validation workflow</strong></h3><p>For decades, clinical and translational researchers have struggled with biomarker verification workflows due to a technology gap. There’s no current technology that simultaneously addresses the scale, sensitivity and throughput demands without some serious drawbacks. You know this well.</p><p>Triple quad technology performing multiple reaction monitoring (MRM) is challenged to keep up with limited capacity to handle massive target lists while quantifying at lower limits using faster LC gradients.</p><p>HRAM MS technology performing parallel reaction monitoring (PRM) are challenged to maintain high sensitivity with high acquisition speeds to function with high throughput at experimental scale.</p><h3 id="h-the-breakthrough-solution-the-first-of-its-kind-verification-class-ms"><strong>The breakthrough solution: The first-of-its kind verification-class MS</strong></h3><p>Researchers struggling to fill the technology gap need not struggle any more. The first-to-market <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1149"><strong>Thermo Scientific Stellar mass spectrometer</strong></a> expertly addresses the shortcomings of both ends of the existing verification-based mass spectrometer spectrum with its:&nbsp;</p><ul><li><strong>Expanded scale </strong>– <strong>The Stellar MS</strong> expands biomarker candidate verification per unit time while covering a wider range of compound classes.&nbsp; For proteomics and metabolomics, the expanded scale enables researchers to include more stable isotope labeled standards (SIS) without having to drop endogenous targets, enabling absolute quantitation for better statistical analysis, plus method standardization.</li><li><strong>Higher sensitivity </strong>– It generates data incredibly fast, but still maintains excellent sensitivity to enable accurate measurements and better putative biomarker stratification. With its impressive quantitative performance, this mass spectrometer minimizes the risk of false negatives. The sensitivity of quantitation extends dynamic range in association with the expanded scale to provide both breadth and depth of sample analysis.</li><li><strong>Greater specificity </strong>– <strong>The Stellar mass spectrometer’s</strong> ability to acquire <strong>full scan MS<sup>2</sup></strong> and <strong>MS<sup>3</sup> </strong>enables greater specificity by measuring all product ions associated with the precursor analyte, ensuring quantitative confidence in your targets of interest. It can detect smaller signal changes between donor groups (e.g., diseased and healthy), which ensures your measured expression levels are attributed to your target compound and not to background isomeric/isobaric interferences.</li><li><strong>Massive throughput </strong>– It provides the capacity to process all the samples in a study faster, which increases the laboratory capacity for more projects or expand the study size which increases statistical power for more confidence. Combined with the <strong>Thermo Scientific Vanquish Neo UHPLC system</strong> that delivers chromatographic performance from 0.1 to 100 µL/min, the <strong>Stellar MS</strong> has the acquisition speed to improve throughput 3-5X compared to methods using existing QQQ and HRAM instrumentation.</li><li><strong>Unrivaled quantitative productivity </strong>– Measuring a large number of targets is one thing, but how do researchers build these highly multiplexed methods? Traditionally, this process has been slow, painful and costly, requiring either direct infusion or many replicate injections followed by manual data evaluation. With the<strong> Stellar MS</strong>, researchers can go from building a method to completing an entire study faster while maintaining high data quality and confidence in results. &nbsp;&nbsp;</li></ul><h3 id="h-bridging-the-gap-between-discovery-and-clinical-validation"><strong>Bridging the gap between discovery and clinical validation</strong></h3><p>Not only does the Stellar MS represent a new class of instrument, it serves as the perfect “companion” product between the upstream HRAM instruments doing discovery and the triple-quad systems performing the downstream validation processes.</p><p>After discovery, the Stellar MS becomes invaluable for the verification phase—using quantitative accuracy to narrow the broad list of candidates with the highest potential down to the best set of markers to move into clinical validation. It can process a large list of potential candidates with the added benefits of higher sensitivity and quantitative accuracy.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Why_You_Need_a_Verification_class_Mass_Spectrometer_2_891de5ae8d.jpg" alt="Thermo Fisher Scientific: Why You Need a Verification-class Mass Spectrometer." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Why_You_Need_a_Verification_class_Mass_Spectrometer_2_891de5ae8d.jpg 245w," sizes="100vw" width="1024" height="576"></p><p>Transitioning from verification to validation may deliver a narrowed set of biomarker candidates that have the greatest potential for specific and sensitive sample classification.