A piece of software which enables researchers worldwide to speed up their work and helps them make scientific discoveries is expanding from science into commerce. <a href="https://lcms.labrulez.com/articles?search=Tomas+pluskal">Dr. Tomáš Pluskal</a>, who leads a <a href="https://pluskal.group.uochb.cz/en">research group</a> at <a href="https://lcms.labrulez.com/companies/62">IOCB Prague</a>, and his colleagues have founded the commercial company mzio. They are thus building on the greatly successful volunteer-driven project MZmine, which expedites and simplifies the interpretation of biological and chemical analyses and which has benefited from contributions made by researchers all over the world.
The software offered by mzio can simultaneously process data from all types of instruments used in mass spectrometry laboratories. These technologies are currently progressing at an explosive rate and the amount of data obtained through them is increasing rapidly. However, this information is becoming increasingly difficult to utilize. One reason is that each make of instrument uses a different format and structure of data, so research teams must understand and master a number of software tools for its interpretation. Therefore, by offering a single universal tool, the mzio project makes things significantly easier.
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Od_vedeckeho_projektu_ke_globalnimu_byznysu_Firma_mzio_se_snazi_zlepsit_analyzu_dat_v_laboratorich_hmotnostni_spektrometrie_Tym_mzio_zleva_Dr_Tomas_Pluskal_Dr_Robin_Schmid_ed2f73c896.jpg" alt="ÚOCHB: mzio team (from the left): Dr.Tomáš Pluskal, Dr. Robin Schmid, Dr. Ansgar Korf, Dr. Steffen Heuckeroth; and Ludger Rothues"/>
The management of mzio is in hold of analyses showing that mass spectrometry facilities worldwide annually spend about USD 300 million on software. According to Tomáš Pluskal, it is likely that mzio will take a significant slice of this pie.
“Our company is an example of a successful bridge between academia and commerce. Progressive reports on the development of MZmine have been published in renowned scientific journals, including Nature Biotechnology and Nature Communications. On the other side of the nexus, the i&amp;i Prague bio-innovation center, affiliated with IOCB Prague and helping bring promising scientific discoveries to the world, has aided us a lot with our navigation in the field of biotechnology business,” says Tomáš Pluskal.
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Od_vedeckeho_projektu_ke_globalnimu_byznysu_Firma_mzio_se_snazi_zlepsit_analyzu_dat_v_laboratorich_hmotnostni_spektrometrie_mzio_6727f00493.jpg" alt="ÚOCHB: From a scientific project to a global business venture. The company *mzio* is striving to improve data analysis in mass spectrometry labs"/>
He founded the <a href="https://mzio.io/">company mzio</a> together with three other colleagues. Robin Schmid and Steffen Heuckeroth come from within academia whereas Ansgar Korf, the CEO of mzio, switched his job from a mass spectrometry vendor. In addition, the company&#39;s management has been joined by the principal investor, German real estate developer Ludger Rothues.
As part of its services, mzio offers user support and consultations in addition to the MZmine software itself. However, the entire package is still free for customers from the academic environment, and the source code of the software remains open to continuous modification by enthusiastic researchers. Scientists around the world can use the tool to process, examine and compare gigabytes of data on molecules analyzed by mass spectrometry.
<blockquote>
mzio website: <a href="https://mzio.io/">mzio.io</a>
</blockquote>

From a scientific project to a global business venture. The company mzio is striving to improve data analysis in mass spectrometry labs

