[ASAP] Residue-Level Determination of Small-Molecule–Protein Affinities by Hydrogen–Deuterium Exchange Mass Spectrometry Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00020

(JASMS) [ASAP] Residue-Level Determination of Small-Molecule–Protein Affinities by Hydrogen–Deuterium Exchange Mass Spectrometry: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00020 (RSS) #MassSpecRSS #JASMS

Hey, #TeamMassSpec! Before you register for San Diego, there’s one step to check off:
Renew your #ASMS membership! It unlocks member rates for the conference and short courses, as well as access to #JASMS and member resources.

Get set for 2026 here: https://bit.ly/47dOKI2

Hey, #TeamMassSpec! Before you register for San Diego, there’s one step to check off:
Renew your #ASMS membership! It unlocks member rates for the conference and short courses, as well as access to #JASMS and member resources.

Get set for 2026 here: https://bit.ly/47dOKI2

[ASAP] Mass Spectrometric Determination of Site-Specific O-Acetylation in Rhamnogalacturonan I Oligomers Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00440

(JASMS) [ASAP] Mass Spectrometric Determination of Site-Specific O-Acetylation in Rhamnogalacturonan I Oligomers: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00440 (RSS) #MassSpecRSS #JASMS

Dr. Ryan Julian will join the #JASMS team as Associate Editor on April 1. He takes over from longtime Associate Editor Facundo Fernandez.

Learn more about JASMS: https://pubs.acs.org/journal/jamsef

#ASMS #TeamMassSpec #JASMS

Dr. Ryan Julian will join the #JASMS team as Associate Editor on April 1. He takes over from longtime Associate Editor Facundo Fernandez.

Learn more about JASMS: https://pubs.acs.org/journal/jamsef

#ASMS #TeamMassSpec #JASMS

[ASAP] Faces of Mass Spectrometry/Jane Gale Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00090

(JASMS) [ASAP] Faces of Mass Spectrometry/Jane Gale: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00090 (RSS) #MassSpecRSS #JASMS

[ASAP] Investigating the Efficiency of Ultraviolet Photodissociation in Peptides Modified with N-Terminal UV-Absorbing Chromophores Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00389

(JASMS) [ASAP] Investigating the Efficiency of Ultraviolet Photodissociation in Peptides Modified with N-Terminal UV-Absorbing Chromophores: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00389 (RSS) #MassSpecRSS #JASMS

[ASAP] In Situ GCIB Cryo-Sectioning Enables Subcellular Cryo-ToF-SIMS Imaging of Arabidopsis Seeds Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00420

(JASMS) [ASAP] In Situ GCIB Cryo-Sectioning Enables Subcellular Cryo-ToF-SIMS Imaging of Arabidopsis Seeds: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00420 (RSS) #MassSpecRSS #JASMS

Investigating the Protonated Cannabinoid Dimer Detected in the Forensic Analysis of Cannabis by DART-MS: A Combined Mass Spectrometry and Computational Study Direct analysis in real time–high-resolution mass spectrometry (DART-HRMS) enables the rapid chemical profiling of Cannabis samples. This approach reveals a prominent signal at nominal m/z 315, charac...

Investigating the Protonated Cannabinoid Dimer Detected in the Forensic Analysis of Cannabis by DART-MS: A Combined Mass Spectrometry and Computational Study #JASMS pubs.acs.org/doi/10.1021/...

[ASAP] Investigating the Protonated Cannabinoid Dimer Detected in the Forensic Analysis of Cannabis by DART-MS: A Combined Mass Spectrometry and Computational Study Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00433

(JASMS) [ASAP] Investigating the Protonated Cannabinoid Dimer Detected in the Forensic Analysis of Cannabis by DART-MS: A Combined Mass Spectrometry and Computational Study: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00433 (RSS) #MassSpecRSS #JASMS

[ASAP] Mapping the Spatial Distribution of Tryptic Peptides in Formalin-Fixed Paraffin-Embedded Tissues Using Desorption Electrospray Ionization Mass Spectrometry Imaging Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00359

