Ask any analytical chemist which hyphenated technique has become indispensable over the past decade, and the answer will almost certainly be the same: tandem chromatography–mass spectrometry. Whether it is <a target="_blank" rel="noopener noreferrer" href="https://www.organomation.com/preparing-samples-for-lc-ms/ms-analysis">LC–MS/MS</a> quantifying a novel biologic’s metabolic fate, or <a target="_blank" rel="noopener noreferrer" href="https://www.organomation.com/preparing-samples-for-gc-ms/ms-analysis">GC–MS/MS</a> chasing per- and polyfluoroalkyl substances (PFAS) down to sub-part-per-trillion levels in municipal water, the combination of chromatographic separation with the specificity of tandem mass detection has become the analytical workhorse of choice across virtually every regulated sector.Below we examine the key forces propelling this expansion, from biopharma pipeline dynamics and PFAS regulatory mandates to AI-driven automation and reshoring of pharmaceutical manufacturing—and explore what each trend means for laboratories managing sample preparation and analytical workflows.<h3>Biopharma: The Engine Room of LC–MS/MS Demand</h3><h4>GLP-1 Agonists and the Metabolomics Gold Rush</h4>The explosive commercial and scientific interest in GLP-1 receptor agonists—<a target="_blank" rel="noopener noreferrer" href="https://www.sepscience.com/advancing-glp-1-peptide-analysis-chromatography-challenges-and-innovations-12163">semaglutide and related peptide therapeutics </a>for diabetes and obesity—has dramatically expanded the analytical demands placed on tandem MS platforms. Discovery programs require precise quantification of peptide drug candidates and endogenous biomarkers across complex biological matrices. These workflows rely on high-sensitivity LC–MS/MS for pharmacokinetic profiling, receptor occupancy studies, and metabolomics characterization. Metabolomics is, in fact, projected to be the fastest-growing application segment in mass spectrometry, driven in part by its growing role in cancer screening, biomarker discovery, and metabolic disease research.I have been spending more time learning about GLP-1s because this is the hot topic that people want to discuss on the Concentrating on <a target="_blank" rel="noopener noreferrer" href="https://open.spotify.com/show/1wZg67rCjoGju4yhqxI3tL?si=n9GLz9zjSCOrVfXPxFPhng&amp;nd=1&amp;dlsi=52868e027aad4d22">Chromatography podcast</a>. With that said, I was astounded looking at CNBC.com during breakfast this morning to see that <a target="_blank" rel="noopener noreferrer" href="https://www.cnbc.com/2026/03/21/glp-1-diets-restaurants-protein-fiber-weight-loss-drugs.html">one in eight Americans are currently taking one of these drugs such as Ozempic</a>.<h4>Antibody–Drug Conjugates and Gene Therapy: Complexity at Every Step</h4>The ascent of antibody–drug conjugates (ADCs) and gene therapies has introduced a new level of analytical complexity. ADCs blend the target specificity of monoclonal antibodies with the cytotoxic potency of small-molecule payloads—and characterizing the linker chemistry, drug-to-antibody ratio (DAR), and conjugate stability demands high-resolution LC–MS/MS at every stage from discovery through QC release testing. Gene therapy vectors require equally rigorous characterization of impurities, aggregates, and empty/full capsid ratios.This translates into a direct need for low-evaporation, high-recovery concentration methods that preserve labile protein structures and maintain sample integrity prior to LC–MS/MS injection. <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/5392">Nitrogen evaporation workflows</a> that minimize oxidative stress and maintain sample temperature are increasingly critical in these pipelines.<h4>Precision Medicine and Multi-Omics Integration</h4>The shift toward precision medicine has accelerated adoption of high-throughput, multi-analyte MS platforms. Proteomics, metabolomics, and lipidomics workflows are converging on a single analytical platform—tandem MS—and generating datasets of a scale and complexity that were unimaginable ten years ago.Make no mistake: the triple quadrupole serves an irreplaceable role in quantitative targeted analysis. At the same time, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products?category=134&amp;manufacturerItems=3">Orbitrap </a>and Q–TOF hybrid platforms are growing rapidly as researchers demand full-scan accurate mass for untargeted discovery.<h3>Environmental Mandates: PFAS Testing Drives Adoption</h3>Environmental testing is something that every person, chemist or not, can understand the importance of. Mounting mandates from the U.S. Environmental Protection Agency and European regulators regarding PFAS—the “forever chemicals” whose extraordinary environmental persistence is matched only by the analytical challenge of detecting them at trace levels—have created immediate, compliance-driven investment in LC–MS/MS infrastructure.<h4>The Regulatory Framework Chemists Need to Know</h4>The EPA has codified a suite of LC–MS/MS-based methods as the analytical standard for PFAS in water and solid matrices:<ul><li><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/epa-533-drying-down-pfas-samples-after-spe">EPA Method 533</a>: Weak anion exchange SPE combined with LC–MS/MS; covers 25 PFAS including short-chain compounds in drinking water.</li><li><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/sample-concentration-epa-method-537-pfas-determination">EPA Method 537.1</a>: Reversed-phase SPE followed by LC–MS/MS; covers 18 PFAS including the GenX compound, with method detection limits in the low ng/L range.</li><li><a target="_blank" rel="noopener noreferrer" href="https://www.agilent.com/en/solutions/environmental/water-testing/pfas-in-water/us-epa-method-8327?srsltid=AfmBOooCY1pcavj7B1PH-75d3HO4BGDglNlhmyTyrpDY3zvUksMO1dlg">EPA Method 8327</a>: LC–MS/MS for selected PFAS in prepared extracts of aqueous and solid matrices.</li><li><a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/preparing-diverse-sample-matrices-for-epa-method-1633">EPA Draft Method 1633</a>: The emerging benchmark for PFAS in non-aqueous matrices—aqueous, solid, biosolids, and tissue—quantifying up to 40 PFAS.</li></ul>All of these methods designate LC–MS/MS, specifically LC coupled to triple quadrupole or tandem-in-time platforms operating in negative electrospray ionization mode with multiple reaction monitoring (MRM), as the required or recommended analytical technique. PFAS analysis is, at its core, an LC–MS/MS problem.