ArticleNature methods2017
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,424 papers, 1 of them a synthesis that pooled it.
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Who cites it
1,424 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An AI-Ready Phosphorylation Meta-Analysis forJournal of proteome research · 2026Pooled it
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- Software Pipelines for Targeted and Untargeted Proteomics in Bioengineering Applications.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Integrated Analysis of Posttranslational Modifications and Total Proteome: Methods for Distinguishing Abundance from Usage Changes.Methods in molecular biology (Clifton, N.J.) · 2027Article
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- Implementation of Nonisobaric TMT Analogs for Accurate Precursor-Level Quantification by plexDIA.Rapid communications in mass spectrometry : RCM · 2026Article
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- Chemogenetic activation of mitochondria counteracts the Warburg effect in tumor cells.Nature chemical biology · 2026Article
- MassNet: billion-scale AI-ready mass spectral corpus empowering scalable deep learning in proteomics.Nature methods · 2026Article
- Mammalian MemPrep establishes the lipid composition of ER membranes in HEK293T cells.EMBO reports · 2026Article
- Unbiased plasma proteomics reveals hemolysis during ADAMTS13 relapse in patients with immune TTP.Blood advances · 2026Article
- Optimized Sample Handling Minimizes Peptide Adsorption to Plastics to Enable High Sensitivity Evosep Based Chemical Proteomics.Proteomics · 2026Article
- Distribution of Big Tau Isoforms in the Human Central and Peripheral Nervous System.Annals of neurology · 2026Article
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- Bacterial stress responses lower mRNA-protein level correlations.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Estimating protein isoform abundances with [Formula: see text].Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Large-scale discovery platform enables identification of peptides targeting drug-resistant candidiasis.Cell reports methods · 2026Article
1,364 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
There is a need to better understand and handle the 'dark matter' of proteomics-the vast diversity of post-translational and chemical modifications that are unaccounted in a typical mass spectrometry-based analysis and thus remain unidentified. We present a fragment-ion indexing method, and its implementation in peptide identification tool MSFragger, that enables a more than 100-fold improvement in speed over most existing proteome database search tools. Using several large proteomic data sets, we demonstrate how MSFragger empowers the open database search concept for comprehensive identification of peptides and all their modified forms, uncovering dramatic differences in modification rates across experimental samples and conditions. We further illustrate its utility using protein-RNA cross-linked peptide data and using affinity purification experiments where we observe, on average, a 300% increase in the number of identified spectra for enriched proteins. We also discuss the benefits of open searching for improved false discovery rate estimation in proteomics.
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