&nbsp; Based on the Stellar mass spectrometer’s work, researchers now know the sample preparation steps, LC methods, retention times, detection range (LLOD/LLOQ) and method robustness that can be carried over to streamline validation.&nbsp;</p><p>In addition, researchers also have the option to directly transition the LC-MS/MS method to&nbsp;the <strong>Thermo Scientific TSQ Altis Plus triple quadrupole mass spectrometer</strong> if expanded laboratory capacity is needed. The ESI source, ion source settings, and <strong>Thermo Scientific Xcalibur software</strong> provide direct overlap to minimize additional method refinement.&nbsp;The <strong>TSQ Altis Plus MS</strong> also has the same robustness to ensure maximum uptime to complete studies with higher throughput. &nbsp;</p><h3 id="h-no-longer-stuck-in-discovery-expanded-capability-across-the-entire-workflow"><strong>No longer stuck in discovery: expanded capability across the entire workflow</strong></h3><p>Many translational researchers have avoided the move to targeted verification methods due to the complexity, as well as the lack of experience operating triple quadrupole systems to create, refine and implement these highly multiplexed methods. The introduction of the Stellar MS workflow streamlines the process while delivering quantitative performance.</p><p>Therefore, researchers can expand their laboratory capacity and advance their research work in house, without the need to add people, learn new skills or devote months to this work. Researchers can cover more of the workflow process themselves—all the way to the validation phase—enabling them to maintain better control, reduce costs and increase confidence in the results.&nbsp;&nbsp;&nbsp;&nbsp;</p><blockquote><p>For more information, explore the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1149">Stellar Mass Spectrometer MS</a> web page or reach out to your Thermo Fisher sales representative.</p><p>Intrigued to learn <strong>more about the Stellar mass spectrometer</strong> and how to streamline your verification process? Watch for more blogs in this series soon.</p></blockquote><blockquote><h5><strong>Visit our&nbsp;</strong><a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/chromatography-&amp;-mass-spectrometry/posts/?feedView=all"><strong>LinkedIn page</strong></a><strong>:</strong> #StellarMassSpec #MassSpectrometry</h5><section><h4><strong>Dr. Scott Peterman</strong></h4><div itemprop="description">Scott Peterman, Ph.D., is Senior Product Marketing Manager for Life Science Mass Spectrometry of the Chromatography and Mass Spectrometry Division of Thermo Fisher Scientific.</div></section></blockquote><p>&nbsp;</p>

Why You Need a Verification-class Mass Spectrometer

<h3><strong>Using Artificial Intelligence to Drive MS Workflow Productivity</strong></h3><p><strong>This is the second in a multi-part blog series highlighting the key attributes and impressive benefits of the Stellar mass spectrometer—the first-of-its-kind instrument designed and optimized for highly multiplexed targeted quantitation, ideally suited—for discovery verification. See Part 1 </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/5077" aria-label="This is the second in a multi-part blog series highlighting the key attributes and impressive benefits of the Stellar mass spectrometer—the first-of-its-kind instrument designed and optimized for highly multiplexed targeted quantitation, ideally suited—for discovery verification" uw-rm-vague-link-id="https://www.thermofisher.com/blog/analyteguru/why-you-need-a-verification-class-mass-spectrometer/$here" data-uw-rm-vglnk=""><strong>here</strong></a><strong> and stay tuned for more blog posts in the series.</strong><i><strong>&nbsp;</strong></i></p><p>As artificial intelligence (AI) continues to take the modern world by storm, a similar concept in the scientific world called “<strong>automated</strong> <strong>intelligence</strong>” is revolutionizing work for research scientists in their transition from discovery to clinical validation. This version of AI enables you to leverage empirical data, user-defined guidance and instrument performance metrics to manage experiments and dramatically improve productivity.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Why_You_Need_a_Verification_class_Mass_Spectrometer_45a584008f.jpg" alt="Thermo Fisher Scientific: Why you need a verification-class mass spectrometer – Part 2" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Why_You_Need_a_Verification_class_Mass_Spectrometer_45a584008f.jpg 207w," sizes="100vw" width="1024" height="773"></p><p>It’s possible with an all-new instrument—the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1149"><strong>Thermo Scientific Stellar mass spectrometer</strong></a> (MS)—which uses AI to transform the process of building methods, data acquisition management and data processing for interpretation and planning next steps.&nbsp; Combined with the unique instrument performance, the Stellar mass spectrometer creates a new paradigm for targeted quantitation.