A critical first step in quantitation is tuning the instrument to identify the optimal fragment ions that deliver both sensitivity and specificity. This is true regardless of the use of triple quadrupoles, ion traps, or accurate mass systems.&nbsp;Traditionally, this process requires physical standards and, in the case of large panels of analytes, can be time-consuming.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Generating_Quantitative_Methods_Automatically_From_Spectral_Library_Data_262243e285.jpg" alt="Thermo Fisher Scientific: Generating Quantitative Methods Automatically From Spectral Library Data" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Generating_Quantitative_Methods_Automatically_From_Spectral_Library_Data_262243e285.jpg 245w," sizes="100vw" width="1024" height="512"><h3>But what if we could generate methods without needing all the standards on hand or even tuning them at all?&nbsp;</h3>Doing so would require having a source of data that captures the optimal fragments and energies for all compounds.&nbsp;Enter <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764">mzCloud</a>, a spectral library that includes up to 20 collision energies for high-energy collisional dissociation MS2 on every compound in the library.Although generated from full scan accurate mass instruments, this information contains the energy-dependent fragment formation using a fragment technique common to triple quadrupoles and other instruments.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_8_9199b4056a.jpg" alt="Thermo Fisher Scientific: Generating Quantitative Methods Automatically From Spectral Library Data: Thermo Scientific mzCloud Mass Spectral Library" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Scientific_mz_Cloud_Mass_Spectral_Library_8_9199b4056a.jpg 224w," sizes="100vw" width="270" height="188"><ul><li>Extensively curated, high-quality free online library</li><li>Multiple fragmentation energy levels represented</li><li>Covers a wide chemical space to include compounds relevant to all applications</li><li>For both research and targeted screening workflows</li><li>Contains over 32,000 compounds and 16,500,000 spectra</li></ul><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Generating_Quantitative_Methods_Automatically_From_Spectral_Library_Data_2_bcac20a85c.jpg" alt="Thermo Fisher Scientific: Generating Quantitative Methods Automatically From Spectral Library Data: Figure 1. Breakdown curves for the top 6 fragment ions from Melatonin showing maximum energy for each fragment ion. X-axis is fragmentation energy, Y-axis is fragment intensity." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Generating_Quantitative_Methods_Automatically_From_Spectral_Library_Data_2_bcac20a85c.jpg 245w," sizes="100vw" width="1024" height="367"><h3>So, could we transfer the information from the library into a usable method for an instrument such as a triple quadrupole?</h3>The answer is yes. The first step is to determine if any offset in the collision energy (eV) exists between the platform used to generate the library and the target quantitative instrument.&nbsp; This can be easily assessed with a small selection of compounds across the mass range to ensure that the optimal collision energy remains the same or, in cases where they are different, a correction factor can be calculated.&nbsp; Once this is done, it is a relatively simple matter of taking the top N most intense fragment ions from the library curves and creating the corresponding quantitative instrument methods.In fact, we have already successfully implemented this approach: all recent triple quadrupoles from Thermo Fisher Scientific now come with a built-in database of methods generated in this fashion.&nbsp; The creation of a quantitative acquisition method is as simple as selecting compounds, polarity, and number of transitions from the database and proceeding with acquisition.By automating the generation of quantitative methods from spectral library data, we significantly reduce the time and effort required for method development. This enables our customers to focus on their core research and analysis, improving productivity and accelerating scientific discovery.For more information, join us at the upcoming <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/events/proteome-discoverer-compound-discoverer-users-meetings.html">user meeting</a> or go to <a target="_blank" rel="noopener noreferrer" href="https://www.mzcloud.org/">mzCloud.org</a> or see the advantages of using mzCloud with Thermo Scientific <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759">Compound Discoverer software</a>.<ul><li>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#mzCloud #MassSpectralLibraries</li></ul><blockquote><h5>Tim Stratton</h5>Tim is a University of Minnesota graduate with over a decade of experience in pharmaceutical analysis and research, specializing in structure elucidation and interpretation of fragmentation. After roles at Solvay Pharmaceuticals and Abbott Laboratories spanning regulated analysis, method validation, and drug metabolism/pharmacokinetics, Tim joined Thermo Fisher Scientific. Over the past decade, he has focused on supporting hardware and software development, as well as building high-resolution, accurate mass spectral libraries to advance unknown identification in research.</blockquote>

