ArticleNature communications2025
MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- AURORA A interacts with DICER and SETD2 to promote S-phase progression.EMBO reports · 2026Article
- Targeted quantification assays for DNA repair and handling proteins and interactions in Huntington's disease models.bioRxiv : the preprint server for biology · 2026Article
- Degradomics for large-scale mechanistic insights on proteases and proteolysis in human health.The FEBS journal · 2026Review
- pmultiqc: An Open-Source, Lightweight, and Metadata-Oriented QC Reporting Library for MS Proteomics.Molecular & cellular proteomics : MCP · 2026Article
- A Framework for Database Search with AI Models in Mass Spectrometry-Based Proteomics.Journal of proteome research · 2026Review
- Rapid photo-crosslinking in living cells reveals protein-nucleic acid dynamics on a timescale of minutes.Nucleic acids research · 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
- Comparison of the Trapping Efficiency for Tryptic Peptides on Particle-Packed and Micro-Pillar Trap Columns for Proteomics Analyses.Proteomes · 2026Article
- Proximity labeling reveals non-catalytic interactions between DPP9 and ubiquitin signaling complexes.Cellular and molecular life sciences : CMLS · 2026Article
- Mass Spectrometry Proteomics: A Key to Faster Drug Discovery.Journal of medicinal chemistry · 2026Review
- Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.BMC bioinformatics · 2026Article
- Proteomic analysis of equine amniotic mesenchymal stromal cells and their extracellular vesicles: comparing their regenerative properties.Extracellular vesicles and circulating nucleic acids · 2026Article
- A subset of type 4 secretion system effectors ofmicroLife · 2026Article
- Article
- Data Processing and Analysis in Positional Proteomics.Proteomics · 2025Review
- Improving Proteomic Dynamic Range with Multiple Accumulation Precursor Mass Spectrometry.Journal of proteome research · 2025Article
- Plasma membrane recycling drives reservoir formation during Toxoplasma gondii intracellular replication.PLoS biology · 2025Article
- Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics.Nature communications · 2025Article
- Trends in Mass Spectrometry-Based Single-Cell Proteomics.Analytical chemistry · 2025Review
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3 authors.
Funding
Abstract
Liquid chromatography-mass spectrometry based proteomics, particularly in the bottom-up approach, relies on the digestion of proteins into peptides for subsequent separation and analysis. The most prevalent method for identifying peptides from data-dependent acquisition mass spectrometry data is database search. Traditional tools typically focus on identifying a single peptide per tandem mass spectrum, often neglecting the frequent occurrence of peptide co-fragmentations leading to chimeric spectra. Here, we introduce MSFragger-DDA+, a database search algorithm that enhances peptide identification by detecting co-fragmented peptides with high sensitivity and speed. Utilizing MSFragger's fragment ion indexing algorithm, MSFragger-DDA+ performs a comprehensive search within the full isolation window for each tandem mass spectrum, followed by robust feature detection, filtering, and rescoring procedures to refine search results. Evaluation against established tools across diverse datasets demonstrated that, integrated within the FragPipe computational platform, MSFragger-DDA+ significantly increases identification sensitivity while maintaining stringent false discovery rate control. It is also uniquely suited for wide-window acquisition data. MSFragger-DDA+ provides an efficient and accurate solution for peptide identification, enhancing the detection of low-abundance co-fragmented peptides. Coupled with the FragPipe platform, MSFragger-DDA+ enables more comprehensive and accurate analysis of proteomics data.
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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.