Improving gene annotation using peptide mass spectrometry

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• dc.contributor.author Tanner, Stephenca
• dc.contributor.author Shen, Zhouxinca
• dc.contributor.author Ng, Julioca
• dc.contributor.author Florea, Lilianaca
• dc.contributor.author Guigó Serra, Rodericca
• dc.contributor.author Briggs, Steven P.ca
• dc.contributor.author Bafna, Vineetca
• dc.date.accessioned 2012-05-21T09:45:03Z
• dc.date.available 2012-05-21T09:45:03Z
• dc.date.issued 2007ca
• dc.description.abstract Annotation of protein-coding genes is a key goal of genome sequencing projects. In spite of tremendous recent advances in computational gene finding, comprehensive annotation remains a challenge. Peptide mass spectrometry is a powerful tool for researching the dynamic proteome and suggests an attractive approach to discover and validate protein-coding genes. We present algorithms to construct and efficiently search spectra against a genomic database, with no prior knowledge of encoded proteins. By searching a corpus of 18.5 million tandem mass spectra (MS/MS) from human proteomic samples, we validate 39,000 exons and 11,000 introns at the level of translation. We present translation-level evidence for novel or extended exons in 16 genes, confirm translation of 224 hypothetical proteins, and discover or confirm over 40 alternative splicing events. Polymorphisms are efficiently encoded in our database, allowing us to observe variant alleles for 308 coding SNPs. Finally, we demonstrate the use of mass spectrometry to improve automated gene prediction, adding 800 correct exons to our predictions using a simple rescoring strategy. Our results demonstrate that proteomic profiling should play a role in any genome sequencing project.
• dc.format.mimetype application/pdfca
• dc.identifier.citation Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V. Improving gene annotation using peptide mass spectrometry. Genome Res. 2007;17(2):231-9. DOI: 10.1101/gr.5646507ca
• dc.identifier.doi http://dx.doi.org/10.1101/gr.5646507
• dc.identifier.issn 1088-9051ca
• dc.identifier.uri http://hdl.handle.net/10230/16474
• dc.language.iso engca
• dc.publisher Cold Spring Harbor Laboratory Press-CSHL Pressca
• dc.relation.ispartof Genome Research. 2007;17(2):231-9
• dc.rights © 2007 Genome Research by Cold Spring Harbor Laboratory Press. Published version available at http://genome.cshlp.org. Aquest document està subjecte a Llicència Creative Commons (Attribution-NonCommercial 3.0 Unported License)ca
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by-nc/3.0/
• dc.subject.other Seqüències de nucleòtids
• dc.subject.other Espectrometria de masses
• dc.title Improving gene annotation using peptide mass spectrometryca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersion