ArticleJournal of proteome research2019
Proteomics Standards Initiative Extended FASTA Format.
Article in Journal of proteome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed.
- Proteoform medicine: characterizing and targeting protein forms in human disease.Nature reviews. Genetics · 2026Review
- Structural information in therapeutic peptides: Emerging applications in biomedicine.FEBS open bio · 2025Review
- ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs.Briefings in bioinformatics · 2024Article
- Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity.Nature communications · 2024Article
- Article
- SeqWiz: a modularized toolkit for next-generation protein sequence database management and analysis.BMC bioinformatics · 2023Article
- Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.Journal of proteome research · 2023Article
- The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.Journal of proteome research · 2023Article
- Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.Journal of proteome research · 2023Review
- Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.Journal of proteome research · 2022Article
- Identification of tumor antigens with immunopeptidomics.Nature biotechnology · 2022Review
- Bioinformatic Prediction and Characterization of Proteins inFrontiers in nutrition · 2022Article
- Rewinding the Molecular Clock: Looking at Pioneering Molecular Phylogenetics Experiments in the Light of Proteomics.Journal of proteome research · 2021Article
- UniProt: the universal protein knowledgebase in 2021.Nucleic acids research · 2021Article
- Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future.Molecular & cellular proteomics : MCP · 2021Article
- Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.Proteomics · 2020Article
- BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks.Genome biology · 2020Article
- The neXtProt knowledgebase in 2020: data, tools and usability improvements.Nucleic acids research · 2020Article
- Assessing Protein Sequence Database Suitability UsingMolecular & cellular proteomics : MCP · 2020Article
Corrections and comments
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Authors and funding
21 authors.
Funding
Abstract
Mass-spectrometry-based proteomics enables the high-throughput identification and quantification of proteins, including sequence variants and post-translational modifications (PTMs) in biological samples. However, most workflows require that such variations be included in the search space used to analyze the data, and doing so remains challenging with most analysis tools. In order to facilitate the search for known sequence variants and PTMs, the Proteomics Standards Initiative (PSI) has designed and implemented the PSI extended FASTA format (PEFF). PEFF is based on the very popular FASTA format but adds a uniform mechanism for encoding substantially more metadata about the sequence collection as well as individual entries, including support for encoding known sequence variants, PTMs, and proteoforms. The format is very nearly backward compatible, and as such, existing FASTA parsers will require little or no changes to be able to read PEFF files as FASTA files, although without supporting any of the extra capabilities of PEFF. PEFF is defined by a full specification document, controlled vocabulary terms, a set of example files, software libraries, and a file validator. Popular software and resources are starting to support PEFF, including the sequence search engine Comet and the knowledge bases neXtProt and UniProtKB. Widespread implementation of PEFF is expected to further enable proteogenomics and top-down proteomics applications by providing a standardized mechanism for encoding protein sequences and their known variations. All the related documentation, including the detailed file format specification and example files, are available at http://www.psidev.info/peff .
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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.