Generating Quantitative Methods Automatically From Spectral Library Data

<h5>Why compromise between performance and price when you can have both?</h5>With Thermo Scientific factory-certified, pre-owned <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=5&amp;manufacturerItems=3">mass spectrometers</a>, you can access legendary LC-MS technology—trusted around the world—at a fraction of the cost of buying new. Our refurb program delivers the quality, precision, and reliability you expect from Thermo Fisher Scientific, while helping you stay within budget and on top of your analytical goals.<h3>Factory-Certified for confidence</h3>Every certified pre-owned system goes through a rigorous factory reconditioning process. From updated hardware and software to comprehensive performance testing, each instrument is restored to meet the same high standards as our new products.<h4>What’s included?</h4>When you choose a certified LC-MS system, you get more than just an instrument—you get the complete Thermo Scientific experience:<ul><li>Full 1-year factory warranty for peace of mind</li><li>29-point inspection checklist, re-certification, and final quality testing</li><li>Software and hardware updates to current revisions</li><li>Re-certification using only genuine Thermo Scientific factory parts</li><li>Professional installation by Unity Lab Services field engineers</li><li>Optional training and application support to get you up and running fast</li></ul><h4>What gets replaced?</h4>Our reconditioning process is comprehensive. These critical components are replaced on every system:<ul><li>All hoses</li><li>Probes</li><li>Ion sources</li><li>Ion transfer tube</li><li>Multiplier</li><li>Mechanical pumps</li><li>Acquisition PC and software</li><li>PCBs (when required for revision)</li></ul><h3>Maximize uptime with expert support</h3>Behind every certified system is a global team of Thermo Fisher specialists committed to helping your lab succeed. Support doesn’t stop after installation:<ul><li>Flexible service contract options through Unity Lab Services</li><li>Guaranteed response times for select contracts</li><li>Financing solutions to meet your budget</li><li>System qualifications and validations</li><li>Technology refresh solutions to keep you ahead of the curve</li></ul><h3>A smarter, more sustainable choice</h3>Investing in a factory-certified pre-owned system isn’t just cost-effective—it’s a sustainable solution that extends the life of high-performance equipment and reduces waste. You get the data quality and instrument reliability your work depends on, while making an environmentally conscious choice.<h3>More ways to access Thermo Scientific excellence—affordably</h3>We understand that every lab’s financial situation is different. That’s why Thermo Fisher offers multiple paths to help you acquire the right mass spectrometry solution, when you need it.<h4>1. <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/mass-spectrometer-price-affordability-programs/factory-certified-refurbished-mass-spectrometers.html">Factory-certified refurbished systems</a></h4>Already covered above, this option gives you fully reconditioned, factory-tested LC-MS instruments at a lower price point—without compromising performance or support.View our brochure for a comprehensive overview.<h4>2. <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/mass-spectrometer-price-affordability-programs/mass-spectrometer-trade-upgrade.html">Trade-in and trade-up</a>: Turn your old into increased productivity</h4>Already own a system—Thermo Fisher or otherwise? Trade it in and upgrade to a newer model with greater capabilities and sensitivity.How it works:<ul><li>Receive a discount on your next system based on the residual value of your current instrument</li><li>Avoid the hassle of selling or decommissioning your old system</li><li>Transition with minimal downtime and disruption</li></ul>Why labs choose this path:<ul><li>Keeps productivity high while moving to new technology</li><li>Eases the financial burden of upgrading</li><li>Helps labs stay competitive with improved system performance</li></ul><h4>3. Personalized equipment <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/products-and-services/services/financial-leasing-services.html">financing &amp; leasing options</a></h4>If upfront capital is limited, our tailored financing and leasing plans offer flexibility that aligns with your lab’s budget and growth plans.<h5>Ready to get started?</h5><ul><li><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">Explore our certified systems, trade-in opportunities, and financing solutions.</a></li></ul>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#affordabiliy #LCMS #sustainability #productivity<blockquote><h5>Ema Ruzic</h5>Vertical Marketing Manager, Chromatography and Mass Spectrometry Division (CMD)</blockquote>

Unlock High-Performance LC-MS with Factory-Certified Systems from Thermo Fisher Scientific

