When I think about what it takes to keep a high-performing MS laboratory running—especially those dealing with tight timelines, strict regulations, and ever-expanding datasets—I’m reminded that the software we rely on isn’t just a tool. It’s the backbone of our workflows, our decisions, and ultimately, our results.Whether you’re in pharma, environmental testing, or food safety, managing the complexity of targeted mass spectrometry workflows while maintaining accuracy, compliance, and efficiency requires a lot of work.That’s where a purpose-built solution makes a difference. I’ve worked closely with labs that are navigating these challenges—and from the many conversations and experiences, I put together five main capabilities you should look for in your software when it comes to targeted MS quantitation:<h3>1. Simplified data and workflow management</h3>Too many labs are still relying on disconnected systems or folder-based setups that can lead to inconsistent methods and reports. When utilizing modern software solutions, everything—methods, templates, data, reports—can be centrally managed, reducing errors and training time while ensuring everyone is working from the same validated workflows.It’s a big plus if the software also supports multi-consensus reporting, making it easy to compare results across sequences and analyses for greater confidence in the data. By packaging complete workflows and setting predefined views, labs can streamline routine operations and ensure method repeatability, so anyone can run the analysis reliably and consistently.<h3>2. Controlled access in and out of the lab</h3>Many labs are still tied to legacy setups that make remote work challenging. Researchers often rely on standalone workstations that store data locally, making it hard to access critical results when off-site. Transferring data via USB drives or external hard disks not only adds inefficiency, but it can also raise serious security concerns. These outdated practices slow down collaboration and increase the risk of data loss or breaches.Hybrid work is here to stay. With the ability to control and access instruments and data, users can securely set up runs, review results, and manage workflows from anywhere. You’re no longer tied to a specific bench, workstation, or even building. Productivity doesn’t have to stop when you step out of the lab.“Managing all our instruments and work with data remotely via a centralized server means we don’t need to be in the laboratory to access our data.” – Dr. Kayleigh Arthur, Owlstone Medical Ltd.<h3>3. It’s built for MS workflows</h3>Whether you’re running triple quads, high-res accurate mass, or both—life’s much easier when working with software solutions that give you native instrument control and deep integration for targeted workflows. That includes support for MSⁿ, intact mass deconvolution, spectral libraries, and high-throughput quantitation.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_5_Things_to_Consider_When_Selecting_Software_for_Targeted_MS_Quantitation_9e5e9dc842.jpg" alt="Thermo Fisher Scientific: 5 Things to Consider When Selecting Software for Targeted MS Quantitation." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_5_Things_to_Consider_When_Selecting_Software_for_Targeted_MS_Quantitation_9e5e9dc842.jpg 245w," sizes="100vw" width="1536" height="411">Just as important is what happens after data acquisition. Integrated, built-in reporting capabilities—paired with customizable reporting options—should make it easy to flag results and automate the necessary calculations, all within the software. You need a powerful combination that can streamline review and ensures consistency across analyses.<h3>4. Scalability</h3>From small bioanalytical teams to global enterprises, can it be scaled up or down without the need for reinstallation or manual data transfer? It should be built to handle complex, multi-site deployments with ease.Add to that network resilience, automated data protection, and centralized updates—and you’ll get a system designed to grow with your organization.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_5_Things_to_Consider_When_Selecting_Software_for_Targeted_MS_Quantitation_2_8ec325678b.jpg" alt="Thermo Fisher Scientific: 5 Things to Consider When Selecting Software for Targeted MS Quantitation." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_5_Things_to_Consider_When_Selecting_Software_for_Targeted_MS_Quantitation_2_8ec325678b.jpg 245w," sizes="100vw" width="1200" height="660"><article><div><h3>5. Stress-free compliance</h3>Let’s face it, if you have to do it, compliance is non-negotiable, but it can be time-consuming. The system should include built-in features that support GxP, 21 CFR Part 11, and audit readiness—like audit trails, version control, and detailed user management.The ability to query and interrogate data within the system would ensure that data integrity requirements are met, delivering full traceability, and verification of data throughout its lifecycle. Your QA team will be very pleased!<h3>Conclusion</h3>Managing targeted MS quantitation shouldn’t feel like assembling a puzzle with missing pieces. A modern software should bring together everything you need—scalable infrastructure, powerful MS data tools, and built-in compliance features—into one cohesive solution. It must support your science, your team, and your business goals.If you’re ready to rethink how your lab handles MS data, this is the right time to explore what’s possible.<blockquote>Join our <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5232">upcoming webinar</a> to learn about networked software for MS labs.Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#targetedquantitation #compliance #massspectrometry #control</blockquote></div></article><section><blockquote><h4>Laercio Fernandes</h4>Laércio Fernandes is a Product Marketing Manager for software at Thermo Fisher Scientific. With a background rooted in analytical chemistry, Laércio has over 20 years of experience in the analytical field with a focus on chromatography instrumentation, enterprise software and compliance. His background in sales and support has enabled him to have a good overview and understanding of different processes and challenges that laboratories may face, which has allowed him to better support our customers in order to improve their workflows and productivity.</blockquote></section>