<h4>The Sample Preparation Bottleneck</h4>Chemists who have worked with PFAS methods understand the particular demands they place on sample preparation. The ubiquity of<a target="_blank" rel="noopener noreferrer" href="https://blog.organomation.com/blog/tackling-pfas-contamination-practical-insights-from-epa-537.1-method-development"> PFAS in laboratory materials</a>—PTFE tubing, some SPE sorbents, standard bench supplies—means that blank contamination control is as analytically demanding as the detection itself. EPA 537.1 requires that sample volumes of approximately 250 mL be extracted and reconstituted in as little as 1 mL, creating a 250:1 concentration factor that can expose even trace contamination in the sample processing chain. The installation of a delay column between the LC pump and autosampler to prevent instrument background interference is now standard practice.This is precisely where robust, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/5385">inert nitrogen evaporation </a>systems earn their keep. PFAS workflows that use nitrogen-assisted evaporation to concentrate extracts prior to reconstitution benefit from materials that avoid PTFE and other fluoropolymers that can leach PFAS background—a consideration Organomation addresses in its concentration system designs.The analytical community is also moving beyond targeted PFAS analysis. High-resolution accurate mass (HRAM) spectrometry via Orbitrap technology, paired with non-targeted screening workflows, is gaining traction for the identification of the more than 5,000 currently catalogued PFAS compounds and the novel structures that continue to emerge. LC–MS/MS remains the quantitative gold standard; HRAM provides the discovery layer.<h3>Technological Trends Reshaping the LC–MS/MS Workflow</h3><h4>Artificial Intelligence and Automated Data Interpretation</h4>The datasets generated by modern tandem MS platforms—particularly in omics applications—are too large and too complex for conventional manual review. AI-driven spectral deconvolution, automated peak integration, and AI-assisted hypothesis generation are now embedded in the software suites accompanying leading instruments. <a target="_blank" rel="noopener noreferrer" href="https://www.agilent.com/about/newsroom/presrel/2022/17feb-gp22004.html?srsltid=AfmBOop3warRIaEojXM2YyMML6RXfMIDzE-Wm0h-SiKkkocBeeET2m7u">Agilent’s acquisition of Virtual Control’s ACIES </a>software specifically to automate LC–MS and GC–MS data analysis is emblematic of this direction.For laboratory managers, AI integration means smaller specialized teams can operate high-throughput multi-analyte workflows—but it also means that the front-end sample preparation must be even more reproducible, since algorithmic interpretation amplifies inconsistencies introduced upstream.<h4>Online SPE Coupling and “Chromatography Without Walls”</h4>A significant trend is the integration of solid-phase extraction directly into the HPLC flow path—so-called online SPE–HPLC coupling. Systems that combine extraction and chromatographic separation in a single analytical instrument reduce manual transfer steps, minimize the risk of sample loss or contamination, and dramatically increase throughput. For analytes at very low concentrations, online SPE provides the on-column concentration capability that traditional offline preparation achieves with manual evaporation steps.That said, offline sample preparation—including <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/article/5392">nitrogen-assisted evaporation</a> under controlled conditions, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/2407">liquid–liquid extraction</a>, and protein precipitation—retains significant advantages in flexibility, matrix handling, and the ability to process sample volumes that exceed online system capacity. The two approaches are increasingly complementary rather than competitive in well-designed analytical laboratories.<h4>High-Purity Solvents and Reference Materials</h4>As detection limits push further into the femtogram range and regulatory methods demand demonstrable blank performance, the quality of analytical consumables—mobile phase solvents, derivatization reagents, reference standards—has moved from background consideration to front-of-mind. Method validation in regulated environments now routinely requires vendor certification of solvent purity at a level that directly interfaces with instrument performance.<h3>The Ever-Present Need for Sample Evaporation</h3>As LC–MS/MS methods push detection limits lower, the analytical burden shifts increasingly upstream. The quality of the concentration, cleanup, and reconstitution steps preceding injection determines whether the instrument’s theoretical sensitivity is achievable in practice.Several specific developments are particularly relevant:<ul><li>ADC and gene therapy characterization workflows require gentle, low-temperature evaporation that preserves protein structure and prevents aggregation prior to LC–MS/MS. Nitrogen evaporation under controlled conditions is the preferred approach.</li><li>PFAS trace analysis demands evaporation systems constructed from PFAS-inert materials, with rigorous attention to avoiding fluoropolymer surfaces throughout the sample path.</li><li>High-throughput pharmaceutical QC driven by reshoring demands parallel processing capability—multi-position evaporators that maintain consistent flow and temperature across all positions simultaneously.</li><li>Multi-omics and metabolomics workflows generate large sample batches that benefit from automated, walk-away evaporation with programmable endpoints to ensure reproducible final volumes across a cohort.</li></ul>Tandem chromatography–mass spectrometry is not merely growing; it is becoming structurally embedded in the analytical workflows of every major regulated industry. The convergence of biopharma complexity, PFAS regulatory mandates, AI-enabled data analysis, and pharmaceutical reshoring is creating a multi-year demand cycle that will require laboratories to invest not only in instruments, but in the entire sample preparation ecosystem that makes those instruments perform.For analytical chemists, the practical takeaway is this: as mass spectrometry sensitivity continues to advance, the sample preparation step becomes the binding constraint on method performance. Whether you are developing a new PFAS method to meet EPA 1633, characterizing an ADC’s drug-to-antibody ratio, or running a 500-sample metabolomics cohort overnight, the reliability and cleanliness of your concentration and cleanup workflow determines the quality of every data point that follows.&nbsp;