In the research article recently published in ACS Analytical Chemistry journal the researchers from the Imperial College London, UK, introduced the J-RESRGAN, an adapted and modified generative adversarial network (GAN) for image super-resolution (SR), which was trained specifically for metabolomic J-Resolved spectra to enhance peak resolution.
J-Resolved (J-Res) NMR spectroscopy is vital for metabolomics research, but it often requires a trade-off between high-resolution but time-intensive experiments and quicker low-resolution experiments prone to peak overlap. To address this, J-RESRGAN, a modified generative adversarial network (GAN), was developed to enhance the resolution of J-Res spectra using deep learning. By training the model on simulated high-resolution spectra and introducing a novel symmetric loss function, J-RESRGAN significantly improved peak resolution across a variety of sample types. The model demonstrated enhanced resolution in over 80% of peak pairs in experimental data, offering quick, accessible improvements for existing datasets. J-RESRGAN, openly accessible on GitHub, presents a promising approach for advancing precision in NMR-based metabolomics.
<blockquote>
<h4>The original article</h4>
</blockquote>
<blockquote>
<h5><a href="https://pubs.acs.org/doi/10.1021/acs.analchem.4c00563">Resolution Enhancement of Metabolomic J-Res NMR Spectra Using Deep Learning</a></h5>
Yan Yan, Michael T. Judge, Toby Athersuch, Yuchen Xiang, Zhaolu Liu, Beatriz Jiménez, and Timothy M. D. Ebbels
Analytical Chemistry 2024 96 (29), 11707-11715
DOI: 10.1021/acs.analchem.4c00563
<h6>licensed under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a></h6>
</blockquote>
<h3>Abstract</h3>
J-Resolved (J-Res) nuclear magnetic resonance (NMR) spectroscopy is pivotal in NMR-based metabolomics, but practitioners face a choice between time-consuming high-resolution (HR) experiments or shorter low-resolution (LR) experiments which exhibit significant peak overlap. Deep learning neural networks have been successfully used in many fields to enhance quality of natural images, especially with regard to resolution, and therefore offer the prospect of improving two-dimensional (2D) NMR data. Here, we introduce the J-RESRGAN, an adapted and modified generative adversarial network (GAN) for image super-resolution (SR), which we trained specifically for metabolomic J-Res spectra to enhance peak resolution. A novel symmetric loss function was introduced, exploiting the inherent vertical symmetry of J-Res NMR spectra. Model training used simulated high-resolution J-Res spectra of complex mixtures, with corresponding low-resolution spectra generated via blurring and down-sampling. Evaluation of peak pair resolvability on J-RESRGAN demonstrated remarkable improvement in resolution across a variety of samples. In simulated plasma data, 100% of peak pairs exhibited enhanced resolution in super-resolution spectra compared to their low-resolution counterparts. Similarly, enhanced resolution was observed in 80.8–100% of peak pairs in experimental plasma, 85.0–96.7% in urine, 94.4–98.9% in full fat milk, and 82.6–91.7% in orange juice. J-RESRGAN is not sample type, spectrometer or field strength dependent and improvements on previously acquired data can be seen in seconds on a standard desktop computer. We believe this demonstrates the promise of deep learning methods to enhance NMR metabolomic data, and in particular, the power of J-RESRGAN to elucidate overlapping peaks, advancing precision in a wide variety of NMR-based metabolomics studies. The model, J-RESRGAN, is openly accessible for download on GitHub at <a href="https://github.com/yanyan5420/J-RESRGAN">https://github.com/yanyan5420/J-RESRGAN.</a>
<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Analytical_Chemistry_Anal_Chem_2024_96_29_11707_11715_Figure_6_Examples_of_peak_pairs_from_experimental_data_For_each_individual_panel_the_upper_row_displays_the_2_D_HR_LR_and_SR_c002ecf982.jpg" alt="Anal. Chem. 2024, 96, 29, 11707-11715: Figure 6. Examples of peak pairs from experimental data. For each individual panel, the upper row displays the 2D HR, LR, and SR spectra respectively; the subsequent row depicts the 1D profiles along the red dashed line; blue─HR, red─LR, and green─SR. Plots (a, b) display two examples of peak pairs aligned along the F1 axis, demonstrating the recovery to doublets in the SR spectra from the singlets observed in LR spectra."/>

