ArticleJournal of proteome research2018
Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper.
Article in Journal of proteome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 22 citations in OpenAlex.
- Wild-AC: A fast, index-free multi-pattern string matching algorithm with wildcard support for proteomics.BMC bioinformatics · 2026Article
- Inhibition of USP7 Destabilizes the Noncanonical PRC1.1 Complex and Induces Neuroblastoma Differentiation.Molecular cancer research : MCR · 2026Article
- Probing the limits of genetic recoding using multi-omics-guided evolution.Nature communications · 2026Article
- TRAINSPOTTER: profiling nascent protein N-termini indicative of bacterial translation initiation via deformylation-assisted N-terminomics.Nucleic acids research · 2026Article
- A Proteogenomic Approach to Discover Novel lncRNA-Derived Microproteins and Their Potential Clinical Utility in Hepatocellular Carcinoma.Molecular & cellular proteomics : MCP · 2026Article
- Article
- Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics.Nature communications · 2026Article
- High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.bioRxiv : the preprint server for biology · 2025Article
- Synthetic genomes unveil the effects of synonymous recoding.bioRxiv : the preprint server for biology · 2024Article
- Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames.Molecular cell · 2023Article
- Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.Journal of proteome research · 2023Article
- Revealing the small proteome ofmicroLife · 2023Article
- Complex regulation of Gephyrin splicing is a determinant of inhibitory postsynaptic diversity.Nature communications · 2022Article
- Advances and Utility of the Human Plasma Proteome.Journal of proteome research · 2021Review
- Extended Spectrum Beta-Lactamase (ESBL) Produced by Gram-Negative Bacteria in Trinidad and Tobago.International journal of microbiology · 2021Review
- A high-stringency blueprint of the human proteome.Nature communications · 2020Review
- Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0.Journal of proteome research · 2019Article
- PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms.Molecular & cellular proteomics : MCP · 2019Article
- Proteomics Standards Initiative Extended FASTA Format.Journal of proteome research · 2019Article
- Toward Completion of the Human Proteome Parts List: Progress Uncovering Proteins That Are Missing or Have Unknown Function and Developing Analytical Methods.Journal of proteome research · 2018Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Bottom-up proteomics relies on the proteolytic or chemical cleavage of proteins into peptides, the identification of those peptides via mass spectrometry, and the mapping of the identified peptides back to the reference proteome to infer which possible proteins are identified. Reliable mapping of peptides to proteins still poses substantial challenges when considering similar proteins, protein families, splice isoforms, sequence variation, and possible residue mass modifications, combined with an imperfect and incomplete understanding of the proteome. The ProteoMapper tool enables a comprehensive and rapid mapping of peptides to a reference proteome. The indexer component creates a segmented index for an input proteome from a FASTA or PEFF file. The ProMaST component provides ultrafast mapping of one or more input peptides against the index. ProteoMapper allows searches that take into account known sequence variation encoded in PEFF files. It also enables fuzzy searches to find highly similar peptides with residue order changes or other isobaric or near-isobaric substitutions within a specified mass tolerance. We demonstrate an example of a one-hit-wonder identification in PeptideAtlas that may be better explained by a combination of catalogued and uncatalogued sequence variation in another highly observed protein. ProteoMapper is a free and open source, available for local use after downloading, embedding in other applications, as an online web tool at http://www.peptideatlas.org/map , and as a web service.
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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.