(JASMS) [ASAP] Mapping the Spatial Distribution of Tryptic Peptides in Formalin-Fixed Paraffin-Embedded Tissues Using Desorption Electrospray Ionization Mass Spectrometry Imaging: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00359 (RSS) #MassSpecRSS #JASMS

[ASAP] Scalable Bayesian Estimation of Multicondition Omics Networks via Clustering and Iterative Merging Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00447

(JASMS) [ASAP] Scalable Bayesian Estimation of Multicondition Omics Networks via Clustering and Iterative Merging: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00447 (RSS) #MassSpecRSS #JASMS

[ASAP] Global Profiling of Post-Translationally Modified Crustacean Neuropeptidome Trends Affiliated with Feeding Activity Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00017

(JASMS) [ASAP] Global Profiling of Post-Translationally Modified Crustacean Neuropeptidome Trends Affiliated with Feeding Activity: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00017 (RSS) #MassSpecRSS #JASMS

Mapping the Spatial Distribution of Tryptic Peptides in Formalin-Fixed Paraffin-Embedded Tissues Using Desorption Electrospray Ionization Mass Spectrometry Imaging Spatial proteomics visualizes protein localization within native cellular and tissue environments, providing critical insights into pathological processes, tissue heterogeneity, and diagnostic biomarkers. Mass spectrometry imaging (MSI) has emerged as a powerful tool for spatial proteomics, with matrix-assisted laser desorption/ionization (MALDI)-MSI being the most widely used platform. Recently, desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) has been explored for mapping proteins and peptides in tissue sections, with distinct sets of proteins detected compared to MALDI MSI. However, current studies have focused on fresh-frozen tissues, and the application of DESI-MSI to formalin-fixed paraffin-embedded (FFPE) tissues, the predominant form of clinical specimens, remains unexplored. Here, we report the optimization and application of DESI-MSI for proteomic analysis of FFPE tissues. Sample pretreatment procedures and DESI parameters were systematically optimized using FFPE mouse brain tissue sections to enhance tryptic peptide detection. The optimized workflow was further applied to FFPE canine melanocytoma tissue to discover protein biomarkers. Protein identification was performed using nanoLC-MS/MS. Overall, we demonstrate the potential of DESI-MSI as a platform for spatial proteomic analysis of FFPE tissues, expanding its applicability to archived clinical specimens.

Mapping the Spatial Distribution of Tryptic Peptides in Formalin-Fixed Paraffin-Embedded Tissues Using Desorption Electrospray Ionization Mass Spectrometry Imaging #JASMS pubs.acs.org/doi/10.1021/...

Global Profiling of Post-Translationally Modified Crustacean Neuropeptidome Trends Affiliated with Feeding Activity Neuropeptides modulate a diverse range of physiological functions, including those associated with feeding. Post-translational modifications (PTMs) contribute significantly to the dynamic nature of neuropeptide isoforms, influencing their functional diversity. Mass spectrometry is the gold-standard analytical technique for peptidomic analyses and is complemented by computational methods for peptide identification; however, the computational search space becomes increasingly difficult to manage as more potential modifications are considered. Using innovative approaches capable of addressing the vast combinations of possible modifications, such as the PEAKS PTM search algorithm, we globally profiled the neuropeptidome ofCancer borealis(Jonah crab) to investigate the role of PTMs in feeding- and appetite-related processes over time. Through an in-depth examination of several notable modifications, we proposed PTM-associated motifs for neuropeptides, which may enhance future identification capabilities. Furthermore, this work revealed neuropeptides that were characteristically modified depending on the crab’s feeding status and time post-feeding, suggesting potential biological significance. This study represents the first large-scale investigation of the modified crustacean neuropeptidome, providing new insights into the regulatory implications of PTMs in biological systems.

Global Profiling of Post-Translationally Modified Crustacean Neuropeptidome Trends Affiliated with Feeding Activity #JASMS pubs.acs.org/doi/10.1021/...

