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BMC Genomics

, 14:141

ProteomicsThe ENCODE project


BackgroundProteogenomic mapping is an approach that uses mass spectrometry data from proteins to directly map protein-coding genes and could aid in locating translational regions in the human genome. In concert with the ENcyclopedia of DNA Elements ENCODE project, we applied proteogenomic mapping to produce proteogenomic tracks for the UCSC Genome Browser, to explore which putative translational regions may be missing from the human genome.

ResultsWe generated ~1 million high-resolution tandem mass MS-MS spectra for Tier 1 ENCODE cell lines K562 and GM12878 and mapped them against the UCSC hg19 human genome, and the GENCODE V7 annotated protein and transcript sets. We then compared the results from the three searches to identify the best-matching peptide for each MS-MS spectrum, thereby increasing the confidence of the putative new protein-coding regions found via the whole genome search. At a 1% false discovery rate, we identified 26,472, 24,406, and 13,128 peptides from the protein, transcript, and whole genome searches, respectively; of these, 481 were found solely via the whole genome search. The proteogenomic mapping data are available on the UCSC Genome Browser at http:-genome.ucsc.edu-cgi-bin-hgTrackUi?db=hg19andg=wgEncodeUncBsuProt.

ConclusionsThe whole genome search revealed that ~4% of the uniquely mapping identified peptides were located outside GENCODE V7 annotated exons. The comparison of the results from the disparate searches also identified 15% more spectra than would have been found solely from a protein database search. Therefore, whole genome proteogenomic mapping is a complementary method for genome annotation when performed in conjunction with other searches.

KeywordsProteogenomic mapping MS-MS spectra Genome annotation Proteomics Genomics AbbreviationsPSMPeptide-spectrum match

ORFOpen reading frame

UTRUntranslated region

MSMass spectrometry

MS-MSTandem mass spectrometry


FDRFalse discovery rate

ENCODEEncyclopedia of DNA elements

UCSC DCCUniversity of California Santa Cruz data coordination center

FASPFilter-aided sample preparation

RPLCReversed-phase liquid chromatography

CIDCollision-induced dissociation.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-141 contains supplementary material, which is available to authorized users.

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Autor: Jainab Khatun - Yanbao Yu - John A Wrobel - Brian A Risk - Harsha P Gunawardena - Ashley Secrest - Wendy J Spitzer - Li

Fuente: https://link.springer.com/

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