News from LabRulezLCMS Library - Week 15, 2025

News from LabRulezLCMS Library - Week 16, 2025

Folin-Ciocâlteu, RP-HPLC (reverse phase-high performance liquid chromatography), and LC-MS (liquid chromatography-mass spectrometry) provide complementary information for describing cider (Malus spp.) apple juice

<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 These outdated practices slow down collaboration and increase the risk of data loss or breaches.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

<p><strong>Our Library never stops expanding. What are the most recent contributions to LabRulezLCMS Library in the week of 30th June 2025? Check out new documents from the field of liquid phase, especially HPLC and LC/MS techniques!</strong></p><blockquote><p><span style="font-size:20px;">👉 </span><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library"><span style="font-size:20px;"><strong>SEARCH THE LARGEST REPOSITORY OF DOCUMENTS ABOUT LCMS AND RELATED TECHNIQUES</strong></span></a></p></blockquote><blockquote><p><strong>👉 Need info about different analytical techniques?</strong> Peek into <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/library"><strong>LabRulezGCMS</strong></a> or <a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/library"><strong>LabRulezICPMS</strong></a> libraries.</p></blockquote><p>This week we bring you other document by <strong>Agilent Technologies </strong>and posters by<strong> Shimadzu / ASMS, Thermo Fisher Scientific / ASMS </strong>and<strong> Waters Corporation / ASMS!</strong></p><h3><strong>1. Agilent Technologies: Agilent InfinityLab Assist Hub: Representing Advancements in Cybersecurity</strong></h3><ul><li>Other document (white paper)</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/wp_infinitylab_assist_cybersecurity_5994_8261en_agilent_310c5c9a6c.pdf"><strong>Full PDF for download</strong></a></li></ul><h4><strong>The laboratory as an operational technology (OT) environment: bridging the gap between OT and IT&nbsp;</strong></h4><p>Compared to connected industrial production environments, the connected laboratory environment closely aligns with an operational technology (OT) environment. OT is defined as "the practice of using hardware and software to control industrial equipment, and it primarily interacts with the physical world" (RedHAT, 2024).&nbsp;</p><p>In the classical Purdue reference model, established in the early 1990s to protect identities, information, and assets, the OT environment is clearly separated and secured from the information technology (IT)/enterprise environment.&nbsp;</p><p>The model only allows direct communication between adjacent levels. OT environments (lab environments) are necessary due to the long life cycles of the systems typically exposed to cybersecurity threats, with the mitigations listed in Table 1.&nbsp;</p><p>Addressing cybersecurity challenges in OT environments requires customized security strategies that incorporate both traditional IT security principles and specific measures for the physical operations they control.&nbsp;</p><p>Unlike some IT system components and devices where complete infrastructure replacement is common, lab devices are typically replaced gradually over years, sometimes even over&nbsp;decades.</p><p>The clear separation between OT and IT is becoming increasingly blurred due to new connectivity requirements, cloud functionality, and Industrial Internet of Things integration. This process, known as IT/OT convergence, is essential for achieving the next level of automation, such as Industry 4.0/5.0 or its counterparts, such as Pharma 4.0. The effectiveness of any new development will be evaluated based on how well it addresses cybersecurity within a converging IT/OT environment.</p><h4><strong>Standards and organizations&nbsp;</strong></h4><p>The diverse standards and organizations can be exemplified by the approaches taken in the U.S., Europe, and China. This summary aims to showcase the complexity of regulatory environments, and is not comprehensive. For specific situations, consulting with dedicated field experts is crucial.</p><h5><strong>Europe&nbsp;</strong></h5><p>European cybersecurity regulations prioritize privacy and data protection, with an emphasis on harmonizing standards across member states.