Development of Low-Flow High-Resolution Desorption Electrospray Ionization Mass Spectrometry Imaging Desorption electrospray ionization mass spectrometry (DESI-MS) imaging is a well-established technique for molecular analysis of biological samples, although its spatial resolution has been limited when compared to other MS imaging techniques. Here, we...

Catch up on trending research! Read more: Development of Low-Flow High-Resolution Desorption Electrospray Ionization Mass Spectrometry Imaging https://bit.ly/3N2pVsm

#ASMS #JASMS #TeamMassSpec #MassSpec

Development of Low-Flow High-Resolution Desorption Electrospray Ionization Mass Spectrometry Imaging Desorption electrospray ionization mass spectrometry (DESI-MS) imaging is a well-established technique for molecular analysis of biological samples, although its spatial resolution has been limited when compared to other MS imaging techniques. Here, we...

Catch up on trending research! Read more: Development of Low-Flow High-Resolution Desorption Electrospray Ionization Mass Spectrometry Imaging https://bit.ly/3N2pVsm

#ASMS #JASMS #TeamMassSpec #MassSpec

[ASAP] Evaluating the Sulfo-Phospho-Vanillin Assay for Total Lipid Sample Normalization as Compared to Gravimetric and Protein Sample Normalization Methods for Untargeted Lipidomic LC–MS/MS Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00429

(JASMS) [ASAP] Evaluating the Sulfo-Phospho-Vanillin Assay for Total Lipid Sample Normalization as Compared to Gravimetric and Protein Sample Normalization Methods for Untargeted Lipidomic LC–MS/MS: Journal of the American Society for Mass SpectrometryDOI:… (RSS) #MassSpecRSS #JASMS

[ASAP] A Universal Buffer System for Native LC–MS Analysis of Antibody-Based Therapeutics Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00028

(JASMS) [ASAP] A Universal Buffer System for Native LC–MS Analysis of Antibody-Based Therapeutics: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00028 (RSS) #MassSpecRSS #JASMS

Evaluating the Sulfo-Phospho-Vanillin Assay for Total Lipid Sample Normalization as Compared to Gravimetric and Protein Sample Normalization Methods for Untargeted Lipidomic LC–MS/MS Sample normalization is essential for lipid quantitation. While normalization methods involving pre- or postgravimetric measurements, counting, or protein prequantitation exist, a single, common sample normalization method is not widely accepted. Previously, we proposed and evaluated the sulfo-phospho-vanillin assay (SPVA), a total lipid quantitation reaction, for prequantifying total lipids for LC–MS/MS sample normalization purposes. This current investigation furthers our evaluation of the SPVA as a sample normalization method in untargeted lipidomic LC–MS/MS by comparing SPVA total lipid prequantitation to protein prequantitation and gravimetric measurements. This study was applied to a wide selection of matrices, including Escherichia coli, plasma, brain, heart, and kidney. Resulting relative lipid concentrations showed smaller bioreplica variation when a prequantitation method was applied, either measuring total lipid or total protein; however, several relative lipid abundances showed inverse concentration relationships when normalizing with total protein compared to total lipid (from SPVA measurements) or gravimetric sample normalization. Further investigation using lipid extracts linearly spiked with pure, non-native lipid showed that gravimetric and protein normalization nonlinearly overproduced significant lipids, while linear increases in significant lipid features were observed from SPVA normalization. Lipid extracts linearly spiked with pure, non-native protein yielded fewer significant lipid features using SPVA normalization, and this was unchanged as protein was added; however, both gravimetric and protein normalization continued to yield large numbers of significant lipid features. Together, these results suggest neither gravimetric nor protein sample normalization appropriately normalizes quantitative lipidomic experiments and greatly overgenerates statistically significant lipid features for biomarker investigation. SPVA normalization more accurately adjusts for lipid changes in bioreplicate samples, leading to fewer but more biologically relevant statistically significant lipid features.

Evaluating the Sulfo-Phospho-Vanillin Assay for Total Lipid Sample Normalization as Compared to Gravimetric and Protein Sample Normalization Methods for Untargeted Lipidomic LC–MS/MS #JASMS pubs.acs.org/doi/10.1021/...