<h5>Beyond the box. Beyond the bottleneck.</h5>Routine laboratories are under constant pressure to do more-more samples, more compounds, more confidence-without sacrificing uptime or usability. That’s why we’re excited to introduce the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2207">Thermo Scientific TSQ Certis Triple Quadrupole Mass Spectrometer</a>, a next-generation QQQ MS designed to keep high-throughput labs running at peak performance.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Introducing_the_new_Thermo_Scientific_TSQ_Certis_Triple_Quadrupole_Mass_Spectrometer_c1abb3fc23.jpg" alt="Thermo Fisher Scientific - Introducing the new Thermo Scientific TSQ Certis Triple Quadrupole Mass Spectrometer" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Introducing_the_new_Thermo_Scientific_TSQ_Certis_Triple_Quadrupole_Mass_Spectrometer_c1abb3fc23.jpg 245w," sizes="100vw" width="1024" height="512">The TSQ Certis MS is built for laboratories that measure success by time, throughput, and results. With a rugged platform engineered for continuous operation and premium quantitative performance, TSQ Certis goes beyond incremental improvements to remove common bottlenecks in everyday LC-MS workflows.<h3>A premium QQQ MS, ready to run</h3>The TSQ Certis MS delivers improved instrument performance and system uptime for applied, clinical research, biopharma, environmental, food safety, and toxicology laboratories. From day one, it is ready to run workflows-no matter who’s at the bench .<h4>Key highlights include:</h4><ul><li>Rugged, unstoppable performance with advanced ion optics designed to extend uptime and reduce maintenance</li><li>Next-generation quantitative performance, powered by the newly engineered OptaMax™ Plus ion source and enhanced ion transmission</li><li>High productivity for demanding multi-analyte methods, enabling fast acquisition speeds and efficient sample throughput</li><li>Enhanced usability, including predictive maintenance tools and ready-to-go method templates that help teams get started faster</li></ul><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Introducing_the_new_Thermo_Scientific_TSQ_Certis_Triple_Quadrupole_Mass_Spectrometer_2_16af5d9816.jpg" alt="Thermo Fisher Scientific - Introducing the new Thermo Scientific TSQ Certis Triple Quadrupole Mass Spectrometer" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Introducing_the_new_Thermo_Scientific_TSQ_Certis_Triple_Quadrupole_Mass_Spectrometer_2_16af5d9816.jpg 245w," sizes="100vw" width="1024" height="512"><h3>Built for routine labs with demanding applications</h3>The TSQ Certis MS is an essential tool for laboratories analyzing hundreds of compounds at high analytical speeds, while maintaining maximum sensitivity and reproducibility. It supports a wide range of applications, including:<ul><li>Robust quantitative bioanalysis for biopharma and CRO laboratories</li><li>PFAS, pesticide, and food safety testing in complex matrices</li><li>Steroid, drugs of abuse, and immunosuppressant analysis in clinical research settings</li><li>High-throughput workflows where reliability and consistency matter most</li></ul><h4>Designed to keep you moving</h4>Every aspect of TSQ Certis was engineered to help labs stay productive. Advanced ion optics, high-capacity ion transfer, and long-life detection components work together to deliver stable, precise measurements over tens of thousands of injections-so your lab spends less time troubleshooting and more time generating results.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Introducing_the_new_Thermo_Scientific_TSQ_Certis_Triple_Quadrupole_Mass_Spectrometer_3_a982011900.jpg" alt="Thermo Fisher Scientific - Introducing the new Thermo Scientific TSQ Certis Triple Quadrupole Mass Spectrometer" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Introducing_the_new_Thermo_Scientific_TSQ_Certis_Triple_Quadrupole_Mass_Spectrometer_3_a982011900.jpg 245w," sizes="100vw" width="1024" height="512">Learn more-and stay tuned Explore the full capabilities of the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2207">Thermo Scientific TSQ Certis Triple Quadrupole Mass Spectrometer</a>.And this is just the beginning. Technical notes, application data, and additional assets are coming soon, highlighting performance across steroids, drugs of abuse, GLP-1, oligonucleotides, PFAS, and more. Stay tuned as we continue to share how TSQ Certis helps routine labs go beyond the box-and beyond the bottleneck.Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#ClinicalBiomarkers #Multiplexed #LCMS #ClinicalResearch<blockquote><h5>Ema Ruzic</h5>Vertical Marketing Manager, Chromatography and Mass Spectrometry Division (CMD)</blockquote>

