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Using RNA-Seq to create sample-specific proteomic databases that enable mass spectrometric discovery of splice junction peptides

ABSTRACT: Many new alternative splice forms have been detected at the transcript level using next generation sequencing (NGS) methods, especially RNA-Seq, but it is not known how many of these transcripts are being translated. Leveraging the unprecedented capabilities of NGS, we collected RNA-Seq and proteomics data from the same cell population (Jurkat cells) and created a bioinformatics pipeline that builds customized databases for the discovery of novel splice-junction peptides. Results: Eighty million paired-end Illumina reads and ~500,000 tandem mass spectra were used to identify 12,873 transcripts (19,320 including isoforms) and 6,810 proteins. We developed a bioinformatics workflow to retrieve high-confidence, novel splice junction sequences from the RNA data, translate these sequences into the analogous polypeptide sequence, and create a customized splice junction database for MS searching.

ORGANISM(S): Homo sapiens

PROVIDER: GSE45428 | GEO | 2013/05/17

SECONDARY ACCESSION(S): PRJNA193719

REPOSITORIES: GEO

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Using RNA-Seq to create sample-specific proteomic databases that enable mass spectrometric discovery of splice junction peptides

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