ArticleNature communications2023
Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 206 papers.
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Who cites it
206 citing papers in PubMed.
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- A single-amino-acid cleavage controls global mitochondrial complex integrity.Nature structural & molecular biology · 2026Article
- Multi-Modal Kinome Profiling Discovers Mesenchymal-Like Polarity Networks that Underly Directed Hepatocellular Carcinoma Cell Migration.bioRxiv : the preprint server for biology · 2026Article
- LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery.bioRxiv : the preprint server for biology · 2026Article
- Engineering editopes through programmable RNA editing toward tumor neoantigen generation.The EMBO journal · 2026Article
- Micro- and Macro-Heterogeneity of N-Glycoproteome Remodeling in Endoplasmic Reticulum Stress.Molecular & cellular proteomics : MCP · 2026Article
- A Spatiotemporal Atlas of the Androgen Receptor Proximal Interactome.bioRxiv : the preprint server for biology · 2026Article
- Differential lipid selectivity of StARD phospholipid transporters revealed by native MS.Nature communications · 2026Article
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- Integrated network pharmacology, transcriptomics and proteomics unveils the mechanisms of Forsythiae Fructus against acute lung injury.Die Naturwissenschaften · 2026Article
- An adipocyte-endothelial framework linking adipose tissue inflammation to cardiometabolic vulnerability in obesity.Research square · 2026Article
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- Beyond Sequence: Posttranslational Remodeling of Antigens in Autoimmunity.Immunological reviews · 2026Review
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146 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we present a fast and sensitive approach for direct peptide identification from DIA data, MSFragger-DIA, which leverages the unmatched speed of the fragment ion indexing-based search engine MSFragger. Different from most existing methods, MSFragger-DIA conducts a database search of the DIA tandem mass (MS/MS) spectra prior to spectral feature detection and peak tracing across the LC dimension. To streamline the analysis of DIA data and enable easy reproducibility, we integrate MSFragger-DIA into the FragPipe computational platform for seamless support of peptide identification and spectral library building from DIA, data-dependent acquisition (DDA), or both data types combined. We compare MSFragger-DIA with other DIA tools, such as DIA-Umpire based workflow in FragPipe, Spectronaut, DIA-NN library-free, and MaxDIA. We demonstrate the fast, sensitive, and accurate performance of MSFragger-DIA across a variety of sample types and data acquisition schemes, including single-cell proteomics, phosphoproteomics, and large-scale tumor proteome profiling studies.
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