Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations.

ABSTRACT:

Background

Current practice in mass spectrometry (MS)-based proteomics is to identify peptides by comparison of experimental mass spectra with theoretical mass spectra derived from a reference protein database; however, this strategy necessarily fails to detect peptide and protein sequences that are absent from the database. We and others have recently shown that customized proteomic databases derived from RNA-Seq data can be employed for MS-searching to both improve MS analysis and identify novel peptides. While this general strategy constitutes a significant advance for the discovery of novel protein variations, it has not been readily transferable to other laboratories due to the need for many specialized software tools. To address this problem, we have implemented readily acces

SUBMITTER: Sheynkman GM 

PROVIDER: S-EPMC4158061 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature