ArticleProteomics2020
Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.
Article in Proteomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Single-cell mapping of alternative splicing linked to checkpoint immunotherapy response.Nucleic acids research · 2025Article
- MHCquant2 refines immunopeptidomics tumor antigen discovery.Genome biology · 2025Article
- Monitoring Functional Posttranslational Modifications Using a Data-Driven Proteome Informatic Pipeline.Proteomics · 2025Article
- Dear-PSM: A deep learning-based peptide search engine enables full database search for proteomics.Smart medicine · 2024Article
- Prediction of glycopeptide fragment mass spectra by deep learning.Nature communications · 2024Article
- Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery.Journal for immunotherapy of cancer · 2023Review
- SeqWiz: a modularized toolkit for next-generation protein sequence database management and analysis.BMC bioinformatics · 2023Article
- Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.Journal of proteome research · 2023Review
- The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.Journal of proteome research · 2023Article
- Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.Journal of proteome research · 2023Article
- Identification of tumor antigens with immunopeptidomics.Nature biotechnology · 2022Review
- The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource.The Plant cell · 2021Article
- Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project.Journal of proteome research · 2020Article
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Authors and funding
2 authors.
Funding
Abstract
Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard for the representation of sequence databases used as input to sequence database search tools is the FASTA format. The Human Proteome Organization's Proteomics Standards Initiative has developed an extension to the FASTA format termed the proteomics standards initiative extended FASTA format or PSI extended FASTA format (PEFF) where additional information such as structural annotations are encoded in the protein description lines. Comet has been extended to automatically analyze the post translational modifications and amino acid substitutions encoded in PEFF databases. Comet's PEFF implementation and example analysis results searching a HEK293 dataset against the neXtProt PEFF database are presented.
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