A Universal Buffer System for Native LC–MS Analysis of Antibody-Based Therapeutics Liquid chromatography coupled to mass spectrometry (LC–MS) is a powerful analytical technique for analyzing biological macromolecules. A long-standing challenge has been applying LC–MS at physiological pH under native conditions using volatile buffers. The predominant “buffer” used, ammonium acetate (AmAc, pKa 4.75 for acetic acid and 9.25 for ammonium), does not offer sufficient buffering capacity in the physiological pH range of 7.0–7.4. To address this, we evaluated a set of fluorinated ethylamines, 2-fluoroethylamine (MFEA), 2,2-difluoroethylamine (DFEA), and 2,2,2-trifluoroethylamine (TFEA), producing conjugate acids with pKa values of 8.9, 7.2, and 5.5, respectively, that together provide buffering across the 4.5–9.8 pH range. We show that protein separations on strong cation- and anion-exchange resins in these volatile mobile phases perform comparably to traditional nonvolatile buffers, with similar elution profiles and analyte elution ranking, albeit with slightly broader peaks. Using fully volatile gradients of pH or ionic strength, we chromatographically resolved charge variants of protein analytes such as mAbs and bovine serum albumin. For many of the eluting LC peaks, we obtained high-resolution mass spectra capable of resolving glycoforms of antibodies. Hydrophobic interaction chromatography (HIC) in volatile mobile phases preserved native separation order and further resolved drug-to-antibody ratio (DAR) species of the antibody-drug conjugate brentuximab-vedotin. For each chromatography modality we further compare innovator and biosimilar antibodies, demonstrating the reproducibility of results in the proposed volatile compounds. Together, our results establish fluorinated ethylamines, in combination with ammonium acetate, as a universal volatile buffer system for native LC–MS, broadly applicable across major chromatographic modalities.

A Universal Buffer System for Native LC–MS Analysis of Antibody-Based Therapeutics #JASMS pubs.acs.org/doi/10.1021/...

A Miniature Ion Trap Particle Mass Spectrometer with an Integrated Optical and Charge Detection System A miniature ion trap particle mass spectrometer with both optical and charge detection systems was constructed in this work. The instrument was initially constructed with an open architecture and mounted on a 600 × 450 mm optical bench. With further compact integration, the system can be accommodated within an aluminum enclosure with dimensions of 333 × 221 × 192 mm and a total mass of approximately 8 kg. In the optical detection mode, the stationary star pattern ion motion was observed by detecting the scattered light, and the m/Z value of the particle ion was calculated accurately. In the charge detection mode, the particle m/Z value, the charge number Z, and the particle mass were determined quickly. These two working modes can be switched freely. By using 3 μm polystyrene size standards and mice red blood cells as the sample, the feasibility of this instrument was demonstrated.

A Miniature Ion Trap Particle Mass Spectrometer with an Integrated Optical and Charge Detection System #JASMS pubs.acs.org/doi/10.1021/...

Dissecting Metabolic Rewiring and Gene-Metabolite Interactions by Utilizing Untargeted Metabolomics and Single-Gene Knockouts in the Model Microorganism E. coli Central carbon metabolism, comprising glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway (PPP), is essential for Escherichia coli survival and growth. While disruptions in these pathways are known to affect cellular physiology, the system-wide metabolite-level consequences of single-gene knockouts remain incompletely understood. Using untargeted LC-MS metabolomics, we systematically profiled E. coli knockouts of TCA core enzymes, isoforms, subunits, bypass routes, and TCA-associated pathways. Core TCA knockouts separated into two major metabolic clusters, with cluster 1 strains displaying strong divergence in amino acid metabolism and cluster 2 retaining partial similarity to the parent strain. Isoform-specific deletions revealed differential roles of aconitases (ΔacnA vs ΔacnB) and fumarases (ΔfumA vs ΔfumC), while subunit knockouts of 2-oxoglutarate dehydrogenase (ΔsucA, ΔsucB) and succinate dehydrogenase (ΔsdhA-D) produced localized but distinct metabolite shifts, particularly around glutamate- and 2-oxoglutarate-linked metabolism. Bypass enzyme deletions (ΔaceA, ΔaceB, ΔglcB, and ΔmaeB) disrupted carbohydrate- and redox-related metabolites, underscoring their role as metabolic safety nets. Importantly, knockouts also triggered off-target effects in glycolysis, PPP, and the electron transport chain, highlighting the interconnectivity of central carbon metabolism. Our systematic approach demonstrated the possibility of utilizing comprehensive and untargeted metabolomics to map gene-metabolite associations and decipher potential metabolic interlinks.

