Lipid-trap mass spectrometry identifies lipid–protein interactions in cells - Nature Cell Biology

Paquola et al. present a technique named lipid-trap mass spectrometry (LTMS) to study lipid–protein interactions directly captured from mammalian cells.

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Reminiscence on Renato Zenobi by Pablo Sinues

Mass Spectrometry Reviews, EarlyView.

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A Special Issue of Mass Spectrometry Reviews to Honor Professor Renato Zenobi: A Lifetime of Mentorship and Innovation in Mass Spectrometry

Mass Spectrometry Reviews, EarlyView.

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GlyComboCLI enables command line-based FAIR workflows for glycan composition assignment in mass spectrometry data

Glycans are integral biomolecules whose presence cannot be predicted from genomic data alone, necessitating experimental characterisation through approaches including mass spectrometry. Assignment of glycan compositions to observed mass to charge ratios is computationally challenging due to the potential monosaccharide diversity and existing tools lack the required flexibility for integration into automated bioinformatic workflows. Here, we present GlyComboCLI, an open-source command-line application for the assignment of glycan compositions to mass spectrometry data which expands upon our previous GUI application, GlyCombo. GlyComboCLI accepts mass lists and vendor-neutral mzML files, supports an extensive range of monosaccharides, derivatisation states, reducing-end modifications, and adducts to ensure compatibility with a breadth of glycomics approaches. Outputs are compatible with downstream tools including Skyline and GlycoWorkBench. This software is deployable as a standalone executable, a Docker container, and a Galaxy tool, adhering to FAIR principles. When applied to 52 raw files from a published mouse glycomics dataset, a local instance completed composition assignment and downstream quality control in under three hours, recovering biologically consistent findings. Furthermore, an integrated Galaxy workflow demonstrated reproducible detection of sialidase treatment effects. GlyComboCLI substantially reduces the pool of spectra requiring manual structural interpretation, offering a flexible and scalable solution for glycomics bioinformatic workflows.

dlvr.it

SpecGP as a transformer-based model for predicting energy-adaptable structural spectra of glycopeptides - Nature Machine Intelligence

SpecGP enhances fragment ion coverage to enable the prediction of N-glycopeptide structural spectra across diverse collision energies, thereby improving isomer discrimination and boosting identification confidence through rescoring.

dlvr.it

Structural promiscuity in the human circulatory IgA1 clonal repertoire | PNAS

Immunoglobulin A (IgA) is the most abundant antibody in humans, with high concentrations in both mucosae/secretions and circulation. While mucosal ...

pnas.org

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A nature-inspired ion trap for parallel manipulation of ions on a massive scale

A nature-inspired ion trap enabling massively parallel mass spectrometry.

science.org

Editorial for the Special Honor Issue Honoring Dr. Carlito B. Lebrilla

Mass Spectrometry Reviews, EarlyView.

dlvr.it

doi.org

Integration of alternative fragmentation techniques into standard LC-MS workflows using a single deep learning model enhances proteome coverage - Nature Methods

An integrated mass spectrometry platform enabling automated collision-, electron- and photon-based fragmentation techniques is presented. A deep learning-based model trained to predict spectra across ...

nature.com

Steve Brunton

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First 20 Years of Orbitrap Mass Spectrometry as the Mainstream Analytical Technique

This review traces the first 20 years of Orbitrap mass spectrometry as a mainstream high‑resolution and accurate‑mass (HR/AM) technology. It outlines the historical development of the Orbitrap analyz...

analyticalsciencejournals.onlinelibrary.wiley.com

Mobilion Demonstrates Feasibility of SLIM Ion Mobility for Proteomics

In a pair of preprints, researchers used the technology for quadrupole-free mass spec-based experiments, an approach that could boost speed and sensitivity.

genomeweb.com

Deep coverage and extended sequence reads obtained with a single archaeal protease expedite de novo protein sequencing by mass spectrometry

Highly efficient hyperthermal acidic proteases combined with hybrid-fragmentation schemes provide five times more unique peptide reads than trypsin or chymotrypsin, greatly boosting confidence in de n...

cell.com

NVMS

Nederlandse Vereniging voor Massaspectrometrie

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A Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics

Accurate and comprehensive peptide spectrum annotation is a crucial step to interpreting mass spectrometry-based proteomics data. While peak assignment in peptide fragmentation spectra is central to a...

pubs.acs.org

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

Mass spectrometry (MS)-based proteomics is a well-established strategy for analyzing complex biological mixtures. Many MS instruments and data acquisition strategies are available, and the data they a...

biorxiv.org

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NVMS

Nederlandse Vereniging voor Massaspectrometrie

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Thermal Tracks: A Gaussian process-based framework for universal melting curve analysis enabling unconstrained hit identification in thermal proteome profiling experiments

Thermal Tracks is a Python-based statistical framework for analyzing protein thermal stability data that overcomes key limitations of existing thermal proteome profiling (TPP) work-flows. Unlike stand...

arxiv.org

NVMS Fall Meeting 2025 – Program Announced! - NVMS

We are pleased to share the full program for the upcoming NVMS Fall Meeting, taking place on Wednesday, November 19, 2025, at the House of Connections in Groningen.

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