PXD001449 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Validation of alternatively spliced protein isoforms in human mesenchymal stem cells |
Description | Alternative splicing of mRNA diversifies the function of human proteins, with tissue- and cell-specific protein isoforms being the most difficult to validate. While transcriptomic experiments enable the detection of many alternatively spliced transcripts, it is not known if these transcripts have protein-coding potential. We recently published the PG Nexus pipeline, which facilitates high confidence validation of exons and exon-exon junctions of spliced transcripts by integrating transcriptomics and proteomics data. Using the PG Nexus, we analyzed undifferentiated human mesenchymal stem cells and compared the number of protein isoforms validated using different protein sequence database, including public online databases and RNA-seq derived databases. With significant overlaps with other databases, we identified 8,011 exons and 3,824 splice junctions with the Ensembl database. Both exonic and junction peptides were important for protein isoform validation. The Ensembl database consistently outperformed the other data sources, but predicted open reading frames from RNA-seq derived transcripts were comparable, with only 6 less splice junctions validated. Using proteotypic and isoform-specific peptides, we validated 462 protein isoforms. This number increases to 1,083 if multiple proteotypic peptides per protein are included. Multiplexing proteotypic peptides in SRM assays or similar experiments will increase the confidence and coverage of protein isoform validation experiments. |
HostingRepository | PRIDE |
AnnounceDate | 2015-05-20 |
AnnouncementXML | Submission_2015-05-20_04:22:45.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD001449 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | A Tay |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | LTQ Orbitrap Velos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2014-10-31 01:51:37 | ID requested | |
⏵ 1 | 2015-05-20 04:22:47 | announced | |
Publication List
Tay AP, Pang CN, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR, Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data. J Proteome Res, 14(9):3541-54(2015) [pubmed] |
Keyword List
curator keyword: Biomedical |
submitter keyword: Human, mesenchymal stem cell, LC-MS/MS |
Contact List
Marc Wilkins |
contact affiliation | School of Biotechnology and Biomolecular Sciences, University of New South Wales |
contact email | m.wilkins@unsw.edu.au |
lab head | |
A Tay |
contact affiliation | School of Biotechnology and Biomolecular Sciences |
contact email | aidan.tay@unsw.edu.au |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD001449
- Label: PRIDE project
- Name: Validation of alternatively spliced protein isoforms in human mesenchymal stem cells