The Continued Rise of Tandem Chromatography–Mass Spectrometry

News from LabRulezLCMS Library - Week 27, 2026

🎤Dr. Christopher Reid (Professor of Chemistry and Biochemistry at Bryant University in Rhode Island)In this episode of Concentrating on Chromatography, host Dave Oliva sits down with Chris Reid to explore how chemical biology and LC-MS are being used to tackle one of the most urgent global challenges: antimicrobial resistance.As antibiotic resistance continues to rise—and new drug development struggles to keep pace—researchers are looking beyond traditional approaches. Instead of targeting how bacteria build their cell walls, Chris’s work focuses on how they break them down, opening the door to entirely new antimicrobial strategies.<h4>What You’ll Learn in This Episode:</h4><ul><li>Why antimicrobial resistance is accelerating globally</li><li>What peptidoglycan is and why it’s essential to bacterial survival</li><li>How targeting cell wall degradation differs from traditional antibiotics</li><li>The strategy behind designing small molecule probes and inhibitors</li><li>How LC-MS is used to analyze peptidoglycan fragments and enzyme activity</li><li>Key analytical challenges: complex mixtures, low-abundance species, and structural similarity</li><li>The importance of sample preparation and reproducibility in LC-MS workflows</li><li>How this research could lead to new antibiotic targets</li></ul><h3>Video Transcription</h3><h4>The Growing Challenge of Antibiotic Resistance</h4>According to Reid, antibiotic resistance is increasing across a broad spectrum of bacterial pathogens that were once readily treated with existing therapies. In some cases, clinicians must now rely on only a handful of last-line antibiotics, while resistance is also rising in diseases such as tuberculosis.One of the major obstacles is the limited commercial incentive to develop entirely new antibiotics. Because bacterial resistance can emerge relatively quickly after a drug reaches the market, pharmaceutical companies often favor modifying existing antibiotics or combining them with resistance-modifying agents rather than investing in completely new drug classes. As a result, genuinely novel antibacterial targets remain urgently needed.<h4>Why the Bacterial Cell Wall Remains an Attractive Target</h4>The bacterial cell wall consists primarily of peptidoglycan, a highly cross-linked polymer that provides structural integrity, maintains cell shape, and enables bacterial growth and division.Many widely used antibiotics—including the β-lactam antibiotics such as penicillins—target enzymes responsible for synthesizing or cross-linking peptidoglycan. These pathways have proven highly successful therapeutic targets because peptidoglycan is unique to bacteria and absent from human cells, minimizing unwanted effects on the host.However, most existing antibiotics target only specific stages of peptidoglycan biosynthesis. Reid's research explores another part of this complex pathway: enzymes responsible for degrading the carbohydrate backbone of peptidoglycan during normal bacterial growth and remodeling. These enzymes may represent an underexplored class of antimicrobial targets capable of overcoming existing resistance mechanisms.<h4>Targeting the Glycan Backbone</h4>A key advantage of focusing on the carbohydrate backbone is its remarkable conservation across both Gram-positive and Gram-negative bacteria.Whereas the peptide components of peptidoglycan vary considerably between bacterial species—and frequently acquire mutations associated with antibiotic resistance—the glycan backbone remains highly conserved and tolerates relatively few structural modifications.This biological constraint makes enzymes acting on the glycan backbone particularly attractive targets. Reid's group developed a series of small-molecule probes and inhibitors designed to recognize enzymes known as N-acetylglucosaminidases, which cleave glycosidic bonds within peptidoglycan and generate soluble degradation products.Rather than beginning with purified enzymes, the researchers adopted a top-down phenotypic screening strategy. Candidate compounds were first evaluated for their ability to inhibit bacterial growth before progressively narrowing the list of potential molecular targets through genetic studies, microscopy, enzyme assays, and biochemical characterization. This iterative workflow ultimately identified compounds capable of inhibiting the desired enzyme class while simultaneously providing valuable chemical probes for studying bacterial cell wall biology.<h4>LC-MS as a Central Analytical Tool</h4>Liquid chromatography coupled with mass spectrometry plays a central role throughout the project by enabling detailed characterization of structural changes occurring within peptidoglycan after bacterial cells are treated with candidate inhibitors.Because intact peptidoglycan is an insoluble polymer, sample preparation begins with isolation of the bacterial cell wall through detergent extraction and differential centrifugation. Additional purification steps remove proteins, nucleic acids, and teichoic acids before enzymatic digestion converts the insoluble material into soluble fragments suitable for chromatographic analysis.The resulting digest is analyzed by LC-MS to examine changes in the distribution of peptidoglycan fragments. Chromatographic retention times provide an immediate indication of changes in cross-linking, with larger oligomers such as trimers and tetramers generally eluting later than monomeric fragments. Mass spectrometry then confirms the identity of these fragments by measuring their intact molecular masses, while tandem MS experiments can provide further structural information when required.<h4>Sample Preparation Determines Data Quality</h4>Reid emphasized that sample preparation represents one of the most critical—and challenging—stages of the entire workflow.Because peptidoglycan analysis involves multiple purification, digestion, and reduction steps, even minor procedural differences between samples can introduce analytical artifacts that complicate biological interpretation.Maintaining strict consistency throughout sample preparation is therefore essential. Appropriate controls must accompany every experiment, ensuring that observed chromatographic and mass spectrometric differences truly reflect biological responses rather than experimental variability. The complexity of bacterial cell wall composition further increases the analytical challenge, as subtle differences in amino acid substitutions and low-abundance cross-linked species can complicate LC-MS data interpretation.<h4>Chemical Biology for Future Antibiotic Discovery</h4>Although the identified compounds may eventually serve as starting points for antibiotic development, Reid views them primarily as chemical biology tools.By selectively inhibiting individual enzymes, these probes allow researchers to investigate previously unexplored aspects of bacterial cell wall remodeling that cannot easily be studied using classical genetic approaches alone.The research team is now expanding this strategy by combining their probes with proximity-labeling proteomics and mass spectrometry, aiming to map protein interaction networks associated with bacterial cell wall degradation. Such studies may reveal entirely new antibacterial targets and provide deeper insight into the biological processes governing bacterial growth and division.Ultimately, the work illustrates how integrating synthetic chemistry, microbiology, molecular biology, and advanced LC-MS can accelerate the search for innovative therapeutic strategies against antimicrobial resistance. As existing antibiotics become progressively less effective, multidisciplinary approaches such as these may play an increasingly important role in identifying the next generation of antibacterial targets.<blockquote>This text has been automatically transcribed from a video presentation using AI technology. It may contain inaccuracies and is not guaranteed to be 100% correct.</blockquote><blockquote><h4>Concentrating on Chromatography Podcast</h4>Dive into the frontiers of chromatography, mass spectrometry, and sample preparation with host David Oliva. Each episode features candid conversations with leading researchers, industry innovators, and passionate scientists who are shaping the future of analytical chemistry. From decoding PFAS detection challenges to exploring the latest in AI-assisted liquid chromatography, this show uncovers practical workflows, sustainability breakthroughs, and the real-world impact of separation science. Whether you’re a chromatographer, lab professional, or researcher you'll discover inspiring content!You can find Concentrating on Chromatography Podcast in podcast apps:<ul><li><a target="_blank" rel="noopener noreferrer" href="https://open.spotify.com/show/1wZg67rCjoGju4yhqxI3tL">Spotify</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://podcasts.apple.com/tz/podcast/concentrating-on-chromatography/id1788429185">Apple podcast</a></li><li><a target="_blank" rel="noopener noreferrer" href="https://podscan.fm/podcasts/concentrating-on-chromatography">podscan</a></li></ul>and on <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/@ChromatographyTalk/videos">YouTube channel</a></blockquote>