Resolution Enhancement of Metabolomic J-Res NMR Spectra Using Deep Learning

<h4>The Science &nbsp;</h4>Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a specialized mass spectrometry technique. It can be used to identify the composition of solid surfaces, providing elemental, isotopic, and molecular information with part per million (ppm) sensitivity. ToF-SIMS spectra, however, may contain numerous individual ion signals, which can be hard to distinguish without dedicated statistical tools. Statistical techniques, such as principal component analysis (PCA), have been widely used to visualize differences of ToF-SIMS spectra and have shown great success. But chemically understanding of these differences, especially for less experienced users, has long been challenging. To solve this issue, a new and flexible software tool based on Python was developed where artificial intelligence (AI)–machine learning functions are incorporated to help users chemically understand complex spectra generated from ToF-SIMS. In this work, AI–machine leaning functions were incorporated to a traditional PCA analysis tool, showing great progress in resolving this issue.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Pacific_Northwest_National_Laboratory_Frepik_New_Software_Tool_Generates_Data_Analysis_for_Complex_To_F_SIMS_A_new_and_flexible_software_tool_based_on_the_Python_computing_language_9205f66a7f.jpg" alt="Pacific Northwest National Laboratory / Freepik: A new and flexible software tool based on the Python computing language was developed by Pacific Northwest National Laboratory researchers where artificial intelligence–machine learning functions are incorporated to help users chemically understand complex spectra generated from time-of-flight secondary ion mass spectrometry." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Pacific_Northwest_National_Laboratory_Frepik_New_Software_Tool_Generates_Data_Analysis_for_Complex_To_F_SIMS_A_new_and_flexible_software_tool_based_on_the_Python_computing_language_9205f66a7f.jpg 244w," sizes="100vw" width="1600" height="1027"><h4>The Impact&nbsp;</h4>Compared to other software packages available, the advantage of the new Python-based package is that a detailed Microsoft Word format data analysis report can be automatically generated, greatly facilitating less experienced users in understanding chemical differences among samples. This saves users a lot of time in data report processing. The new package is free, open-source software that comes with a detailed manual, making it user-friendly and straightforward to understand. The new package is flexible, powerful, and extensible. For example, most exported parameters can be customized. Additionally, some basic AI functions have been integrated into the software package, and many other AI/machine learning functions in the Python system are available for exploring more powerful capabilities. In principle, the software package can be used to treat many types of spectra data, such as Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS), matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), infrared spectroscopy (IR), and X-ray photoelectron spectroscopy (XPS).&nbsp;<h4>Summary&nbsp;</h4>So far, several software tools have been developed for PCA of ToF-SIMS spectra; however, none of them are freely available. Such a situation leads to some difficulties in extending applications of PCA to various research fields. More importantly, it has long been challenging for common researchers to understand PCA plots and extract chemical differences among samples. In this work, a team of researchers from Pacific Northwest National Laboratory and the <a target="_blank" rel="noopener noreferrer" href="https://www.emsl.pnnl.gov/">Environmental Molecular Sciences Laboratory</a>, a Department of Energy Office of Science user facility, developed a new and flexible software tool called “Advanced Spectra PCA Toolbox.” The software is based on Python for PCA of complex ToF-SIMS spectra and features an easy-to-read manual. It can generate data analysis reports automatically to explain chemical differences among samples, helping less experienced researchers easily understand tricky PCA results. Moreover, it is expandable and compatible with AI/machine learning functions. Pure goethite and different lignin-adsorbed goethite samples were used as a model system to demonstrate the software tool, showing that it can be readily used in complex spectra data processing. Our software tool is open-source, flexible, and expandable. The research team expects this open-source tool will benefit not only the ToF-SIMS community, but also other spectrometry techniques (such as FTICR-MS, MALDI-MS, IR, and XPS).&nbsp;<h4>PNNL Contact</h4>Zihua Zhu, Pacific Northwest National Laboratory and Environmental Molecular Sciences Laboratory,&nbsp;<a href="mailto:zihua.zhu@pnnl.gov">zihua.zhu@pnnl.gov</a>&nbsp;<h4>Funding&nbsp;</h4>This research was supported by the Laboratory Directed Research and Development program in the Earth and Biological Sciences Directorate at Pacific Northwest National Laboratory and was performed on a project award from the Environmental Molecular Sciences Laboratory, a Department of Energy Office of Science user facility sponsored by the Biological and Environmental Research program.

