ArticleMolecular & cellular proteomics : MCP2023
MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics.
Article in Molecular & cellular proteomics : MCP, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 40 citations in OpenAlex.
- NuXLApp: Interactive data analysis and visualization for protein-nucleic acid crosslinking mass spectrometry.Protein science : a publication of the Protein Society · 2026Article
- Alveolar Cytochrome P450 Mediates Butylated Hydroxytoluene-Induced Electrophilic Injury and Apoptosis.bioRxiv : the preprint server for biology · 2026Article
- CLASPP: A unified model for predicting post-translational modifications.PLoS computational biology · 2026Article
- Harnessing Tumor-Specific Transcript Diversity Uncovers a Shared Neoantigen Reservoir for Pancreatic Ductal Adenocarcinoma.MedComm · 2026Article
- Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics.Nature chemistry · 2026Article
- Article
- A comprehensive landscape of human organ N-glycoproteome.Nature communications · 2026Article
- CLASPP: A unified model for predicting post-translational modifications.bioRxiv : the preprint server for biology · 2026Article
- Improved Peptide Search for Identification of SUMO and Sequence-Based Modifiers, in MaxSBM.Molecular & cellular proteomics : MCP · 2026Article
- End-to-end deep attention-based multitask pipeline for predicting uncertainty-quantified peptide properties from mass spectrometry data.Scientific reports · 2026Article
- Quantitative Mapping of NHS Ester-Protein Reactivity Using Native Top-Down Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2026Article
- Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.Nature communications · 2026Article
- Navigating Challenges in Mass Spectrometry Analysis of Endogenous and Synthetic Protein Modifications.Biomolecules · 2026Review
- High-throughput chemical proteomics workflow for profiling protein citrullination dynamics.Nature communications · 2026Article
- A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs.Journal of proteome research · 2026Article
- Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.Nucleic acids research · 2025Article
- Dynamic Changes in Antibodies and Proteome in Breast Milk of Mothers Infected with Wild-Type SARS-CoV-2 and Omicron: A Longitudinal Study.Nutrients · 2025Article
- MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search.Nature communications · 2025Article
- Quantitative proteome-wide O-glycoproteomics analysis with FragPipe.Analytical and bioanalytical chemistry · 2025Article
- diaTracer enables spectrum-centric analysis of diaPASEF proteomics data.Nature communications · 2025Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Posttranslational modifications of proteins play essential roles in defining and regulating the functions of the proteins they decorate, making identification of these modifications critical to understanding biology and disease. Methods for enriching and analyzing a wide variety of biological and chemical modifications of proteins have been developed using mass spectrometry-based proteomics, largely relying on traditional database search methods to identify the resulting mass spectra of modified peptides. These database search methods treat modifications as static attachments of a mass to particular position in the peptide sequence, but many modifications undergo fragmentation in tandem mass spectrometry experiments alongside, or instead of, the peptide backbone. While this fragmentation can confound traditional search methods, it also offers unique opportunities for improved searches that incorporate modification-specific fragment ions. Here, we present a new labile mode in the MSFragger search engine that provides the flexibility to tailor modification-centric searches to the fragmentation observed. We show that labile mode can dramatically improve spectrum identification rates of phosphopeptides, RNA-crosslinked peptides, and ADP-ribosylated peptides. Each of these modifications presents distinct fragmentation characteristics, showcasing the flexibility of MSFragger labile mode to improve search for a wide variety of biological and chemical modifications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.