High-throughput proteomics detection of novel splice isoforms in human platelets.
Affiliation
UCD Conway Institute and UCD School of Biomolecular & Biomedical Sciences, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland.Issue Date
2009MeSH
Amino Acid SequenceBlood Platelets
Databases, Factual
Exons
Genome, Human
Humans
Mass Spectrometry
Metalloendopeptidases
Peptides
Protein Isoforms
Proteomics
RNA, Messenger
Metadata
Show full item recordCitation
High-throughput proteomics detection of novel splice isoforms in human platelets. 2009, 4 (3):e5001 PLoS ONEJournal
PloS oneDOI
10.1371/journal.pone.0005001PubMed ID
19308253Abstract
Alternative splicing (AS) is an intrinsic regulatory mechanism of all metazoans. Recent findings suggest that 100% of multiexonic human genes give rise to splice isoforms. AS can be specific to tissue type, environment or developmentally regulated. Splice variants have also been implicated in various diseases including cancer. Detection of these variants will enhance our understanding of the complexity of the human genome and provide disease-specific and prognostic biomarkers. We adopted a proteomics approach to identify exon skip events - the most common form of AS. We constructed a database harboring the peptide sequences derived from all hypothetical exon skip junctions in the human genome. Searching tandem mass spectrometry (MS/MS) data against the database allows the detection of exon skip events, directly at the protein level. Here we describe the application of this approach to human platelets, including the mRNA-based verification of novel splice isoforms of ITGA2, NPEPPS and FH. This methodology is applicable to all new or existing MS/MS datasets.Language
enISSN
1932-6203ae974a485f413a2113503eed53cd6c53
10.1371/journal.pone.0005001
Scopus Count
Collections
Except where otherwise noted, this item's license is described as https://creativecommons.org/licenses/by/4.0/
Related articles
- PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.
- Authors: Zhou A, Zhang F, Chen JY
- Issue date: 2010 Oct 7
- Detection of alternative splice variants at the proteome level in Aspergillus flavus.
- Authors: Chang KY, Georgianna DR, Heber S, Payne GA, Muddiman DC
- Issue date: 2010 Mar 5
- SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.
- Authors: Zhu Y, Hultin-Rosenberg L, Forshed J, Branca RM, Orre LM, Lehtiö J
- Issue date: 2014 Jun
- Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data.
- Authors: Tay AP, Pang CN, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR
- Issue date: 2015 Sep 4
- A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.
- Authors: Mo F, Hong X, Gao F, Du L, Wang J, Omenn GS, Lin B
- Issue date: 2008 Dec 16