New Software Tool Generates Data Analysis for Complex ToF-SIMS

<h3>Mnova 15.1 is Here!</h3>We’re excited to announce the release of <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/4evoo5H">Mnova 15.1</a>, packed with new tools, enhanced features, and powerful algorithms designed to enhance your analytical workflows.&nbsp;Whether you're focused on NMR, LC/GC-MS or Electronic &amp; Vibrational Spectroscopic techniques, Mnova 15.1 has something to boost your analytical data analyses and streamline your workflows.<h4>What’s New in Mnova 15.1?</h4>Get a glimpse of the <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/48InTUC">Top features in Mnova 15.1</a>Mnova 15.1 brings significant updates and improvements across our suite of plugins including Mnova NMR, <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/products/1077">MSChrom</a>, DB, Advanced Chemometrics, BioHOS, StereoFitter, <a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/products/1128">qNMR</a>, Structure Elucidation, IUPAC Name, NMRPredict, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1081">Mgears</a>, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1084">Affinity Screen</a>, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1079">Chrom Best Method</a>, and <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1085">Reaction Optimization</a>. These updates introduce new functionalities, performance enhancements, and essential bug fixes to optimize your analytical workflows.For a detailed overview of all new enhancements and improvements check out our complete <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/3O1mGhF">Changelog</a>.<h4>Ready to Upgrade?</h4>Don’t miss out on these cutting-edge innovations. Visit our website to <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/4evoo5H">Download Mnova 15.1</a> and take your analytical workflows to the next level.<blockquote><h4>Watch showcase videos of a novel tool for Peak Purity Assessment</h4><ul><li><a target="_blank" rel="noopener noreferrer" href="https://youtu.be/FkJ43lQrMwI">Our solution for LCMS and GCMS included in Mnova MSChrom</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://youtu.be/nab8pR2RAbE">Our solution for chemometrics included in Mnova Advanced Chemometrics and Mnova BioHOS</a></li></ul></blockquote>

What's New in Mnova 15.1?

This year, Mestrelab turns 20, and to celebrate this milestone, we’re excited to announce a special 20% discount offer on new annual licenses purchased at the <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/4eUDVfX">Mestrelab Store</a>.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Mestrelab_Research_Celebrate_Mestrelab_s_Anniversary_with_Exclusive_Store_Offers_cover_image_72f6e1331a.jpg" alt="Mestrelab Research: Celebrate Mestrelab’s Anniversary with Exclusive Store Offers! " srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Mestrelab_Research_Celebrate_Mestrelab_s_Anniversary_with_Exclusive_Store_Offers_cover_image_72f6e1331a.jpg 245w," sizes="100vw" width="1920" height="1080">This exclusive offer is open to everyone - whether you're an industry professional, researcher, or part of an academic institution, it's the perfect opportunity to upgrade your toolkit with powerful solutions or begin your journey with our cutting-edge tools.But hurry - these anniversary offers won’t last long! Celebrate with us and take advantage of these deals before they end on November 30, 2024.Visit the <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/4eUDVfX">Mestrelab Store</a> today and join us in making our 20th anniversary memorable.Stay tuned for more surprises and updates as we continue to innovate and grow together.<blockquote>About <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/companies/298">Mestrelab Research</a>:For two decades, we have provided cutting-edge tools to enhance analytical data processing, analysis, and reporting experience. Today, our comprehensive range of products and solutions extends beyond NMR to include LC/GC-MS and other spectroscopies. These tools empower users to automate routine tasks, streamline workflows, and focus on what truly matters—extracting meaningful insights from their data.</blockquote>

Celebrate Mestrelab’s Anniversary with Exclusive Store Offers!

