<p><strong>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.</strong></p><p>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.</p><p>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:</p><h3><strong>1. Simplified data and workflow management</strong></h3><p>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.</p><p>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.</p><h3><strong>2. Controlled access in and out of the lab</strong></h3><p>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 These outdated practices slow down collaboration and increase the risk of data loss or breaches.</p><p>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.</p><p><i>“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.</i></p><h3><strong>3. It’s built for MS workflows</strong></h3><p>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.</p><p><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"></p><p>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.</p><h3><strong>4. Scalability</strong></h3><p>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.</p><p>Add to that network resilience, automated data protection, and centralized updates—and you’ll get a system designed to grow with your organization.</p><p><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"></p><article><div><h3><strong>5. Stress-free compliance</strong></h3><p>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.</p><p>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!</p><h3><strong>Conclusion</strong></h3><p>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.</p><p>If you’re ready to rethink how your lab handles MS data, this is the right time to explore what’s possible.</p><blockquote><p>Join our <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/5232"><strong>upcoming webinar</strong></a> to learn about networked software for MS labs.</p><p><strong>Visit us on&nbsp;</strong><a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/"><strong>LinkedIn:</strong></a>&nbsp;#targetedquantitation #compliance #massspectrometry #control</p></blockquote></div></article><section><blockquote><h4><strong>Laercio Fernandes</strong></h4><p>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.</p></blockquote></section>

5 Things to Consider When Selecting Software for Targeted MS Quantitation

<h4><strong>Have you explored what’s new in </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Thermo Scientific Compound Discoverer software</strong></a><strong>, version 3.4?</strong></h4><p>In case you missed it, earlier this year we released version 3.4 – bringing new capabilities to small molecule researchers. Get ready to elevate your compound identification and analysis experience with this new version packed with groundbreaking features and enhancements.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Why_Compound_Discoverer_3_4_Software_is_Worth_Your_Attention_c08c06da12.jpg" alt="Thermo Fisher Scientific: Why Compound Discoverer 3.4 Software is Worth Your Attention!" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Why_Compound_Discoverer_3_4_Software_is_Worth_Your_Attention_c08c06da12.jpg 245w," sizes="100vw" width="1536" height="614"></p><article><div><h3><strong>Here’s a look at some of the key updates and why you should be excited:</strong></h3><h4><strong>1.&nbsp;LipidSearch (MKI) is now integrated</strong></h4><ul><li>The new <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1740"><strong>LipidSearch </strong></a>(MKI) node simplifies lipid identification, making it faster and more accurate. And here’s the best part: you don’t need to install separate software!</li></ul><h4><strong>2. Improved quality control for small molecule experiments</strong></h4><ul><li>A new QC node leverages internal standards to automatically detect and group in-source fragments, ensuring accurate and reliable results.</li></ul><h4><strong>3.&nbsp;Improved compound identification</strong></h4><ul><li>Connect to the latest version of the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1764"><strong>mzCloud </strong></a>Spectral database (2.0), which includes over 16.5 million spectra, 32,000 MS<sup>n</sup> trees and extensive metadata such as compound classes and CAS numbers. Providing deeper insight and better identification confidence.</li></ul><h4><strong>4.&nbsp;Performance boost</strong></h4><ul><li>Experience up to 8x faster processing speeds for various nodes, including alignment, detecting compounds, fill gaps, and <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1762"><strong>mzLogic</strong></a>, ensuring that your data analysis is completed in record time.</li></ul><h4><strong>5. New spectral library and mass list parameters</strong></h4><ul><li>Now, you can use different sets of parameters for various spectral libraries or mass lists, allowing for precise matching and prioritization.</li></ul><h4><strong>6. Smarter feature detection and component assembly</strong></h4><ul><li>Separate feature detection and component assembly for greater flexibility and performance. New nodes streamline the creation of grouped feature tables and efficiently group ions and in-source fragments.</li></ul><h4><strong>7.&nbsp;New molecular networking capabilities</strong></h4><ul><li>Inject seed compounds (a compound of interest that is not present in the data set) into your molecular networks to form clusters with related compounds, helping you interpret complex networks more effectively. This feature is particularly useful for PFAS-related studies!</li></ul><h4><strong>8.</strong>&nbsp;<strong>Seamless Integration with the Thermo Scientific Ardia Platform</strong></h4><ul><li>Connect to the<strong> </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1821"><strong>Ardia Platform</strong></a> for direct raw data access and result file uploads, streamlining your workflow and enabling easy sharing of result files!</li></ul><blockquote><h3><strong>Excited to learn more?</strong></h3><ul><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/webinar/4863"><strong>Take a look at our webinar</strong></a> where we dive deep into these new features and demonstrate how Compound Discoverer 3.4 Software can elevate your workflows, including pesticides. &nbsp;&nbsp;</li><li>Stay ahead with <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Compound Discoverer Software</strong></a> —where innovation meets precision!</li><li><strong>Visit us on&nbsp;</strong><a target="_blank" rel="noopener noreferrer" href="https://www.linkedin.com/showcase/72003132/admin/dashboard/"><strong>LinkedIn:</strong></a><strong>&nbsp;</strong>#CompoundDiscoverer #SmallMolecules #Software</li></ul></blockquote></div></article><section><blockquote><h5><strong>Zoe Julian</strong></h5><p>Zoe Julian is a Product Marketing Manager for Chromatography and Mass Spectrometry software at Thermo Fisher Scientific. With over 12 years' experience of working with chromatography and mass spectrometry techniques with a background in GC and GC-MS(/MS) organic environmental analysis, she has helped many laboratories and industries improve their workflows through a unique understanding of their challenges. Transitioning to a focus on Chromeleon CDS she has shown customers how software solutions can improve their productivity and support their day-to-day operations.</p></blockquote></section>

Why Compound Discoverer 3.4 Software is Worth Your Attention!

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News from LabRulezLCMS Library - Week 44, 2025

Why Compound Discoverer 3.4 Software is Worth Your Attention!

5 Things to Consider When Selecting Software for Targeted MS Quantitation

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Understanding quantification algorithms

36th MassSpec Forum Vienna 2026

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PFAS in Food & Food Contact Material