</p><h3 id="h-garbage-in-garbage-out"><strong>Garbage in, garbage out</strong></h3><p>Scientific research is all about data, and just like with any computational work, poor-quality input will always produce faulty or unusable output. This idea is especially true for clinical and translational researchers who perform biomarker verification. The quality of your method development and research will always be determined by several things: <strong>(1)</strong> your existing data (e.g., compound databases, empirical data, in silico predictive models), <strong>(2)</strong> your guidance (e.g., real-time decision-making parameters) and <strong>(3) </strong>the experimental capabilities of your instrument platform.</p><h3 id="h-another-challenge-limitations-in-the-discovery-to-validation-workflow"><strong>Another challenge: limitations in the discovery-to-validation workflow</strong></h3><p>Poor quality input for method development is one challenge, but it’s not the only one. As we discussed in our <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/5077">first blog post </a>researchers have long struggled with a technology gap in available instrument platforms. Until recently, there were no single-vendor solutions that offered excellent performance for both discovery and targeted verification. This was a serious limitation that impacted how much researchers could rely on AI for method-building. The old process still required a lot more hands-on optimization, which seriously limited productivity.</p><h3 id="h-finally-automated-intelligence-without-the-drawbacks"><strong>Finally: automated intelligence without the drawbacks</strong></h3><p>With the advent of automated intelligence available on Stellar MS to build targeted methods and manage data acquisition, it’s a whole new ball game. Stellar MS software leverage automated intelligence to boost laboratory productivity, capacity, and lab reputation for high-quality data with faster turnaround times. As a researcher, you can now use automated intelligence to “feed in” your previous work and provide instructions about how to use that information to make decisions and generate new data. Here’s how it works:</p><h3 id="h-how-ai-speeds-method-creation-and-optimization"><strong>How AI speeds method creation and optimization</strong></h3><p>Stellar MS come with the Thermo Scientific software tool <strong>PRM Conductor </strong>in Skyline software for automated method building. It uses automated intelligence to build highly effective, targeted acquisition methods from your discovery data (from either<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?instrumentationItems=33&amp;manufacturerItems=3&amp;search=Thermo+Scientific+Orbitrap"><strong> Thermo Scientific Orbitrap</strong></a>-based MS systems or the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1149"><strong>Stellar MS</strong></a>).</p><p>PRM Conductor aids in the generation of targeted-MS2 and MS3 assays. The creation of an assay is broken into three main parts:</p><ol><li>Skyline metadata describing precursor-to-product transitions is used to filter transitions against a set of thresholds. The filters are based on integrated peak area, relative area, signal-to-background, correlation to median transition, LC base peak width, and retention time. Precursors are filtered by whether they have at least a certain number of qualifying transitions, typically three for peptides and two for small molecules.</li><li>Targeted assays are created with a visualization that depicts the concurrency of the assay in terms of how long the instrument would take to acquire data for the precursors as a function of retention time. Given a desired number of acquired points per LC peak and corresponding cycle time, you can see how various experimental parameters affect the feasibility of acquiring data for the qualifying precursors, such as linear ion trap scan rate and acquisition window width.</li><li>Finally, you can decide whether to create multiple assays for all qualifying precursors, or a single assay with a “balanced load” that picks the best N peptides per protein. Instrument methods for the final assay(s) can then be exported, based on a user-defined template method.</li></ol><p>In addition, Stellar MS solutions use <a target="_blank" rel="noreferrer noopener" aria-label="Normalized Collision Energy - open in a new tab" data-uw-rm-ext-link="" uw-rm-external-link-id="https://assets.thermofisher.com/tfs-assets/cmd/warranties/psb104-normalized-collision-energy-technology-en.pdf$normalizedcollisionenergy"><a target="_blank" rel="noopener noreferrer" href="https://assets.thermofisher.com/TFS-Assets/CMD/Warranties/PSB104-Normalized-Collision-Energy-Technology-EN.pdf"><strong>Normalized Collision Energy</strong></a></a><strong> (NCE)</strong> – a well-established principle that automatically compensates for mass dependency by automatically estimating all of the collision energies. NCE bypasses the need for optimization per precursor-to-product ion transition performed by a triple quadrupole mass spectrometer which takes much longer to perform, multiplies the experimental cost due to replicate injections of standards and dedicated research staff time.