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J Proteome Res. 2015 Sep 4;14(9):3710-9. doi: 10.1021/acs.jproteome.5b00541. Epub 2015 Aug 19.

GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project.

Author information

1
Yonsei Proteome Research Center and Biomedical Proteome Research Center , 50 Yonsei-Ro, Seodaemun-gu, Seoul 120-749, Korea.
2
Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 12 Oxford Street, Boston, Massachusetts 02115, United States.
3
Department of Biochemistry, Department of Integrated Omics for Biomedical Science (World Class University Graduate Program), Yonsei University , 50 Yonsei-Ro, Sudaemoon-ku, Seoul 120-749, Korea.

Abstract

Since the launch of the Chromosome-centric Human Proteome Project (C-HPP) in 2012, the number of "missing" proteins has fallen to 2932, down from ∼5932 since the number was first counted in 2011. We compared the characteristics of missing proteins with those of already annotated proteins with respect to transcriptional expression pattern and the time periods in which newly identified proteins were annotated. We learned that missing proteins commonly exhibit lower levels of transcriptional expression and less tissue-specific expression compared with already annotated proteins. This makes it more difficult to identify missing proteins as time goes on. One of the C-HPP goals is to identify alternative spliced product of proteins (ASPs), which are usually difficult to find by shot-gun proteomic methods due to their sequence similarities with the representative proteins. To resolve this problem, it may be necessary to use a targeted proteomics approach (e.g., selected and multiple reaction monitoring [S/MRM] assays) and an innovative bioinformatics platform that enables the selection of target peptides for rarely expressed missing proteins or ASPs. Given that the success of efforts to identify missing proteins may rely on more informative public databases, it was necessary to upgrade the available integrative databases. To this end, we attempted to improve the features and utility of GenomewidePDB by integrating transcriptomic information (e.g., alternatively spliced transcripts), annotated peptide information, and an advanced search interface that can find proteins of interest when applying a targeted proteomics strategy. This upgraded version of the database, GenomewidePDB 2.0, may not only expedite identification of the remaining missing proteins but also enhance the exchange of information among the proteome community. GenomewidePDB 2.0 is available publicly at http://genomewidepdb.proteomix.org/.

KEYWORDS:

Chromosome-Centric Human Proteome Project; GenomewidePDB; alternative splicing; database; missing protein; proteomics

PMID:
26272709
DOI:
10.1021/acs.jproteome.5b00541
[Indexed for MEDLINE]

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