 Fighting Antibiotic Resistance with LC-MS: Targeting Bacterial Cell Walls

Article

Application

Academy

Video

Scientists

Interview

Poster

Everything from the world of analytical chemistry in one place. We connect people in solving their problems. At Labrulez you will find all the necessary information easily, quickly and clearly. Stop searching and start finding.

LabRulez

Organomation, founded in 1959, designs and manufactures high-quality nitrogen evaporators and extraction systems. Known for innovation and durability, their lab instruments are used globally for efficient sample preparation with strong customer support.

Organomation

Separation Science

The Analytical Scientist

Agilent Technologies

Technology Networks

Bruker

SelectScience

Evosep Biosystems

Dear user and other PaSER interested customers,
You are hereby invited to our 2nd Virtual PaSER Workshop. A lot of new possibilities has been introduced since last time – including, but not limited to PaSER Novor for de novo sequencing of dda-PASEF® data on the PaSER Box as well as TIMS DIA-NN 2.0 -which will be demonstrated during this Workshop. Data virtualization has been a requested feature – and this is now possible with Mass Dynamics for PaSER. Not limited to above – stay tuned for even more approaching features, we will discuss as well.
<h3>The tentative agenda looks like this:</h3>
<h5>1:00 – 1:15 pm: Introduction</h5>
<ul>
<li>Willy Bjørklund</li>
</ul>
<h5>1:15 – 1: 35pm: New Applications on the timsTOF Platform</h5>
<ul>
<li>Lars Kristensen (Field Application Specialist)</li>
</ul>
<h5>1:35 – 1:55 pm: PaSER as a bioinformatic platform - what’s new and what’s coming</h5>
<ul>
<li>Jonathan Krieger (Software R&amp;D Department)</li>
</ul>
<h5>5 minute break</h5>
<h5>2:00 – 2:20 pm: Live Demo/workshop of PaSER</h5>
<ul>
<li>Tharan Srikumar (Software R&amp;D Department)</li>
</ul>
<h5>2:20 – 2:50 pm: Mass Dynamics</h5>
<ul>
<li>Mark Condina and Giuseppe Infusini</li>
</ul>
<h5>2:50 – 3:10 pm: Questions and discussions</h5>
<h5>3:10 – 3:15 pm: Conclusion</h5>
<ul>
<li>Willy Bjørklund</li>
</ul>
We aim for a lively interaction so take the timing as an indication. Please feel free to share with colleagues or others you think could benefit from attending this workshop. Looking forward to “meet”

Bruker Virtual PaSER Workshop

Dear user and other PaSER interested customers, You are hereby invited to our 2nd Virtual PaSER Workshop. 

A novel spatial technique, DISCO-MS, combines whole-organ/whole-organism clearing and imaging, deep-learning-based image analysis, robotic tissue extraction, and ultra-high-sensitivity mass spectrometry with the Bruker timsTOF instrument family. This combination enables DISCO-MS to perform unbiased proteome analysis of preclinical and clinical tissues from quantity-limited materials after unbiased imaging of entire specimens in 3D.
In this webinar, you will learn about a new experimental approach that combines whole tissue clearing, dia-PASEF®, and trapped ion mobility spectrometry (TIMS) mass spectrometry to analyze the spatial proteome of complex tissue structures. The webinar will detail how with this technique, researchers were able to:
<ul>
<li>Analyze the proteome of preclinical and clinical tissues after identification of regions of interest using 3D imaging, followed by robotic tissue extraction</li>
<li>Achieve early unbiased detection and characterization of subtle tissue perturbations across pathologies</li>
<li>Benefit from the use of ultra-high sensitivity and robust timsTOF mass spectrometers</li>
</ul>
<h5>Key learning objectives</h5>
<ul>
<li>Discover the new experimental approach that combines whole tissue clearing, dia-PASEF®, and TIMS mass spectrometers can be used to analyze the spatial proteome of complex tissue structures</li>
<li>Understand how researchers were able to analyze the proteome of specific tissue regions following 3D imaging to enable robotic tissue extraction</li>
<li>Learn about the unparalleled sensitivity and robustness the timsTOF platform offers with 4D-Proteomics™ which enables researchers to delve deeper into proteome analysis and gain greater insights</li>
</ul>
<blockquote>
Presenter: Dr. Harsharan Singh Bhatia (Institute for Tissue Engineering and Regenerative Medicine (iTERM))
</blockquote>
<blockquote>
Dr. Harsharan Singh Bhatia is the Omics technologies team leader at the Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Munich. He completed his Ph.D. at the University of Freiburg, Germany, studying the neuroprotective role of dietary antioxidants. Bhatia worked as a postdoctoral researcher at UCLA, where he investigated the impact of dietary manipulations on rodent behavior. He later returned to the University of Freiburg to work as a research associate at the University Clinic, exploring epigenetic factors&#39; regulation of microglial function. In 2017, Bhatia joined iTERM to study chronic neuroinflammation using DISCO tissue clearing and spatial-omics tools.
</blockquote>
<blockquote>
Presenter: Jemima Arnold (Editorial Team, SelectScience)
</blockquote>
<blockquote>
Jemima studied Cellular and Molecular Medicine at the University of Bristol, UK, and as a member of the Editorial team, she now plays an integral role in shaping the content on SelectScience.
</blockquote>

