title: Improving gene annotation using peptide mass spectrometry.
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.
authors.affiliation: Bioinformatics Program, University of California, San Diego, La Jolla, California 92093-0419, USA. stanner@ucsd.edu
authors.forename: Stephen
authors.initials: S
authors.lastname: Tanner
authors.forename: Zhouxin
authors.initials: Z
authors.lastname: Shen
authors.forename: Julio
authors.initials: J
authors.lastname: Ng
authors.forename: Liliana
authors.initials: L
authors.lastname: Florea
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.forename: Steven P
authors.initials: SP
authors.lastname: Briggs
authors.forename: Vineet
authors.initials: V
authors.lastname: Bafna
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D000595:Amino Acid Sequence; D030562:Databases, Protein; D005091:Exons; D005821:Genetic Techniques; D006801:Humans; D007438:Introns; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040081:Protein Array Analysis / Q000379:methods / Q000706:statistics & numerical data; D040901:Proteomics / Q000379:methods* / Q000706:statistics & numerical data; D016415:Sequence Alignment
chemical_list: D010455:Peptides