From December 1st to December 31st, 2024, when you purchase any new Mnova license, you'll receive an additional plugin of your choice FREE for 1 year.<blockquote><h5>Check out our tutorial videos for Peak Purity Assessment in LCMS with Mnova MSChrom, Advanced Chemometrics, and BioHOS.</h5><ul><li><a target="_blank" rel="noopener noreferrer" href="https://youtu.be/FkJ43lQrMwI">Peak Purity Assessment for LCMS using MCR mode in Mnova MSChrom</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://youtu.be/nab8pR2RAbE">MCR tool in Mnova chemometric solutions: Advanced Chemometrics and BioHOS</a></li></ul></blockquote>&nbsp;<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Mestrelab_Research_Mestrelab_Holiday_Special_Get_More_from_Mnova_This_December_Buy_1_Get_1_255c1413bd.jpg" alt="Mestrelab Research: Mestrelab Holiday Special - Get More from Mnova This December: Buy 1 - Get 1!" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Mestrelab_Research_Mestrelab_Holiday_Special_Get_More_from_Mnova_This_December_Buy_1_Get_1_255c1413bd.jpg 245w," sizes="100vw" width="1920" height="1080">Whether you're in industry, government, or academia, this limited-time offer is the perfect way to enhance your analysis toolkit with our powerful suite of tools for NMR, LC/GC-MS, and Electronical &amp; Vibrational Spectroscopic techniques. It’s also an excellent choice for exploring our solutions tailored to specific applications, such as <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/3VgxIne">prediction</a>, <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/4eYNRoC">reaction monitoring</a>, <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/49iDUBh">structure elucidation</a> and <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/3CUNxd6">verification</a>, <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/49gfisB">quantification</a> and <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/3Zu3EHs">mixture analysis</a>, <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/3B8Jvx9">screening</a>, <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/3CQKwuv">chemometrics</a>, <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/41ddyOV">database management</a>, and <a target="_blank" rel="noopener noreferrer" href="https://bit.ly/3ZB1aWL">more</a>!<h4>How It Works:</h4><ol><li>Buy any new Mnova license.</li><li>Choose an additional plugin (of equal or lesser value) for free for 1 year.</li><li>Expand your research capabilities with unmatched tools!</li></ol>Don’t wait—claim your offer now!<h4>Offer Details:</h4><ul><li>Valid: December 1–31, 2024</li><li>Exclusions: Mnova Gears and its plugins/bricks, USP-ID, Mnova Web, Mbook.</li><li>Discounts: Cannot be combined with other discounts (except volume discounts).</li></ul>Act now and give yourself the gift of innovation this holiday season.<a target="_blank" rel="noopener noreferrer" href="https://bit.ly/41euuVs">Visit our web store</a> or <a href="mailto:sales@mestrelab.com" target="_blank" rel="noopener noreferrer">contact</a> us directly to claim your offer now!<blockquote><h4>About <a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/companies/298">Mestrelab Research</a>:</h4>For two decades, we have provided cutting-edge tools to enhance analytical data processing, analysis, and reporting experience. Today, our comprehensive range of products and solutions extends beyond NMR to include LC/GC-MS and other spectroscopies. These tools empower users to automate routine tasks, streamline workflows, and focus on what truly matters—extracting meaningful insights from their data.</blockquote>

Mestrelab Holiday Special - Get More from Mnova This December: Buy 1 - Get 1!

