ArticleNature biotechnology2015
A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides.
Article in Nature biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 197 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
197 citing papers in PubMed.
- PSMatch: An R/Bioconductor Package to Explore Proteomics Identification Data.Methods in molecular biology (Clifton, N.J.) · 2027Article
- ProteoRift Protocols: A Deep Learning Filtering Workflow for Peptide Identification in Mass Spectrometry Data.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Discovery of Post-Translationally Modified Epitopes in Autoimmunity: Someone Has to Fish so Everyone Can Eat.Immunological reviews · 2026Review
- Estimating protein isoform abundances with [Formula: see text].Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- CLASPP: A unified model for predicting post-translational modifications.PLoS computational biology · 2026Article
- Advancing proteomic discovery through optimized multi-stage scoring and deep learning-enhanced open search.Bioinformatics (Oxford, England) · 2026Article
- Characterizing the Effects of Protein Glycosylation Perturbation on Phosphorylation Signaling.Analytical chemistry · 2026Article
- A decision-driven framework for the mass spectrometry analysis of previously uncharacterized protein modifications.STAR protocols · 2026Review
- Integrated top-down and bottom-up proteomics enables precise characterization of proteoforms within the protein corona.Nature communications · 2026Article
- CLASPP: A unified model for predicting post-translational modifications.bioRxiv : the preprint server for biology · 2026Article
- pAnno: a comprehensive, precise, and fast proteogenomic workflow for the discovery of novel coding regions.Genome biology · 2026Article
- A Viral Mutation Profiling and Discovery Strategy for Sensitive Multiplex Detection of Viruses and Variants in Saliva by Proteomics.bioRxiv : the preprint server for biology · 2026Article
- In Depth Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2.Molecular & cellular proteomics : MCP · 2026Article
- A Framework for Database Search with AI Models in Mass Spectrometry-Based Proteomics.Journal of proteome research · 2026Review
- Identification of non-canonical peptides with moPepGen.Nature biotechnology · 2026Article
- Generalizable Direct Protein Sequencing With InstaNexus.Molecular & cellular proteomics : MCP · 2026Article
- Global Profiling of Post-Translationally Modified Crustacean Neuropeptidome Trends Affiliated with Feeding Activity.Journal of the American Society for Mass Spectrometry · 2026Article
- End-to-end deep attention-based multitask pipeline for predicting uncertainty-quantified peptide properties from mass spectrometry data.Scientific reports · 2026Article
- Navigating Challenges in Mass Spectrometry Analysis of Endogenous and Synthetic Protein Modifications.Biomolecules · 2026Review
- A New Detailed Mass Offset Search in MSFragger for Improved Interpretation of Complex PTMs.Journal of proteome research · 2026Article
137 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
- Erratum issued
- Erratum issued
Authors and funding
7 authors.
Funding
Abstract
Fewer than half of all tandem mass spectrometry (MS/MS) spectra acquired in shotgun proteomics experiments are typically matched to a peptide with high confidence. Here we determine the identity of unassigned peptides using an ultra-tolerant Sequest database search that allows peptide matching even with modifications of unknown masses up to ± 500 Da. In a proteome-wide data set on HEK293 cells (9,513 proteins and 396,736 peptides), this approach matched an additional 184,000 modified peptides, which were linked to biological and chemical modifications representing 523 distinct mass bins, including phosphorylation, glycosylation and methylation. We localized all unknown modification masses to specific regions within a peptide. Known modifications were assigned to the correct amino acids with frequencies >90%. We conclude that at least one-third of unassigned spectra arise from peptides with substoichiometric 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.