&nbsp;</p><ul><li><strong>General Data Protection Regulation (GDPR): </strong>GDPR is the cornerstone of data protection in the European Union (EU). It sets strict rules on handling personal data, including requirements for data breach notifications, data minimization, and individual rights over personal data. Noncompliance can result in severe fines.</li><li><strong>Network and Information Security Directive (NIS&nbsp;Directive): </strong>Adopted in 2016, the NIS Directive focuses on the cybersecurity of essential services (such as energy, transportation, and finance) and digital service providers. It requires member states to strengthen their national cybersecurity capabilities and cooperation.&nbsp;</li><li><strong>European Union Agency for Cybersecurity (ENISA):</strong> ENISA is the EU's dedicated cybersecurity agency, helping to develop and promote cybersecurity standards across Europe, including guidelines for incident reporting and cybersecurity&nbsp;certifications.</li><li><strong>ISO/IEC 27001: </strong>While ISO/IEC 27001 is a global standard for information security management systems, it is heavily adopted in Europe. This standard outlines processes for systematically managing sensitive company information, ensuring its security.&nbsp;</li><li><strong>Cybersecurity Act (EU): </strong>The Cybersecurity Act establishes a framework for cybersecurity certification for products, services, and processes, ensuring they meet recognized EU-wide standards.</li></ul><h4><strong>Conclusion&nbsp;</strong></h4><p>With the initial release of the InfinityLab Assist Control Software, the InfinityLab Assist Hub offers plenty of cybersecurity features that can be leveraged for a secure lab network environment founded on a customer-specific OT/IT security strategy.</p><h3><strong>2. Shimadzu / ASMS: Single Quadrupole Mass Spectrometry Quick Workflows Specified to Oligonucleotides Screening&nbsp;</strong></h3><ul><li>Poster</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/ASMS_25_TP_605_fa8deb906e.pdf"><strong>Full PDF for download</strong></a></li></ul><p>A workflow has been developed to deliver molecular mass information on the full-length product and related impurities for chemically synthesized oligonucleotides by applying a deconvolution algorithm to all detected components within a targeted data stream (UV/PDA, TIC or BPC). It has been designed to simplify the data processing experience without the need for a sequence input delivering results quickly by automating mass assignment of all detected components in a data stream.</p><h4><strong>2. Materials and Methods&nbsp;</strong></h4><h5><strong>2.1 LC-MS/MS method&nbsp;</strong></h5><p><strong>20-mer sample.</strong> A phosphorothioate-modified oligonucleotide purified was used as a model sample (20-mer anti-sense oligo; C229 H316 N69 O121 P19 S19; average mass 7168.05, Te-smCe-sTe-sTe-sGe-sGd-sTd-sTd-sAd-sCd-sAd-sTd-sGd-sAd-sAd-sAe-sTe-smCe-smCesmCe) spiked with 10% impurities (N-1(5’) and N-3(5’) shortmers) to the full-length product.&nbsp;</p><p><strong>80-mer antisense DNA sample</strong>. 80-mer PolyT oligonucleotide sample (C800 H1041 N160 O558 P79; average mass 24273.62) was also analyzed was analyzed by ion-pair reversedphase chromatography mode using HFIP (hexafluoroisopropanol) and 10 mM TEA (triethylamine).</p><p><strong>LC Separation</strong>. Components were separated using the Shimadzu <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?manufacturerItems=3&amp;search=Nexera+XS"><strong>Nexera XS</strong></a> inert LC and Shim-pack Scepter Claris column using HFIP (hexafluoroisopropanol) and 10 mM TEA (triethylamine) as ion pair additives.&nbsp;</p><p><strong>Mass Spectrometry Detection. </strong>Shimadzu Single Quadrupole<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?manufacturerItems=3&amp;search=+LCMS-2050"><strong> LCMS-2050</strong></a>. Data acquired in profile mode. MS mass scan m/z 600-2000; 1 secs; negative ion mode.