title: Application of quantitative proteomics to the integrated analysis of the ubiquitylated and global proteomes of xenograft tumor tissues.
abstract: BACKGROUND
  Post-translational modification by ubiquitin is a fundamental regulatory mechanism that is implicated in many cellular processes including the cell cycle, apoptosis, cell adhesion, angiogenesis, and tumor growth. The low stoichiometry of ubiquitylation presents an analytical challenge for the detection of endogenously modified proteins in the absence of enrichment strategies. The recent availability of antibodies recognizing peptides with Lys residues containing a di-Gly ubiquitin remnant (K-ε-GG) has greatly improved the ability to enrich and identify ubiquitylation sites from complex protein lysates via mass spectrometry. To date, there have not been any published studies that quantitatively assess the changes in endogenous ubiquitin-modification protein stoichiometry status at the proteome level from different tissues.
  
  
  RESULTS
  In this study, we applied an integrated quantitative mass spectrometry based approach using isobaric tags for relative and absolute quantitation (iTRAQ) to interrogate the ubiquitin-modified proteome and the cognate global proteome levels from luminal and basal breast cancer patient-derived xenograft tissues. Among the proteins with quantitative global and ubiquitylation data, 91 % had unchanged levels of total protein relative abundance, and less than 5 % of these proteins had up- or down-regulated ubiquitylation levels. Of particular note, greater than half of the proteins with observed changes in their total protein level also had up- or down-regulated changes in their ubiquitylation level.
  
  
  CONCLUSIONS
  This is the first report of the application of iTRAQ-based quantification to the integrated analysis of the ubiquitylated and global proteomes at the tissue level. Our results underscore the importance of conducting integrated analyses of the global and ubiquitylated proteomes toward elucidating the specific functional significance of ubiquitylation.
authors.affiliation: Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, 1550 Orleans Street CRBII Room 3M06, Baltimore, MD 21231 USA.
authors.forename: Stefani N
authors.initials: SN
authors.lastname: Thomas
authors.affiliation: Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine, 1550 Orleans Street CRBII Room 3M06, Baltimore, MD 21231 USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Cotter
keywords: Mass spectrometry; Proteomics; Quantification; Tissue; Ubiquitylation; Xenograft; iTRAQ