Dataset Information

Validation of alternatively spliced protein isoforms in human mesenchymal stem cells

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Bone Marrow

SUBMITTER: A Tay

LAB HEAD: Marc Wilkins

PROVIDER: PXD001449 | Pride | 2015-05-20

REPOSITORIES: Pride

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Publications

Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data.

Tay Aidan P AP Pang Chi Nam Ignatius CN Twine Natalie A NA Hart-Smith Gene G Harkness Linda L Kassem Moustapha M Wilkins Marc R MR

Journal of proteome research 20150520 9

Human proteome analysis now requires an understanding of protein isoforms. We recently published the PG Nexus pipeline, which facilitates high confidence validation of exons and splice junctions by integrating genomics and proteomics data. Here we comprehensively explore how RNA-seq transcriptomics data, and proteomic analysis of the same sample, can identify protein isoforms. RNA-seq data from human mesenchymal (hMSC) stem cells were analyzed with our new TranscriptCoder tool to generate a data ...[more]

PMID: 25961807

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Dataset Information

Validation of alternatively spliced protein isoforms in human mesenchymal stem cells

Publications

Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data.

Similar Datasets

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