</p><h4><strong>3.Results&nbsp;</strong></h4><h5><strong>3.1 Workflows and Methods&nbsp;</strong></h5><p>Insight Biologics software application supports two workflows to help accelerate oligonucleotide characterization. The default data processing behavior was driven by a defined FLP sequence to confirm sequence composition, identify product related impurities and assess impurity profiles. Data processing has been further augmented by enabling automated deconvolution routines to be applied without a defined FLP sequence input to help workflows that need to quickly check on molecular mass information in a synthesis (Figure 2).</p><h4><strong>4. Conclusions&nbsp;</strong></h4><ul><li>LabSolutions Insight Biologics offers flexibility by supporting both user-defined and automated deconvolution workflows for comprehensive oligonucleotide analysis.&nbsp;</li><li>A Quick Picking algorithm has been developed and applied to the analysis of 20-mer and 80-mer antisense DNA. In the case of a 20-mer sample, the FLP and associated impurities were also automatically detected and molecular weight information reported. The analysis showed high correspondence with data processing results using a defined FLP sequence input.&nbsp;</li><li>The Quick Picking algorithm enables a molecular weight confirmation of any detected peak and can be a powerful tool for synthesis confirmation in cases where the product is not as intended.&nbsp;</li><li>This LC-MS analysis platform provides a rapid and cost-effective solution for purity analysis and molecular weight confirmation, making it ideal for quality control environments.</li></ul><h3><strong>3. Thermo Fisher Scientific / ASMS: Comprehensive data acquisition workflow on a modified Orbitrap Astral MS to achieve deep lipidome coverage with high confidence annotations</strong></h3><ul><li>Poster</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/PO_003964_ms_ASMS_25_Astral_Zoom_Lipidomics_po003964_na_en_0ccd4bd053.pdf"><strong>Full PDF for download</strong></a></li></ul><p>Lipid identification is often considered the most challenging and bottleneck of the lipidomics workflow. This is due to the vast diversity of lipid structures, isomers and varying concentrations. Fragmentation of lipids generate characteristic fragments that help in lipid annotation, structural elucidation, isomer differentiation, and improved confidence in lipid identification. Having fragmentation for most of the lipids detected in a sample hence is highly desirable. This requires fast and sensitive instrumentation. Here we evaluated the new Orbitrap Astral Zoom mass spectrometer (Figure 1) for deeper lipidome coverage and confident lipid identification from 73 mice plasma extracts.</p><h4><strong>Materials and methods&nbsp;</strong></h4><h5><strong>Sample Preparation&nbsp;</strong></h5><p>Lipids were extracted from plasma samples obtained from 73 mice fed with a high fat diet and a normal diet. Lipid standards and bovine liver lipid extracts were purchased from Avanti Polar Lipids.&nbsp;</p><h5><strong>LCMS Method&nbsp;</strong></h5><p>Plasma lipid extract was separated using Thermo Scientific nanoLC PepMap (C18, 75µmx150mm, 2µm) column connected to a <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/398"><strong>Vanquish Neo UHPLC system</strong></a>. Data acquisition was carried out on the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1959"><strong>Orbitrap Astral Zoom mass spectrometer</strong></a> using full-scan Orbitrap MS1 in parallel with data-dependent Astral MS2.</p><h5><strong>Data Analysis&nbsp;</strong></h5><p>Data processing was performed using <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1759"><strong>Thermo Scientific Compound Discoverer 3.4 software</strong></a>. Compound Discoverer 3.4 software includes new features such as Thermo Scientific LipidSearch software node for simplified lipid identification, QC for small molecule experiments using internal standards, automatically detects and groups MS1 fragments and other performance improvements.</p><h4><strong>Results&nbsp;</strong></h4><h5><strong>Orbitrap Astral Zoom mass spectrometer DDA MS2 scan rate&nbsp;</strong></h5><p>The Orbitrap Astral Zoom mass spectrometer offers an enhanced MS2 scan rate compared to the already high-speed Orbitrap Astral MS system, enabling DDA with Top 30, Top 40, or even Top 50 MS2 scans (Figure 2) without compromising data quality. This advancement delivers unprecedented speed, achieving faster DDA MS2 scan rates than ever before.