Introducing the new Thermo Scientific TSQ Certis Triple Quadrupole Mass Spectrometer

In today’s forensic and clinical toxicology labs, productivity is more than just speed—it’s about accuracy, flexibility, and the ability to keep pace with an ever-expanding universe of analytes. Whether processing high-throughput urine samples or evaluating oral fluid, labs are under pressure to deliver reliable results faster, with fewer resources, and across a wide range of complex drug panels. Thermo Fisher Scientific is addressing this challenge head-on, delivering complete LC-MS/MS workflows, solution guides, and databases that prioritize throughput and robustness without sacrificing sensitivity or selectivity. Workflows that include over 100 to 2000 drugs allow for single injection assays that mitigate the need to extract and analyze each drug class individually. The fast speed of the mass spectrometers gives users the ability to speed up gradients, leading to shorter run times.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Boosting_Productivity_in_Toxicology_Labs_7d80cfd388.jpg" alt="Thermo Fisher Scientific: Boosting Productivity in Toxicology Labs." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Boosting_Productivity_in_Toxicology_Labs_7d80cfd388.jpg 245w," sizes="100vw" width="1024" height="512"><h3>A unified workflow for broad drug coverage in urine</h3>Urine remains the cornerstone matrix for drug testing, offering a long detection window for many commonly abused substances. However, with over 100 frequently tested drugs and a growing list of synthetic analogs, labs need streamlined methods capable of handling this analytical diversity. A recent method developed by application scientist Courtney Patterson using <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/chromatography/chromatography-sample-preparation/sample-preparation-consumables/solid-phase-extraction-consumables/sola-spe-plates-cartridges.html">Thermo Scientific SOLAµ SPE plates</a>, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=37&amp;manufacturerItems=3&amp;search=vanquish">Thermo Scientific Vanquish UHPLC</a>, and both <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=22&amp;manufacturerItems=3&amp;search=orbitrap">Thermo Scientific HRAM Orbitrap</a> and <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=20&amp;manufacturerItems=3&amp;search=tsq">Thermo Scientific TSQ triple quadrupole</a> mass spectrometry platforms, delivers a compelling solution. This workflow (linked in the resources section below), utilizes both HRAM Orbitrap and triple quadrupole mass spectrometers, quantified 106 drugs—including 15 isomers—across 10 drug classes, including drugs in both positive and negative polarities, in just 7 minutes per sample. Notably, it demonstrated strong chromatographic resolution for challenging isomeric pairs like codeine/hydrocodone and methamphetamine/phentermine. Lower limits of quantitation (LOQs) ranged from 0.1 to 100 ng/mL, meeting stringent ANSI and forensic standards. Wide dynamic ranges, such as 0.5 to 5,000 ng/mL for norbuprenorphine, enabled labs to confidently report both trace and high-concentration results with minimal rework.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Boosting_Productivity_in_Toxicology_Labs_2_0e2f7432b4.jpg" alt="Thermo Fisher Scientific: Boosting Productivity in Toxicology Labs: Figure 1 Extracted ion chromatogram of 106 drugs of abuse in urine from TN002363." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Boosting_Productivity_in_Toxicology_Labs_2_0e2f7432b4.jpg 220w," sizes="100vw" width="672" height="476">What makes this method stand out is its dual-platform compatibility. The same sample preparation and chromatography approach has been validated on both high-resolution Orbitrap and triple quadrupole systems, giving laboratories the freedom to select instrumentation that best aligns with their throughput needs and budget constraints.And speaking of budgets… Be sure to explore our latest promotions, including <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/o/b/clinical-lcms-discounts.html">complete LC-MS toxicology configurations</a> and <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">affordability programs</a>. You can aim high without overspending by:<ul><li>Investing in certified refurbished instruments at a fraction of the cost</li><li>Trading in older instruments for credit toward the latest models, regardless of manufacturer</li><li>Taking advantage of flexible leasing and financing options, including 0% interest and deferred payment plans</li></ul><h3>Meeting new demands in oral fluid testing with Stellar MS</h3>As oral fluid gains traction for workplace drug testing, roadside