5 Things to Consider When Selecting Software for Targeted MS Quantitation

News from LabRulezLCMS Library - Week 14, 2026

Metabolomics researchers are often forced to choose between two powerful but different approaches. <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/metabolomics-lipidomics/metabolomics/untargeted-metabolomics.html">Untargeted metabolomics</a> is great for discovery: it surveys as many metabolites as possible to reveal biology you didn’t know to look for. <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/metabolomics-lipidomics/metabolomics/targeted-metabolomics.html">Targeted metabolomics</a> is built for precision: it measures a defined list of metabolites with high sensitivity and quantitative confidence. The challenge is that running both typically costs time, sample, and can introduce variability between workflows.In order to deal with this the researchers at Thermo Fisher Scientific have developed <a target="_blank" rel="noopener noreferrer" href="https://www.thermofisher.com/content/lifetech/global/en/home/industrial/mass-spectrometry/metabolomics-lipidomics/simultaneous-quantitation-discovery-squad.html">Simultaneous Quantitation and Discovery (SQUAD)</a> analysis as shown in this technical note <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/tn_004327_ov_squad_metabolomics_orbitrap_astral_tn004327_na_en_290c75edd9.pdf">Simultaneous Quantitation and Discovery Analysis: Combining Targeted and Untargeted Metabolomics on Orbitrap Mass Spectrometers</a>, a hybrid strategy that combines targeted quantitation and untargeted discovery in a single experiment. In practice, SQUAD lets you quantify a predefined metabolite panel using calibration curves built from authentic standards and isotopically labeled internal standards, while still capturing rich full-scan data that supports retrospective mining and identification of unknowns.A key theme of the technical note is that results are only as strong as the experiment design and quality controls. The workflow emphasizes calibration strategy, careful extraction choices (aligned to metabolite classes), and the smart use of blanks, pooled QCs, and system suitability tests to monitor drift, contamination, and reproducibility across a batch.SQUAD is also designed to scale across different Thermo Scientific Orbitrap mass spectrometers. The technical note outlines how the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1491">Thermo Scientific Orbitrap Exploris mass spectrometers</a> can use MS1-based SQUAD with polarity switching and optionally add tSIM/tMS2 for targeted sensitivity, while the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=5&amp;manufacturerItems=3&amp;search=Tribrid">Thermo Scientific Orbitrap Tribrid mass spectrometers</a> can pair high-resolution MS1 discovery with rapid ion-trap tMS2 quantitation, boosted by tools like <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1763">Thermo Scientific AcquireX Intelligent Data Acquisition</a> and Real-Time Library Search (RTLS).Finally, the data story comes together in software: <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/77">Thermo Scientific TraceFinder Software</a> for targeted quantitation and <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759">Thermo Scientific Compound Discoverer Software </a>for untargeted discovery, annotation, and statistics, turning one injection into both confident numbers and new biological leads.<blockquote><div><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/tn_004327_ov_squad_metabolomics_orbitrap_astral_tn004327_na_en_290c75edd9.pdf">Download the SQUAD technical note</a></div></blockquote>Visit us on&nbsp;<a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/">LinkedIn:</a>&nbsp;#SQUAD #Metabolomics #Lipidomics

One Injection, Two Answers: Introducing Squad Metabolomics on Orbitrap Mass Spectrometers

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