SelectScience: Spatial proteomics in three-dimensional intact specimens

Spatial proteomics in three-dimensional intact specimens

A new experimental approach that combines whole tissue clearing, dia-PASEF®, and TIMS MS to analyze the spatial proteome of complex tissue structures.

<ul>
<li>Wait what?! Who knew!? There are so many things that a mass spec can do.
</li>
<li>I&#39;ve used it for years, yes this may be true.
</li>
<li>I&#39;ve processed some samples, more than a few.
</li>
<li>But between me and you, I had no idea all the things it could do!
</li>
<li>From sample prep to separation, you just won&#39;t believe…
</li>
<li>All of the tips and tricks we have up our sleeve.
</li>
<li>So, take a few minutes, about 15 should do.
</li>
<li>And learn all the things your mass spec can do.
</li>
</ul>
An easy to follow guide detailing how to set MS scan parameters for an LCMS experiment will be presented. Scan speeds for reproducible quantitation, chromatographic resolution, retention time definition, proper threshold adjustment for optimum datafile size, and how this can result in faster processing times will all be discussed.
<blockquote>
Presenter: Rebecca Glaskin, Ph.D. (LC/MS Application Scientist, Agilent Technologies, Inc.)
</blockquote>
<blockquote>
Rebecca Glaskin is an LC/MS Application Scientist at Agilent with a focus on BioPharma applications supporting the LC-Q/TOF and IM-QTOF platforms. Prior to joining Agilent, Rebecca received her Ph.D. in analytical chemistry from Indiana University in the lab of Professor David Clemmer. While there she designed and constructed home-built instruments, pushing the limits of the mobility resolution that can be obtained with a circular drift tube for the separation of biomolecules (peptides, proteins, carbohydrates, and metabolites). While there, she also studied hydrogen/deuterium exchange of proteins in the gas-phase as a function of time and pressure. Rebecca then went to Boston University as a Postdoctoral Associate in the lab of Professor Catherine Costello to develop a database containing collision cross section values for glycans, peptides, and glycopeptides utilizing Agilent Technologies 6560 IM-QTOF. This database can be used to determine how the collision cross section is altered with the addition of individual saccharide units. The trendlines obtained from this database will be used to predict collision cross sections for glycopeptides based on the conformation and structure of the specific glycoform.
</blockquote>
<blockquote>
Presenter: Jim Lau, PhD (HRAMS LC/MS Application Engineer, Agilent Technologies, Inc.)
</blockquote>
<blockquote>
Jim Lau received his Ph.D. From the University of Colorado. There he worked in the laboratories of Peter Albersheim and Robert Shapiro. This work involved the structure elucidation of plant natural products and, in particular, elucidating the structures of oligosaccharides derived from plant cell wall polysaccharides. This work was done in the early days of LCMS and made use of DLI-LCMS and (at the time) recently invented Thermospray-LCMS.
</blockquote>
<blockquote>
After the completion of his Ph.D., Jim joined Hewlett-Packard to work on LCMS ionization techniques with Paul Goodley during the early days of Electrospray-LCMS. He then moved to work on field applications and collaborations with Hewlett-Packard’s LCMS customers. More than 30 years later, Jim continues to work with Agilent’s customers in High Resolution Accurate Mass applications of LCMS. While involved in many areas of HRAMS LCMS, his recent work has focused on the area of Screening/Qual&amp;Quant of small molecules and on the high throughput confirmation of oligonucleotide synthesis.
</blockquote>

Agilent Technologies: How to set MS Scan Parameters for your LCMS Experiment

How to set MS Scan Parameters for your LCMS Experiment

An easy to follow guide detailing how to set MS scan parameters for an LCMS experiment will be presented.