&nbsp;</p><h3 id="h-how-ai-streamlines-data-acquisition"><strong>How AI streamlines data acquisition</strong></h3><p>With the Stellar MS automated intelligence capabilities, scientists can also speed data acquisition with these tools:</p><p><strong>Dynamic AGC</strong> (automated gain control) helps the system maintain constant ion count and high data quality regardless of ion flux. Essentially, the Stellar MS regulates the number of charges or ions per spectrum by employing a hyper-fast ion gate managing ion accumulation to pass an ideally constant number of ions per spectrum.</p><figure class="image"><img style="aspect-ratio:400/443;" src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Why_you_need_a_verification_class_mass_spectrometer_Part_2_2db3d7d0df.jpg" alt="Thermo Fisher Scientific: Figure 1: a) Theoretical depiction of how AGC expands the accessible quantitative range of concentrations. b) Assessment of active targets at the start of a cycle, with their minimum acquisition times on the y-axis, and where more intense precursors are white. 3) Expansion of injection times inverse-proportionally to target abundance. " srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Why_you_need_a_verification_class_mass_spectrometer_Part_2_2db3d7d0df.jpg 141w," sizes="100vw" width="400" height="443"></figure><p>As depicted in Figure 1, the ability to vary the injection time expands the dynamic range of quantitation, from a base range given by just the storage and detector saturation limits and multiplies it by the gate linearity range. In the case of the Stellar MS, the pulsed nature of ion trap mass analysis limits the intra-scan dynamic range to about three orders (from 1 to 25k ions in a peak), while the gate can give a linear response from about 3d-6 seconds up to a practical experimental limit, for example 3e-1 seconds.</p><p>Another tool, <strong>Adaptive RT</strong>, dynamically manages PRM acquisition, which means you’ll nearly eliminate the risk of missing data while maximizing target capacity.&nbsp; Missing data requires you to re-run samples, costing time and money. Using the method (generated by PRM Conductor software), you can run one representative sample on the gradient and product ion distribution profiles as a function of retention time are built into the instrument editor, which combines PRM settings and Adaptive RT to manage every microsecond of sample acquisition. The system will continue to update and modify the method to adjust for any unexpected LC perturbation or manage data acquisition across multi-channel UHPLC column formats. For a more in-depth description, check out the <a target="_blank" rel="noreferrer noopener" aria-label="newly published BioRxiv paper - open in a new tab" data-uw-rm-ext-link="" uw-rm-external-link-id="https://www.biorxiv.org/content/10.1101/2024.05.31.596848v1$newlypublishedbiorxivpaper"><a target="_blank" rel="noopener noreferrer" href="https://www.biorxiv.org/content/10.1101/2024.05.31.596848v1">newly published BioRxiv paper</a></a>.</p><h3 id="h-conclusion-automated-intelligence-maximizes-workflow-performance"><strong>Conclusion: Automated intelligence maximizes workflow performance</strong></h3><p>In order to maximize LC-MSn workflow performance for translational verification, you need solutions that streamline all steps while meeting experimental expectations—scale, sensitivity, specificity, throughput, and ease-of-use. Together, automated intelligence on the Stellar MS combined with unique instrument performance can help deliver the ultimate performance to boost your lab’s productivity and prestige.</p><blockquote><p>For more information, explore the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1149">Stellar Mass Spectrometer MS</a> or <a target="_blank" rel="noreferrer noopener" aria-label="reach out to your Thermo Fisher Scientific sales representative - open in a new tab" data-uw-rm-ext-link="" uw-rm-external-link-id="https://www.thermofisher.com/us/en/home/global/forms/industrial/stellar-mass-spectrometer-contact.html$reachouttoyourthermofisherscientificsalesrepresentative"><a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/us/en/home/global/forms/industrial/stellar-mass-spectrometer-contact.html">reach out to your Thermo Fisher Scientific sales representative</a></a>.</p><p>Intrigued to learn more about the Stellar MS and how it can improve your work? Watch for more blog posts in this series soon.</p><h5><strong>Visit our&nbsp;</strong><a target="_blank" rel="noreferrer noopener" aria-label="LinkedIn page - open in a new tab" data-uw-rm-ext-link="" uw-rm-external-link-id="https://www.linkedin.com/showcase/chromatography-&amp;-mass-spectrometry/posts/?feedview=all$linkedinpage"><a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/chromatography-&amp;-mass-spectrometry/posts/?feedView=all"><strong>LinkedIn page</strong></a></a><strong>:</strong> #StellarMassSpec #MassSpectrometry #TranslationalResearch</h5><h4><strong>Dr. Scott Peterman</strong></h4><div itemprop="description">Scott Peterman, Ph.D., is Senior Product Marketing Manager for Life Science Mass Spectrometry of the Chromatography and Mass Spectrometry Division of Thermo Fisher Scientific.</div></blockquote>

Why you need a verification-class mass spectrometer – Part 2

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