evaluations, and rapid screening, labs face a different set of challenges—chief among them, the need for highly sensitive and selective methods to meet SAMHSA detection thresholds. Patterson’s oral fluid workflow, powered by the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1149">Thermo Scientific Stellar mass spectrometer</a>, addresses these needs with precision in a 5-minute method. Using DPX Technology’s INTip™ SCX/WAX SPE tips for extraction and an<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/424"> Accucore Biphenyl column</a> for separation, this method quantified 31 drugs—including THC, opioids, stimulants, and cocaine—at LOQs as low as 0.25 ng/mL. The Stellar system’s targeted-MS2 (tMS2) acquisition mode delivered confident identification with full-scan MS2 spectra, resolving issues like matrix suppression common in oral fluid analysis.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Boosting_Productivity_in_Toxicology_Labs_3_146d0fde1c.jpg" alt="Thermo Fisher Scientific: Boosting Productivity in Toxicology Labs: Figure 2 Schematic of XTR tip extraction protocol with mixed mode SCX/WAX chemistry for INTip dispersive solid phase extraction followed by analysis using the Vanquish Horizon UHPLC system and Stellar Mass Spectrometer from TN003851. Artwork provided by DPX Technologies." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Boosting_Productivity_in_Toxicology_Labs_3_146d0fde1c.jpg 245w," sizes="100vw" width="867" height="375">Importantly, the method achieved baseline separation of structural isomers and provided flexibility in fragmentation, using either HCD or CID based on compound-specific needs. Ten real-world case study samples were analyzed successfully, confirming all compounds with robust retention times and fragment ion ratios.<h3>Productivity without compromise</h3>Together, these two workflows—one for urine and one for oral fluid—showcase how Thermo Fisher Scientific is redefining productivity in toxicology. By combining smart sample preparation, fast chromatography, and high-resolution mass spectrometry platforms, these solutions enable:<ul><li>Rapid turnaround times with sub-10-minute methods</li><li>High-confidence results for complex drug panels, including isomers</li><li>Flexible instrumentation to meet the needs of both high-resolution and triple quadrupole users</li><li>Regulatory readiness with LOQs meeting ANSI and SAMHSA guidelines</li></ul>In a world where toxicology labs must do more with less, Thermo Fisher’s comprehensive solutions empower teams to work faster, smarter, and with greater confidence.Learn more about how Thermo Fisher Scientific’s toxicology solutions can help your lab stay ahead: <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/forensics/forensic-toxicology.html">Forensic Toxicology</a><h3>Resources</h3><ul><li>Past blogs in this series<ul><li>Sample prep – <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6189">Sample Preparation Strategies Demystified: Choosing the Right Fit for Your Toxicology Workflow</a></li><li>Tox Explorer – <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6587">Beyond Blood: Sheffield Teaching Hospitals NHS Foundation Trust Develops HRAM-Powered Method for Post-Mortem Toxicology Analysis</a></li><li>VeriSpray – <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6860">Advancing Drug Analysis with PaperSpray MS</a></li></ul></li><li>On-demand workshop – <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>Technical note – <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/paper/32266">Quantitation of an oral fluid drug panel including THC using the new Stellar mass spectrometer</a></li><li>Technical note – <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/paper/32265">Utilizing HRAM Orbitrap mass spectrometry to quantitate 106 drugs of abuse in urine</a></li><li>Technical note – <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/paper/32265">Utilizing triple quadrupole mass spectrometry to quantitate 106 drugs of abuse in urine</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/paper/32265">Drug screening and confirmation workflows</a></li><li>Promotions<ul><li><a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/o/b/clinical-lcms-discounts.html">Save up to 40% on complete LC-MS toxicology configurations</a></li><li><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</a><ul><li>Refurbished MS</li><li>Trade-in</li><li>Financing/ leasing</li></ul></li></ul></li></ul>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#ForensicToxicology #MassSpectrometry #LabProductivity<blockquote><h5>Ema Ruzic</h5><div>Vertical Marketing Manager, Chromatography and Mass Spectrometry Division (CMD)</div></blockquote>