<ul>
<li>Wait what?! Who knew!? There are so many things that a mass spec can do.
</li>
<li>I&#39;ve used it for years, yes this may be true.
</li>
<li>I&#39;ve processed some samples, more than a few.
</li>
<li>But between me and you, I had no idea all the things it could do!
</li>
<li>From sample prep to separation, you just won&#39;t believe…
</li>
<li>All of the tips and tricks we have up our sleeve.
</li>
<li>So, take a few minutes, about 15 should do.
</li>
<li>And learn all the things your mass spec can do.
</li>
</ul>
The acquisition parameters for an LCMSMS experiment can seem overwhelming. This presentation will examine the scan parameters available for designing an MSMS, explain their intended function, and suggest approaches to use based on the goal of the LCMSMS experiment. Parameters for MSMS trigger thresholds, active exclusion settings for different types of experiments and variable weighting of precursors will be discussed.
<blockquote>
Presenter: Rebecca Glaskin, Ph.D. (LC/MS Application Scientist, Agilent Technologies, Inc.)
</blockquote>
<blockquote>
Rebecca Glaskin is an LC/MS Application Scientist at Agilent with a focus on BioPharma applications supporting the LC-Q/TOF and IM-QTOF platforms. Prior to joining Agilent, Rebecca received her Ph.D. in analytical chemistry from Indiana University in the lab of Professor David Clemmer. While there she designed and constructed home-built instruments, pushing the limits of the mobility resolution that can be obtained with a circular drift tube for the separation of biomolecules (peptides, proteins, carbohydrates, and metabolites). While there, she also studied hydrogen/deuterium exchange of proteins in the gas-phase as a function of time and pressure. Rebecca then went to Boston University as a Postdoctoral Associate in the lab of Professor Catherine Costello to develop a database containing collision cross section values for glycans, peptides, and glycopeptides utilizing Agilent Technologies 6560 IM-QTOF. This database can be used to determine how the collision cross section is altered with the addition of individual saccharide units. The trendlines obtained from this database will be used to predict collision cross sections for glycopeptides based on the conformation and structure of the specific glycoform.
</blockquote>
<blockquote>
Presenter: Jim Lau, PhD (HRAMS LC/MS Application Engineer, Agilent Technologies, Inc.)
</blockquote>
<blockquote>
Jim Lau received his Ph.D. From the University of Colorado. There he worked in the laboratories of Peter Albersheim and Robert Shapiro. This work involved the structure elucidation of plant natural products and, in particular, elucidating the structures of oligosaccharides derived from plant cell wall polysaccharides. This work was done in the early days of LCMS and made use of DLI-LCMS and (at the time) recently invented Thermospray-LCMS.
</blockquote>
<blockquote>
After the completion of his Ph.D., Jim joined Hewlett-Packard to work on LCMS ionization techniques with Paul Goodley during the early days of Electrospray-LCMS. He then moved to work on field applications and collaborations with Hewlett-Packard’s LCMS customers. More than 30 years later, Jim continues to work with Agilent’s customers in High Resolution Accurate Mass applications of LCMS. While involved in many areas of HRAMS LCMS, his recent work has focused on the area of Screening/Qual&amp;Quant of small molecules and on the high throughput confirmation of oligonucleotide synthesis.
</blockquote>

Agilent Technologies: How to design an LCMSMS Experiment

How to design an LCMSMS Experiment

The scan parameters available for designing an MSMS, explain their intended function, and suggest approaches to use based on the goal of the LCMSMS experiment.

Targeted workflows are particularly interesting for identifying established biomarkers in various applications. The focus on these workflows, coupled with technological advancements, is continually expanding the boundaries of high-throughput targeted analysis.
<h3>Next Generation of absolute protein Quantitation in Biological Matrixes; higher multiplexicity while faster, robust and sensitive</h3>
<ul>
<li>Presenter: Dr. Christoph Borchers (Mcgill university)</li>
</ul>
The accurate and rapid determination of protein concentrations using multiplexed multiple reaction monitoring (MRM) with isotope-labeled internal standards has the potential to revolutionize biochemistry and medical sciences. The combination of an Evosep One LC with an Agilent QQQ6495C allows a several-fold reduction of analysis time while maintaining high multiplexicity. As an example, we show the use of a multi-protein method for the absolute quantitation of 270 proteins, combined with metabolomics and Artificial Intelligence (AI), to analyze the plasma of a COVID cohort for prediction of survival. Moreover, optimization of the Evosep/6495C combination allowed adaptation of the 270-protein MRM method to a 24-minute gradient, thus doubling the throughput compared to before.
<h3>Development of a LC-MS/MS Method for Measurement of Fusion Sarcoma Proteins in Plasma</h3>
<ul>
<li>Presenter: Phd. AnThony Maus (Clinical Mass Spec. Development Laboratory, Mayo Clinic)</li>
</ul>
Sarcoma is general term for a group of over 70 cancers that are classified using genomic techniques to identify characteristic gene fusions in tumor tissues. However, this technique requires relatively invasive biopsies and is not conducive to monitoring disease progression or response to treatment. Measurements of fusion protein biomarkers in plasma would overcome these limitations. We sought to develop an LC-MS/MS method capable of performing these measurements by conducting discovery experiments on cell lines with an EvoSep coupled to an Exploris 480 mass spectrometer. Using these data, we developed a targeted method and performed measurements in plasma samples.

Targeted Workflows

Targeted workflows are particularly interesting for identifying established biomarkers in various applications.

Targeted LC/MS Workflows

Webinar in collaboration with the Polish Society of Metabolomics.
<h3>14:00 - 14:20 Benefits of Trapped Ion Mobility Spectrometry (TIMS) for Metabolomics and Lipidomics</h3>
<ul>
<li>Presenter: Dr. Stefanie Wernisch ( Business Development Manager Metabolomics/Multiomics, Bruker Daltonics Bremen, Germany)</li>
</ul>
After revolutionizing the area of proteomics, trapped ion mobility spectrometry (TIMS) is now conquering the fields of metabolomics and lipidomics. Bruker&#39;s unique timsTOF technology addresses the complexity of biological samples by adding an orthogonal dimension of separation before mass spectrometric analysis, thus reducing the complexity of MS/MS data and improving annotation confidence for untargeted analysis. The ability to determine Collisional Cross Sections (CCS) can further aid identification and outlier detection in lipidomics studies.
<h3>14:20 - 14:40 SpatialOMx® for in-depth 4D-Lipidomics™</h3>
<ul>
<li>Presenter: Dr. Janina Oetjen (Application Specialist MALDI Imaging, Bruker Daltonics Bremen, Germany)</li>
</ul>
The combined possibilities of ESI and MALDI in one instrument enables powerful SpatialOMx® applications. In short, ion mobility-based annotation can connect confident LC-TIMS-MS/MS identification with meaningful spatial information from MALDI Imaging, specifically in the field of lipidomics. Further, segmentation results based on lipid imaging can define specific regions of interest for subsequent, in-depth analysis. Thus, the information content of MALDI Imaging can be enhanced with SpatialOMx® workflows on the timsTOF fleX platform.
<h3>14:40 - 15:00 Application Round-up: 4D-Metabolomics™ and 4D-Lipidomics™</h3>
<ul>
<li>Presenter: Dr. Matthias Szesny (Application Scientist Metabolomics, Bruker Daltonics Bremen, Germany)</li>
</ul>
We will highlight the capabilities of the timsTOF platform and introduce new applications, method developments, and software solutions in the field of metabolomics and lipidomics. Those help scientists gain a faster and deeper understanding of diverse research areas such as health and disease as well as agriculture.