</p><h5><strong>Unprecedented speed and depth: dual analyzer power of Orbitrap Astral Zoom MS</strong></h5><p>The parallel data acquisition on Orbitrap Astral Zoom MS using both the Thermo Scientific Orbitrap analyzer and Thermo Scientific Astral analyzer, enables a higher number of Orbitrap HRAM MS1 full scans with sub-ppm mass accuracy. Simultaneously, the fast Astral analyzer delivers a significantly greater number of highquality MS2 scans at 80k resolution (77% more) compared to Orbitrap-Orbitrap configurations, which is essential for deep coverage and confident lipid identification (Figure 3).</p><h4><strong>Conclusions&nbsp;</strong></h4><ul><li>The novel Orbitrap Astral Zoom mass spectrometer provides deeper lipidome coverage and confident identification, utilizing the parallel operation of Orbitrap and Astral analyzers.&nbsp;</li><li>The enhanced MS2 speed in Orbitrap Astral Zoom mode, coupled with Stepped NCE, enables efficient data acquisition and comprehensive lipidome coverage with a 15% increase with grade A and B lipid annotation.&nbsp;</li><li>The use of nano-flow increased the sensitivity and the number of detected lipids while achieving a significant reduction in the use of sample and solvent.&nbsp;</li><li>A significant difference was observed between control and high fat diet mice samples with potential biomarker upregulated neutral lipids (triglycerides and cholesterol esters) in the high fat diet.</li></ul><h3><strong>4. Waters Corporation / ASMS: Routine EPA 1633 PFAS Analysis with a Novel Slotted Bandpass Ion Guide to Improve Signal Response Robustness</strong></h3><ul><li>Poster</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/labrulez-bucket-strapi-h3hsga3/720008888_65b495feb8.pdf"><strong>Full PDF for download</strong></a></li></ul><p>With increasing regulatory pressure around PFAS monitoring, this study evaluates a robust and long-term solution for EPA 1633A-compliant PFAS analysis. It focuses on how the StepWave XR ion guide, integrated into the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?manufacturerItems=5&amp;search=Xevo+TQ+Absolute+XR"><strong>Waters Xevo TQ Absolute XR tandem quadrupole mass spectrometer,</strong></a> improves signal robustness and method stability across demanding environmental matrices such as river water, biosolids, and landfill leachate.</p><h4><strong>Materials and Methods</strong></h4><p>Samples included NIST-certified biosolids, landfill leachate, and spiked river water. Solid-phase extraction (SPE) was followed by LC-MS/MS analysis on an <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/191"><strong>ACQUITY Premier System</strong></a> with BEH C18 columns and detection via the <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/library?manufacturerItems=5&amp;search=Xevo+TQ+Absolute+XR"><strong>Xevo TQ Absolute XR</strong></a> using negative electrospray ionization and MRM. The robustness of the method was assessed over 12 weeks with over 9,000 injections and weekly calibrations, using <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1544"><strong>waters_connect for Quantitation Software</strong></a> for data processing and review.</p><h4><strong>Results</strong></h4><p>Throughout the 12-week study, all sample types showed high consistency and low variability. For example, L-PFHxS in biosolids averaged 8.78 µg/kg (%RSD 7.2%) compared to the certified 9.39 µg/kg, while PFOA in landfill leachate showed a mean of 2.52 ng/mL (%RSD 2.7%). QC plots confirmed that all monitored PFAS met trueness and ion ratio targets across thousands of injections with no unscheduled downtime, highlighting the system’s long-term reliability.</p><h4><strong>Conclusion</strong></h4><p>The StepWave XR ion guide enabled reliable, high-throughput PFAS analysis with minimal maintenance and excellent reproducibility. The Xevo TQ Absolute XR maintained calibration stability, accurate quantitation, and strong matrix resilience across diverse sample types. Combined with streamlined software workflows, this setup is well-suited for routine EPA 1633A PFAS analysis in environmental labs.</p>

News from LabRulezLCMS Library - Week 27, 2025

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PFAS & Our Planet: Food and Food Contact Materials

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