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

<h3>Lunch &amp; learn tips &amp; tricks series 2026 – part 1</h3>In modern analytical laboratories, efficiency, consistency, and data confidence are essential. Whether you are operating an ICP-OES or ICP-MS system, the way you use your software can significantly influence productivity and analytical performance. In the first session of our Lunch &amp; Learn Tips &amp; Tricks Series, we focused on one of the most common themes raised by users: how to navigate <a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/products/1489">Qtegra </a>software more effectively and optimize everyday workflows.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Thermo_Fisher_Scientific_Mastering_Qtegra_Software_Practical_Strategies_to_Improve_Your_Daily_Lab_Workflow_3d35454782.jpg" alt="Thermo Fisher Scientific: Mastering Qtegra Software: Practical Strategies to Improve Your Daily Lab Workflow" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Thermo_Fisher_Scientific_Mastering_Qtegra_Software_Practical_Strategies_to_Improve_Your_Daily_Lab_Workflow_3d35454782.jpg 245w," sizes="100vw" width="1024" height="512">This session explored three key areas in detail: understanding the structure of Qtegra and the Configurator, using the Dashboard as your operational control center, and building smarter, more efficient LabBooks. Below is a structured recap of the key insights shared during Part 1.<h3>Understanding the structure of Qtegra</h3>One of the most valuable features of Qtegra software is its consistency across multiple instrument platforms. Whether you are working with the <a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/products?category=227&amp;instrumentationItems=84&amp;manufacturerItems=3&amp;search=icap+pro">iCAP PRO ICP-OES</a>, the <a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/products?category=232&amp;instrumentationItems=83&amp;manufacturerItems=3">iCAP MX ICP-MS</a>, the iCAP 7000 OES, or Qnova ICP-MS systems, the interface and workflow logic remain familiar. This consistency reduces the learning curve when transitioning between instruments and supports standardised training across laboratories.Qtegra consists of two primary components: the Qtegra application itself and the Configurator.<ul><li>The Qtegra application is where you directly interact with your instrument. It is used to create LabBooks, control the instrument, execute analyses, and review results.</li><li>The Configurator, in contrast, defines how your system behaves at a deeper level. It controls system-level settings that underpin daily operation. Within the Configurator, users can manage features such as Fast Uptake setup, drain sensor configuration, wavelength libraries for ICP-OES systems, the Reaction Database for ICP-MS systems, and user access permissions.</li></ul>Understanding the distinction between these two components helps users troubleshoot more effectively and ensures that system configuration aligns with laboratory requirements.<h3>Using the dashboard as your central hub</h3>When Qtegra is opened, the first screen presented is the Dashboard. The Dashboard functions as the central hub for instrument monitoring and control. From this location, users can view instrument status, monitor live operating parameters, access tuning tools, review performance checks, and identify error or interlock notifications.<ul><li>For ICP-OES users, the Dashboard provides access to tune sets, source settings, AutoPeak alignment, autotuning functions, and live views such as Plasma TV. These tools allow users to confirm that the plasma and optical system are performing as expected before analysis begins.</li><li>For ICP-MS users, the Instrument tab within the Dashboard provides access to autotune routines, performance report summaries, gas flow settings, nebuliser adjustments, operating mode selection such as Standard, KED, or CCT modes, IntelliLens control, and real-time data streams.</li></ul>The Dashboard should be used as a structured checkpoint before running any analysis. Confirming that all parameters are within acceptable ranges reduces the likelihood of interruptions and supports consistent performance throughout the run.<h3>The get ready workflow: structured instrument preparation</h3><ul><li>The Get Ready function, which is launched directly from the Dashboard, provides a guided preparation workflow. This feature is designed to ensure that the instrument is fully configured and operating correctly for the selected method before analysis begins.</li><li>Within Get Ready, users can access scheduling tools that automate warmups, standby routines, shutdowns, and maintenance checks. These tools are particularly beneficial for laboratories operating multiple shifts or managing variable workloads.</li></ul>For ICP-MS systems, the Get Ready workflow includes automated performance checks, autotune routines, and controlled warm-up conditions. These routines verify that the instrument is operating within its expected performance range.By following the structured steps within Get Ready, laboratories can reduce the risk of missed preparation tasks and maintain day-to-day analytical consistency.<h3>Building smarter LabBooks</h3>The LabBook forms the foundation of every analytical sequence in Qtegra. A carefully constructed LabBook improves efficiency, reduces setup errors, and simplifies data review.Users can create a LabBook from scratch or begin with a template. Templates are particularly useful for laboratories that integrate with LIMS systems or import sample lists via CSV files, as they promote standardisation and consistency.<h4>Defining analytes</h4><ul><li>For ICP-OES methods, users must select appropriate wavelengths and evaluate potential spectral interferences.