Matching peptide mass spectra to EST and genomic DNA databases
- PMID: 11780965
- DOI: 10.1016/S0167-7799(01)01795-4
Matching peptide mass spectra to EST and genomic DNA databases
Abstract
The use of mass spectrometry data to search molecular sequence databases is a well-established method for protein identification. The technique can be extended to searching raw genomic sequences, providing experimental confirmation or correction of predicted coding sequences, and has the potential to identify novel genes and elucidate splicing patterns.
Similar articles
-
Error-tolerant EST database searches by tandem mass spectrometry and multiTag software.Proteomics. 2005 Nov;5(16):4118-22. doi: 10.1002/pmic.200401262. Proteomics. 2005. PMID: 16121338
-
Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics.Genes Cells. 2012 Aug;17(8):633-44. doi: 10.1111/j.1365-2443.2012.01615.x. Epub 2012 Jun 12. Genes Cells. 2012. PMID: 22686349
-
[Analysis, identification and correction of some errors of model refseqs appeared in NCBI Human Gene Database by in silico cloning and experimental verification of novel human genes].Yi Chuan Xue Bao. 2004 May;31(5):431-43. Yi Chuan Xue Bao. 2004. PMID: 15478601 Chinese.
-
A hitchhiker's guide to expressed sequence tag (EST) analysis.Brief Bioinform. 2007 Jan;8(1):6-21. doi: 10.1093/bib/bbl015. Epub 2006 May 23. Brief Bioinform. 2007. PMID: 16772268 Review.
-
Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry.Methods Mol Biol. 2000;146:41-61. doi: 10.1385/1-59259-045-4:41. Methods Mol Biol. 2000. PMID: 10948496 Review. No abstract available.
Cited by
-
Comparative Proteogenomic Approaches for Mapping the Global Proteome of the Unsequenced Leishmania Vector Phlebotomus papatasi.Methods Mol Biol. 2025;2859:265-277. doi: 10.1007/978-1-0716-4152-1_15. Methods Mol Biol. 2025. PMID: 39436607
-
A ranking-based scoring function for peptide-spectrum matches.J Proteome Res. 2009 May;8(5):2241-52. doi: 10.1021/pr800678b. J Proteome Res. 2009. PMID: 19231891 Free PMC article.
-
Generation of a predicted protein database from EST data and application to iTRAQ analyses in grape (Vitis vinifera cv. Cabernet Sauvignon) berries at ripening initiation.BMC Genomics. 2009 Jan 26;10:50. doi: 10.1186/1471-2164-10-50. BMC Genomics. 2009. PMID: 19171055 Free PMC article.
-
Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry.Mol Cell Proteomics. 2010 Jun;9(6):1157-66. doi: 10.1074/mcp.M900426-MCP200. Epub 2010 Feb 5. Mol Cell Proteomics. 2010. PMID: 20139370 Free PMC article.
-
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.Genome Res. 2011 May;21(5):756-67. doi: 10.1101/gr.114272.110. Epub 2011 Apr 1. Genome Res. 2011. PMID: 21460061 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Research Materials