title: 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 accessible, modifiable, and extensible workflows within Galaxy-P, short for Galaxy for Proteomics, a web-based bioinformatic extension of the Galaxy framework for the analysis of multi-omics (e.g. genomics, transcriptomics, proteomics) data.
  
  
  RESULTS
  We present three bioinformatic workflows that allow the user to upload raw RNA sequencing reads and convert the data into high-quality customized proteomic databases suitable for MS searching. We show the utility of these workflows on human and mouse samples, identifying 544 peptides containing single amino acid polymorphisms (SAPs) and 187 peptides corresponding to unannotated splice junction peptides, correlating protein and transcript expression levels, and providing the option to incorporate transcript abundance measures within the MS database search process (reduced databases, incorporation of transcript abundance for protein identification score calculations, etc.).
  
  
  CONCLUSIONS
  Using RNA-Seq data to enhance MS analysis is a promising strategy to discover novel peptides specific to a sample and, more generally, to improve proteomics results. The main bottleneck for widespread adoption of this strategy has been the lack of easily used and modifiable computational tools. We provide a solution to this problem by introducing a set of workflows within the Galaxy-P framework that converts raw RNA-Seq data into customized proteomic databases.
authors.forename: Gloria M
authors.initials: GM
authors.lastname: Sheynkman
authors.forename: James E
authors.initials: JE
authors.lastname: Johnson
authors.forename: Pratik D
authors.initials: PD
authors.lastname: Jagtap
authors.forename: Michael R
authors.initials: MR
authors.lastname: Shortreed
authors.forename: Getiria
authors.initials: G
authors.lastname: Onsongo
authors.forename: Brian L
authors.initials: BL
authors.lastname: Frey
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Griffin
authors.affiliation: Chemistry Department, University of Wisconsin-Madison, 1101 University Ave,, Madison, WI 53706, USA. smith@chem.wisc.edu.
authors.forename: Lloyd M
authors.initials: LM
authors.lastname: Smith
mesh_terms: D017398:Alternative Splicing; D019943:Amino Acid Substitution; D000818:Animals; D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D019169:Jurkat Cells; D051379:Mice; D020641:Polymorphism, Single Nucleotide; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics; D020543:Proteome / Q000737:chemistry / Q000235:genetics; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D020033:Protein Isoforms; D020543:Proteome