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Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data
- Source :
- Tay, A P, Pang, C N I, Twine, N A, Hart-Smith, G, Harkness, L, Kassem, M & Wilkins, M R 2015, ' Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data ', Journal of Proteome Research, vol. 14, no. 9, pp. 3541-3554 . https://doi.org/10.1021/pr5011394
- Publication Year :
- 2015
-
Abstract
- 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 database of protein isoform sequences. MS/MS data from matching hMSC samples were then matched against the TranscriptCoder-derived database, along with Ensembl and the neXtProt database. Querying the TranscriptCoder-derived or Ensembl database could unambiguously identify ∼450 protein isoforms, with isoform-specific proteotypic peptides, including candidate hMSC-specific isoforms for the genes DPYSL2 and FXR1. Where isoform-specific peptides did not exist, groups of nonisoform-specific proteotypic peptides could specifically identify many isoforms. In both the above cases, isoforms will be detectable with targeted MS/MS assays. Unfortunately, our analysis also revealed that some isoforms will be difficult to identify unambiguously as they do not have peptides that are sufficiently distinguishing. We covisualize mRNA isoforms and peptides in a genome browser to illustrate the above situations. Mass spectrometry data is available via ProteomeXchange (PXD001449).
- Subjects :
- Proteomics
Gene isoform
Protein isoform
Genetics
NeXtProt
Sequence Analysis, RNA
RNA Splicing
Alternative splicing
Exons
General Chemistry
Genome browser
Biology
Biochemistry
Open Reading Frames
Tandem Mass Spectrometry
Human proteome project
Humans
Protein Isoforms
Ensembl
RNA, Messenger
Codon
Cells, Cultured
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Tay, A P, Pang, C N I, Twine, N A, Hart-Smith, G, Harkness, L, Kassem, M & Wilkins, M R 2015, ' Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data ', Journal of Proteome Research, vol. 14, no. 9, pp. 3541-3554 . https://doi.org/10.1021/pr5011394
- Accession number :
- edsair.doi.dedup.....e079e4c289020bef3ef8f70329eb1202