&nbsp;</li><li>For ICP-MS methods, users select the required masses, consider isobaric and polyatomic interferences, and use the Reaction Database to support reaction mode selection.</li></ul>Careful analyte selection at this stage helps prevent complications later in the analytical workflow.<h4>Configuring acquisition parameters</h4>Acquisition parameters define how the instrument collects data.<ul><li>For ICP-OES systems, this includes selecting viewing modes, choosing wavelength ranges such as iFR or eUV, and defining integration times.</li><li>For ICP-MS systems, this includes selecting operating modes such as Standard, KED, or CCT, configuring Reaction Finder options, enabling Intelligent Matrix Handling, and defining digital trigger settings.</li></ul>Thoughtful parameter configuration ensures that data quality objectives are met without unnecessary reanalysis.<h4>Using intelligent uptake and rinse</h4>The Intelligent Uptake and Rinse feature detects when the sample or rinse solution reaches the nebuliser. This ensures consistent timing across samples and improves overall throughput. In high-throughput environments, this feature contributes to both efficiency and reproducibility.<h4>Calibration and quantification strategy</h4>Calibration design is central to reliable quantification. Qtegra allows users to manage global standards, configure dilution tools, select calibration fit types, assign internal standards, and establish quality control samples.For ICP-OES systems, users can define standard ranges and switch points. For SemiQuant workflows, Relative Sensitivity Factors can be applied.Establishing these parameters during LabBook creation ensures that data validation is straightforward once analysis is complete.<h4>Autosampler and sample list setup</h4>For laboratories using the <a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/products/1715">iSC-65 autosampler</a>, features such as StepAhead, custom rack definitions, colour-coded sample views, and visual integrity checks support efficient sequence management.When constructing the sample list, users should clearly define sample types, establish a logical sequence order, and configure column layouts appropriately. Setting flags and limits during initial setup simplifies the data review process and supports quality assurance.<h3>Why workflow optimisation matters</h3>Optimising Qtegra usage does not require learning new software features. Instead, it involves using existing tools more strategically. By treating the Dashboard as a pre-run checkpoint, using Get Ready consistently, and constructing LabBooks with long-term efficiency in mind, laboratories can reduce downtime, improve reproducibility, and strengthen confidence in analytical results.<h3>Looking ahead to part 2</h3><blockquote>In Part 2 of the Qtegra Tips &amp; Tricks series, we will focus on post-analysis best practices. Topics will include interpreting signal intensities, reviewing calibration performance, evaluating recoveries and readbacks, applying flags effectively, exporting data, and implementing practical workflow improvements discussed in Part 1.</blockquote>By building a structured approach to both preparation and data review, laboratories can transform routine analysis into a streamlined, reliable, and repeatable process.We look forward to continuing the discussion in Part 2.<h5>Acknowledgement</h5>I would like to thank Matthew Gregory Field Applications Scientist, North EMEA, Trace Elemental Analysis and David Fishwick Field Applications Scientist, North EMEA, Trace Elemental Analysis for the support on this blog and the webinars<h4>Sign up for our webinars live and on demand.</h4>English<ul><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/5795">Lunch and Learn Tips and Tricks Series: Qtegra Part 1</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/5976">Lunch and Learn Tips and Tricks Series: Qtegra Part 2</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/5977">Lunch and Learn Tips and Tricks Series: Trace Elemental Analysis (ICP-OES &amp; ICP-MS)</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/5978">Trace Elemental Analysis: Ask the Expert</a></li></ul>Deutsch<ul><li>19. März 2026 <a target="_blank" rel="noopener noreferrer" href="https://event.on24.com/wcc/r/5179134/393E071E3B501943730958BA6203F477">Interne Standards in der ICP-OES: Ein Praxisguide für zuverlässige Qualitätssicherung im Labor</a></li><li>18. Juni 2026 <a target="_blank" rel="noopener noreferrer" href="https://event.on24.com/wcc/r/5179292/AE4C576B6A54D1AC182F7F77573D380F">Fehler reduzieren, Durchsatz steigern: Autoverdünnung mit PrepFast am ICP-MS</a></li><li>17. September 2026 <a target="_blank" rel="noopener noreferrer" href="https://event.on24.com/wcc/r/5179423/B5019C560431BADCA2A76E54E4EFE56F">ICP-OES smarter nutzen: Probendurchsatz erhöhen, Ressourcen sparen</a></li><li>17. Dezember 2026 <a target="_blank" rel="noopener noreferrer" href="https://event.on24.com/wcc/r/5179530/94EEDD1F56138F5EEE2AF24E29E6C12A">Qtegra ISDS Software Unlocked – Live im Expertengespräch</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;#Qtegra, #ICPMS, #ICPOES, #TraceElementalAnalysis<blockquote><h5>Petra Gerhards</h5>Petra Gerhards, Dipl-Ing, is Regional Marketing Manager of GC and GC-MS for EMEA at Thermo Fisher Scientific. She has more than 29 years of experience in the fields of GC-MS, SPE and LC-MS. Since joining the regional team she has contributed to workflow solutions combining vials and closures with SPE solutions, GC-MS and LC-MS. She works with KOL's on data for regional specific marketing campaigns, organizes in-house seminars and works on customer specific solutions. Her main expertise is in the field of doping and drugs-of-abuse analysis.</blockquote>

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