Article

ProteoMeter: A pipeline for integrating multi-PTM and limited proteolysis data to reveal modification-structure coupling at the residue level

2025-07-18

Abstract excerpt

Systemic perturbations trigger extensive changes across the proteome–altering protein abundance, post-translational modifications (PTMs), conformational states, and complex assembly. Interpreting these effects demands computational pipelines capable of integrating diverse proteomics modalities, such as multi-PTM profiling, limited proteolysis mass spectrometry (LiP-MS), and cross-linking mass spectrometry (XL-MS),...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 48195c9a-ce62-5b52-a799-ed9b196ad65b
DOI: 10.1101/2025.07.14.664747

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

ProteoMeter: A pipeline for integrating multi-PTM and limited proteolysis data to reveal modification-structure coupling at the residue levelDOI 10.1101/2025.07.14.664747Read

HXMS: a standardized file format for HX-MS dataSemantic proximity Read

High Sensitivity Crosslink Detection Coupled With Integrative Structure Modeling in the Mass Spec Studio.Semantic proximity Read

ProteoSushi: a software tool to biologically annotate and quantify modification-specific, peptide-centric proteomics datasetsSemantic proximity Read

A peptide-centric local stability assay to unveil protein targets of diverse ligandsSemantic proximity Read

Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptidesSemantic proximity Read

The SysteMHC Atlas project.Semantic proximity Read

ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and PeptidomicsSemantic proximity Read

Integrated top-down and bottom-up mass spectrometry enables precise characterization of proteoforms and their post-translational modifications within the protein coronaSemantic proximity Read

SpecGlob: rapid and accurate alignment of mass spectra differing from their peptide models by several unknown modificationsSemantic proximity Read

Pyntheon: A Functional Analysis Framework for Protein Modifications and Mutations of 83 Model OrganismsSemantic proximity Read

Scop3P-Toolkit: executable structure-aware workflows linking PTMs, peptides, and mutations to protein functionSemantic proximity Read

Complex-centric proteome profiling by SEC-SWATH-MSSemantic proximity Read