ArticleNucleic acids research2017
dbSAP: single amino-acid polymorphism database for protein variation detection.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 32 citations in OpenAlex.
- Molecular Tracing and Comparative Genomics Analysis ofPathogens (Basel, Switzerland) · 2025Article
- Review
- Multiaspect Examinations of Possible Alternative Mappings of Identified Variant Peptides: A Case Study on the HEK293 Cell Line.ACS omega · 2022Article
- Personalized Proteome: Comparing Proteogenomics and Open Variant Search Approaches for Single Amino Acid Variant Detection.Journal of proteome research · 2021Article
- Secretome Proteomic Approaches for Biomarker Discovery: An Update on Colorectal Cancer.Medicina (Kaunas, Lithuania) · 2020Review
- XMAn v2-a database of Homo sapiens mutated peptides.Bioinformatics (Oxford, England) · 2020Article
- Beyond Genes: Re-Identifiability of Proteomic Data and Its Implications for Personalized Medicine.Genes · 2019Review
- dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.Nucleic acids research · 2019Article
- Single Amino Acid Variant Discovery in Small Numbers of Cells.Journal of proteome research · 2019Article
- High throughput discovery of protein variants using proteomics informed by transcriptomics.Nucleic acids research · 2018Article
- Article
- Comparative Proteome Profiling and Mutant Protein Identification in Metastatic Prostate Cancer Cells by Quantitative Mass Spectrometry-based Proteogenomics.Cancer genomics & proteomicsArticle
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Millions of human single nucleotide polymorphisms (SNPs) or mutations have been identified so far, and these variants could be strongly correlated with phenotypic variations of traits/diseases. Among these variants, non-synonymous ones can result in amino-acid changes that are called single amino-acid polymorphisms (SAPs). Although some studies have tried to investigate the SAPs, only a small fraction of SAPs have been identified due to inadequately inferred protein variation database and the low coverage of mass spectrometry (MS) experiments. Here, we present the dbSAP database for conveniently accessing the comprehensive information and relationships of spectra, peptides and proteins of SAPs, as well as related genes, pathways, diseases and drug targets. In order to fully explore human SAPs, we built a customized protein database that contained comprehensive variant proteins by integrating and annotating the human SNPs and mutations from eight distinct databases (UniProt, Protein Mutation Database, HPMD, MSIPI, MS-CanProVar, dbSNP, Ensembl and COSMIC). After a series of quality controls, a total of 16 854 SAP peptides involving in 439 537 spectra were identified with large scale MS datasets from various human tissues and cell lines. dbSAP is freely available at http://www.megabionet.org/dbSAP/index.html.
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