Bruker: Expanding the Horizons of 4D-Metabolomics and 4D-Lipidomics

Expanding the Horizons of 4D-Metabolomics and 4D-Lipidomics

Benefits of TIMS for Metabolomics and Lipidomics. SpatialOMx for in-depth 4D-Lipidomics, Application Round-up: 4D-Metabolomics and 4D-Lipidomics.

Studies on drug metabolism aid in evaluating the pharmacokinetics, pharmacodynamics and safety during discovery and development. In vitro studies of drug metabolism are essential for identifying major metabolism pathways. These studies often use accurate mass spectrometry to ensure comprehensive profiling and identification of drug metabolites. However, confident identification of drug metabolites remains challenging due to insufficient fragment ion coverage.
Here, an alternative fragmentation technique is applied to produce additional fragment ions and an informative MS/MS spectra for metabolite identification. An end-to-end workflow is demonstrated for streamlined method development and metabolite identification from high-quality and more informative electron activated dissociation (EAD) MS/MS spectra. 
Attend this webinar to learn how to:
<ul>
<li>Perform confident drug metabolite identification using alternative fragmentation mechanism</li>
<li>Harness the informative and rich data collection from the latest generation QTOF technology for sensitive drug metabolite identification</li>
<li>Employ an end-to-end workflow for drug metabolite identification, from method development to data analysis</li>
</ul>
<blockquote>
Presenter: Rahul Baghla (Global Pharma Applications Lead, SCIEX)
</blockquote>

Technology Networks: Improving End-to-End Metabolite Identification by LC-MS/MS

Improving End-to-End Metabolite Identification by LC-MS/MS

Here, an alternative fragmentation technique is applied to produce additional fragment ions and an informative MS/MS spectra for metabolite identification. 

Mass spectrometry is a powerful analytical tool used to study the properties of chemical substances and their interactions with other molecules. In this forum, you will learn more about mass spectroscopy and its potential applications to the proteomics field.
Our expert speakers will share their knowledge and experience, and also discuss the latest advances in the field. Their respective talks are titled:
Whether you are a student, researcher, or an analytical science professional, this forum is an excellent opportunity to learn more about mass spectroscopy and its potential (plasma) proteomics applications.
Don&#39;t miss this chance to gain valuable insights and expand your knowledge in the fascinating field of mass spectrometry. Register now and secure your spot!
<h3>Unleashing the Power of 4D-Proteomics™ Ecosystem for Plasma Analysis: Pioneering Precision Medicine Research</h3>
<h5>Presenter: Torsten Müller (Business Development Manager - Proteomics, Bruker Life Sciences Mass Spectrometry)</h5>
LC-MS enthusiast with strong interest in sample preparation, method and workflow optimization in the field of proteomics.
<h3>Taking plasma biomarker discovery to the next level with TrueDiscovery™, a DIA-based platform for deep and unbiased proteome profiling</h3>
<h5>Presenter: Yuehan Feng, PhD (Director, Scientific Alliances, Biognosys)</h5>
Yuehan Feng, PhD is Senior Director, Application Sciences at Biognosys. His scientific expertise is centered around proteomics technologies and applications with a strong emphasis on mass spectrometry and chemical biology.
Yuehan obtained his BSc, MSc in interdisciplinary sciences from the Department of Chemistry at ETH Zurich. He stayed at ETH for his PhD training at the Institute for Biochemistry and contributed to the initial development of LiP-MS as well as structural biomarkers for protein misfolding in the lab of Paola Picotti.
Before joining Biognosys in 2018, he was a postdoctoral researcher at the Stanford Genome Technology Center.”
<h3>Pushing the boundaries for robust and high-throughput single cell analysis with Whisper Flow technology powered by dia-PASEF</h3>
<h5>Presenter: Dorte Bekker-Jensen (Senior Scientist, Evosep Biosystems)</h5>
Dorte Bekker-Jensen is a senior scientist in the Application Development team at Evosep Biosystems. She works on technology development with a focus on developing simple and automated workflows for high-throughput proteomics.
<h3>Streamlined &amp; automated sample processing for in-depth proteomic analyses</h3>
<h5>Presenter: Dr. Garwin Pichler (Co-founder and CEO, Preomics)</h5>
Dr. Garwin Pichler is the co-founder and CEO of PreOmics.
Out of Matthias Mann&#39;s lab at the MPI for Biochemistry in Munich he started with Nils A. Kulak PreOmics based on their propriety iST technology in 2016.
PreOmics thereby is a company dedicated to setting the standard for protein analysis by offering highly efficient proteomic sample preparation solutions.
Dr. Pichler holds a PhD in Biochemistry from LMU Munich (Germany) and is responsible for Sales, Finances, Business Development, Investor Relationships and HR.

The Analytical Scientist: Mass Spec Technology Forum

Mass Spec Technology Forum

Our expert speakers will share their knowledge and experience, and also discuss the latest advances in the field.