Boosting Productivity in Toxicology Labs

This is the second part of a multi-part Library blog series. For additional information, see blog <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/6709">Part 1- Generating Quantitative Methods Automatically From Spectral Library Data </a>and stay tuned for more blogs on our website.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_58afeccc3e.jpg" alt="Thermo Fisher Scientific: Identification of Substructures in Unknowns Through MSn Data." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_58afeccc3e.jpg 216w," sizes="100vw" width="1024" height="740">While identification of unknowns remains a significant challenge, it has become easier over the years with the growth of large MSn spectral libraries. These libraries, such as <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764">mzCloud</a>, can provide substructure data on unknowns.&nbsp; Such information can help us to elucidate the structure of compounds that would previously remain unknown.Substructure identification such as this takes advantage of the fact that a structure will always create the same fragments under a given set of fragmentation conditions regardless of if that structure was from MS1 or an MSn level of fragmentation.&nbsp; While no library will ever contain fragmentation data on all possible chemicals, what we need with this approach is enough breadth of coverage in the various substructures commonly occurring to “build up” larger molecules.&nbsp; What that means is we can take the MSn data on many structurally diverse molecules and use it to identify substructures in our unknown.As an example of using MSn data in this fashion, figure 1 shows the query MSn spectra for an unknown and two of the library hits.&nbsp; The hits are from MSn spectra of two known compounds and the precursor of the specific MSn fragment spectra is shown.&nbsp; Both hits from the library provide a similar structure – an aromatic benzyne linked to either an amide or linked to a carbonyl and amine group.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_2_010011961a.jpg" alt="Thermo Fisher Scientific: Identification of Substructures in Unknowns Through MSn Data: Figure 1: The MS3 spectra of the unknown (A) and two matching fragment spectra from the library search along with the precursors of those spectra (B)." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_2_010011961a.jpg 245w," sizes="100vw" width="1024" height="288">While in this example, the specific orientation could not be determined, we have at least a very good starting point in our structure determination by knowing at least one piece of our unknown.&nbsp; Further searches with other MSn spectra from our molecule may uncover other substructures bringing us close to a final identification.&nbsp; In fact, the unknown in this case was isoproturon (Figure 2) which indeed has the substructure indicated from the search.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_3_72dbd5fcef.jpg" alt="Thermo Fisher Scientific: Identification of Substructures in Unknowns Through MSn Data: Figure 2: Structure of Isoproturon." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Identification_of_Substructures_in_Unknowns_Through_M_Sn_Data_3_72dbd5fcef.jpg 245w," sizes="100vw" width="1024" height="578">By utilizing a large library of MSn reference data and acquiring the same MSn query data on our unknowns, we can begin to build up a picture based on substructures we identify.&nbsp; Visit <a target="_blank" rel="noopener noreferrer" href="https://www.mzcloud.org/">mzCloud </a>to see the breadth of MSn fragmentation spectra on a diverse range of chemicals that can be used for such an approach.<ul><li>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#mzCloud #MassSpectralLibraries</li></ul><blockquote><h5>Tim Stratton</h5>Tim is a University of Minnesota graduate with over a decade of experience in pharmaceutical analysis and research, specializing in structure elucidation and interpretation of fragmentation. After roles at Solvay Pharmaceuticals and Abbott Laboratories spanning regulated analysis, method validation, and drug metabolism/pharmacokinetics, Tim joined Thermo Fisher Scientific. Over the past decade, he has focused on supporting hardware and software development, as well as building high-resolution, accurate mass spectral libraries to advance unknown identification in research.</blockquote>

