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De novo derivation of proteomes from transcriptomes for transcript and protein identification.

ABSTRACT: Identification of proteins by tandem mass spectrometry requires a reference protein database, but these are only available for model species. Here we demonstrate that, for a non-model species, the sequencing of expressed mRNA can generate a protein database for mass spectrometry-based identification. This combination of high-throughput sequencing and protein identification technologies allows detection of genes and proteins. We use human cells infected with human adenovirus as a complex and dynamic model to demonstrate the robustness of this approach. Our proteomics informed by transcriptomics (PIT) technique identifies >99% of over 3,700 distinct proteins identified using traditional analysis that relies on comprehensive human and adenovirus protein lists. We show that this approach can also be used to highlight genes and proteins undergoing dynamic changes in post-transcriptional protein stability.

SUBMITTER: Evans VC

PROVIDER: S-EPMC3581816 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

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De novo derivation of proteomes from transcriptomes for transcript and protein identification.

Evans Vanessa C VC Barker Gary G Heesom Kate J KJ Fan Jun J Bessant Conrad C Matthews David A DA

Nature methods 20121111 12

Identification of proteins by tandem mass spectrometry requires a reference protein database, but these are only available for model species. Here we demonstrate that, for a non-model species, the sequencing of expressed mRNA can generate a protein database for mass spectrometry-based identification. This combination of high-throughput sequencing and protein identification technologies allows detection of genes and proteins. We use human cells infected with human adenovirus as a complex and dyna ...[more]

PMID: 23142869

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