Accurate reconstruction of metabolic pathways is an important prerequisite for interpreting metabolomics changes and understanding the diverse biological processes in disease models. A tracer-based metabolomics strategy utilizes stable isotope labeled precursors to resolve complex pathways by tracing the labeled atom(s) to downstream metabolites through enzymatic reactions. Isotope enrichment analysis is informative and achieved by counting total labeled atoms and acquiring the mass isotopologue distribution (MID) of the intact metabolite. However, quantitative analysis of labeled metabolite substructures/moieties can offer more valuable insights into the reaction connections through measuring metabolite transformation.
In this webinar, you will see how we developed a method that couples hydrophilic interaction liquid chromatography (HILIC) with Zeno trap-enabled high-resolution multiple reaction monitoring (MRMHR) in order to acquire the isotopic labeling information at the intact metabolite and moiety level simultaneously.
We will show the method performance of HILIC-Zeno MRMHR compared to that of the HILIC-SWATH and HILIC-general MRMHR with regards to the aspects of sensitivity, accuracy, and fragmentation reproducibility in MID analysis based on the measurement of 13C or 15N-labeled cellular samples.
Further method application will be demonstrated using a classic neuronal model of rotenone-induced neurodegeneration and reveal diverse flux regulations via glucose and glutamine metabolism into glutathione metabolism related to neurodegeneration.
<h5>By attending this presentation you will learn about:</h5>
<ul>
<li>utilizing the HILIC-Zeno MRMHR method for doing structurally-resolved mass isotopologue distribution analysis of metabolites</li>
<li>tracing the labeled 13C/15N atoms in the moieties of metabolite isotopologues to reconstruct the cell-type and condition-specific pathways of glutathione metabolism</li>
<li>quantitative isotopologue analysis to elucidate glutathione metabolism regulation at both metabolite and enzyme level</li>
</ul>
<blockquote>
Presenter: Luojiao Huang (Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden)
</blockquote>
<blockquote>
Luojiao Huang studied traditional Chinese pharmacy at China Pharmaceutical University, and obtained her BSc degree with honors in 2015. In 2018, she started her PhD work at Leiden University and during her research has developed a comprehensive analytical strategy for characterizing the metabolic activity related to PD neurodegeneration, tackling the current analytical challenges faced in selecting an appropriate polar stationary phase used in polar metabolome analysis, advancing the analytical method for tracer-based metabolome analysis, and developing a computational workflow for metabolic flux analysis.
</blockquote>

Separation Science: Understanding Metabolic Pathways Using Mass Isotopologue Analysis with HILIC Zeno MRM High-Resolution

Understanding Metabolic Pathways Using Mass Isotopologue Analysis with HILIC Zeno MRM High-Resolution

You will see how we developed a method that couples HILIC with Zeno trap-enabled MRMHR in order to acquire the isotopic labeling information.

Metabolic Pathways Using HILIC Zeno MRM High-Resolution

In extractables studies, LC/UV/MS is commonly used to detect and annotate the non-volatile fraction of compounds. Industry guidance and regulatory requirements indicate an analytical evaluation threshold (AET), above which compounds need to be identified to allow for toxicological risk assessment, requiring estimated quantitation before their identity is known. UV and MS detector response is known to vary for analytes, requiring the use of an uncertainty factor to account for difference in response relative to a reference standard at the AET.
In this webinar, we will discuss the challenges associated with these analyses and present strategies that can be deployed to reduce uncertainty in LC/MS extractable studies, including the combination of the three detection techniques in one system to allow the concurrent measurement of UV absorption, CAD signal, and high resolution-accurate mass (HRAM) mass spectra from one injection.
<h5>By attending this presentation you will learn about:</h5>
<ul>
<li>Ways to decrease analytical uncertainty in quantitation of unknown extractables by LC/MS</li>
<li>How incorporating UV, CAD, and MS in one system provides orthogonal detection based on different properties, increasing compound coverage and annotation confidence</li>
<li>How the universal response of the CAD detector, when used with the Vanquish Duo for inverse gradient system, enables semi-quantitation of unknown compounds against surrogate standards with lower uncertainty</li>
</ul>
<blockquote>
Presenter: Chongming Liu
</blockquote>
<blockquote>
Chongming Liu is currently a Supervisor in the Extractables and Leachables (E&amp;L) team at SGS Health Science in Fairfield, New Jersey, USA. At SGS, his daily responsibility is to assist the team members in performing E&amp;L testing on pharmaceutical containers and medical devices and to elucidate structures for compounds of interest based on high-resolution GC-FID/MS and LC-PDA/MS data. Prior to that, he joined the E&amp;L team at SGS in 2018 as an Instrumentation Chemist. Chongming holds a PhD degree in Analytical Chemistry from Stevens Institute of Technology, in Hoboken, New Jersey and a BSc degree in Chemistry from the University of Science and Technology of China (USTC), in Hefei, China.
</blockquote>
<blockquote>
Presenter: Sven Hackbusch
</blockquote>
<blockquote>
Sven Hackbusch is currently a Senior Application Scientist at Thermo Fisher Scientific, responsible for the development of LC/MS applications related to structural elucidation for and in collaboration with customers in the Pharma/Biopharma markets. He joined Thermo Fisher Scientific in 2017 as an Application Scientist in the LC/MS product demonstration laboratory, focusing on untargeted small molecule applications using Thermo Scientific Orbitrap technology. Sven holds a PhD in Pharmaceutical and Chemical Sciences from the University of the Pacific in Stockton, California, USA and a BSc in Chemistry from the Justus Liebig Universität Gießen in Gießen, Germany.
</blockquote>

Pixabay/Jan Felix Christiansen: Practical strategies to decrease uncertainty in comprehensive extractables and leachables analysis by LC/MS

Practical strategies to decrease uncertainty in comprehensive extractables and leachables analysis by LC/MS

We will discuss the challenges associated with these analyses and present strategies that can be deployed to reduce uncertainty in LC/MS extractable studies.

LCMS webinars focusing on LC/HRMS - page 41