Identification of Substructures in Unknowns Through MSn Data

News from LabRulezLCMS Library - Week 11, 2026

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Whether you’re facing performance bottlenecks, rising maintenance costs, or simply ready to scale up, Thermo Fisher Scientific’s Trade-In / Trade-Up Program offers a seamless, cost-effective path to advanced LC-MS technology.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Upgrade_Smarter_Trade_In_Your_Current_LC_MS_System_and_Boost_Lab_Performance_Without_Breaking_Budget_a54b9c7019.jpg" alt="Thermo Fisher Scientific: Upgrade Smarter: Trade In Your Current LC-MS System and Boost Lab Performance Without Breaking Budget" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Upgrade_Smarter_Trade_In_Your_Current_LC_MS_System_and_Boost_Lab_Performance_Without_Breaking_Budget_a54b9c7019.jpg 245w," sizes="100vw" width="1024" height="512"><h3>Elevate lab productivity at a lower cost</h3>With the Trade-In program, you can turn your existing LC-MS, HPLC system, or Orbitrap mass analyzer—regardless of brand—into savings toward a newer, more powerful instrument. We’ll evaluate your current system’s residual value and apply it directly to your upgrade, helping you offset the cost while avoiding the hassle of selling, shipping, or decommissioning the old instrument yourself.Why Trade-In?Upgrading through the Trade-In program means more than saving money—it’s about gaining lab efficiency, performance, and peace of mind.Benefits of Trading In:<ul><li>Access high-performing Thermo Scientific mass spectrometers</li><li>Increase throughput, sensitivity, and data quality</li><li>Reduce total cost of ownership through improved reliability</li><li>Streamline the upgrade with free instrument removal</li><li>Simplify the process—no third-party brokers or middlemen</li></ul><h3>Explore our full range of MS instrumentation</h3>When you’re ready to upgrade, Thermo Scientific offers an extensive portfolio of cutting-edge LC-MS systems built to support high-throughput labs, complex workflows, and evolving analytical challenges.<ul><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=5&amp;manufacturerItems=3&amp;search=astral">Orbitrap Astral MS</a> Ultra-sensitive, high-throughput mass spectrometry for Omics and BioPharma applications</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=134&amp;manufacturerItems=3&amp;search=tribrid">Orbitrap Tribrid MS</a> Measure low-abundance molecules and characterize structural isomers and native complexes</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=5&amp;manufacturerItems=3&amp;search=Exploris+">Orbitrap Exploris MS</a> High-performance mass spectrometry with streamlined workflows and broad dynamic range</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=22&amp;manufacturerItems=3&amp;search=Stellar">Stellar MS</a> Robust quantitation and rapid full-scan MSn for improved productivity</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=20&amp;manufacturerItems=3&amp;search=plus">TSQ Plus Triple Quadrupole MS</a> Fast, reliable, and precise targeted quantitation for all molecule types</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=5&amp;manufacturerItems=3&amp;search=Exactive">Q Exactive Plus MS</a> Versatile solution for discovery and quantitation workflows, all in one instrument</li></ul>Take the next step toward modernizing your labWhether you’re working in pharma, biotech, academic research, or clinical research, modern LC-MS platforms deliver the sensitivity, resolution, and throughput required for today’s most demanding applications.And with the Trade-In program, you don’t have to delay progress due to cost.<h3>Looking for other affordable options?</h3>If a trade-in isn’t the right fit for your current needs, explore these additional affordability programs:<ul><li><a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/mass-spectrometer-price-affordability-programs/certified-pre-owned-lc-ms.html">Explore refurbished systems</a></li></ul>Access factory-certified, reconditioned LC-MS systems at a fraction of the cost—fully tested and ready to deliver high-quality data.<ul><li><a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/mass-spectrometer-price-affordability-programs/thermo-scientific-financial-solutions.html">Explore leasing &amp; financing solutions</a></li></ul>Flexible payment plans, leasing options, and deferred payments designed to meet your financial and operational needs.<h3>Upgrade now, pay less, get more</h3>It’s never been easier to transition your lab to next-gen mass spectrometry. Trade in your current system—Thermo Fisher Scientific or otherwise—and gain access to our latest technology, expert support, and proven reliability, all while staying within budget.<a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/mass-spectrometer-price-affordability-programs/mass-spectrometer-trade-upgrade.html">Start your trade-in today</a> Let us help you turn today’s tools into tomorrow’s capabilities.Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#LCMS #promotions #affordability #TradeIn<blockquote><h5>Ema Ruzic</h5>Ema Ružić is a molecular biologist with a background in forensic biology who has transitioned into strategic marketing within the clinical research and toxicology space. 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Upgrade Smarter: Trade In Your Current LC-MS System and Boost Lab Performance Without Breaking Budget

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Upgrade Smarter: Trade In Your Current LC-MS System and Boost Lab Performance Without Breaking Budget

Identification of Substructures in Unknowns Through MSn Data

News from LabRulezLCMS Library - Week 11, 2026

Boosting Productivity in Toxicology Labs

Introducing the new Thermo Scientific TSQ Certis Triple Quadrupole Mass Spectrometer

Unlock High-Performance LC-MS with Factory-Certified Systems from Thermo Fisher Scientific

Generating Quantitative Methods Automatically From Spectral Library Data

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