Dissecting Metabolic Rewiring and Gene-Metabolite Interactions by Utilizing Untargeted Metabolomics and Single-Gene Knockouts in the Model Microorganism E. coli #JASMS pubs.acs.org/doi/10.1021/...

[ASAP] Dissecting Metabolic Rewiring and Gene-Metabolite Interactions by Utilizing Untargeted Metabolomics and Single-Gene Knockouts in the Model Microorganism E. coli Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00454

(JASMS) [ASAP] Dissecting Metabolic Rewiring and Gene-Metabolite Interactions by Utilizing Untargeted Metabolomics and Single-Gene Knockouts in the Model Microorganism E. coli: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00454 (RSS) #MassSpecRSS #JASMS

[ASAP] A Miniature Ion Trap Particle Mass Spectrometer with an Integrated Optical and Charge Detection System Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00399

(JASMS) [ASAP] A Miniature Ion Trap Particle Mass Spectrometer with an Integrated Optical and Charge Detection System: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00399 (RSS) #MassSpecRSS #JASMS

Higher-Energy Collisional Dissociation Mass Spectrometry Fragmentation Enables Distinguishing O-GlcNAc from Tn Antigen in Cancer Cells Protein glycosylation plays essential roles in various biological processes, and thus determining the glycan structure present on the protein is essential to comprehensively understand these events. However, distinguishing saccharide stereoisomers is ch...

Selected as #ACS Editors’ Choice and free for a limited time!

This #JASMS paper demonstrates how HCD MS can distinguish O-GlcNAc from the Tn antigen in cancer cells, advancing glycoproteomics research.

Read it while it’s free: https://pubs.acs.org/doi/10.1021/jasms.5c00378

A Computational Model for Determining Labeling Duration in Protein Turnover Studies Using a Single Deuterated Water Labeled Sample The time course of metabolic labeling using deuterated water, followed by liquid chromatography coupled with mass spectrometry, is employed to investigate the turnover rates of individual proteins in vivo. These labeling experiments are resource intensive. Computational methods that can determine turnover rates from a single and labeled for a short duration sample will help reduce these demands. We evaluated linear and logarithmic models to estimate protein turnover rates based on two samples (one nonlabeled and one labeled). Key factors such as the number of exchangeable hydrogens, body water enrichment in deuterium, protein turnover rate, and necessary changes in monoisotopic relative abundance established a range of labeling durations for the two-sample approach. We provide two inequalities that formally define this range of labeling duration for each peptide, which is integrated into an R Shiny App. We applied this two-sample approach to four murine tissues. By adjusting the labeling duration according to the turnover of the tissue proteome, the two-sample approach was able to analyze over 60% (1221 murine liver proteins) of the proteome previously assessed using a multisample approach.

A Computational Model for Determining Labeling Duration in Protein Turnover Studies Using a Single Deuterated Water Labeled Sample #JASMS pubs.acs.org/doi/10.1021/...

Faces of Mass Spectrometry/Chris Crittenden

Faces of Mass Spectrometry/Chris Crittenden #JASMS pubs.acs.org/doi/10.1021/...

[ASAP] Faces of Mass Spectrometry/Chris Crittenden Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00074

(JASMS) [ASAP] Faces of Mass Spectrometry/Chris Crittenden: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00074 (RSS) #MassSpecRSS #JASMS