title: Label-free proteomic methodology for the analysis of human kidney stone matrix composition.
abstract: BACKGROUND
  Kidney stone matrix protein composition is an important yet poorly understood aspect of nephrolithiasis. We hypothesized that this proteome is considerably more complex than previous reports have indicated and that comprehensive proteomic profiling of the kidney stone matrix may demonstrate relevant constitutive differences between stones. We have analyzed the matrices of two unique human calcium oxalate stones (CaOx-Ia and CaOx-Id) using a simple but effective chaotropic reducing solution for extraction/solubilization combined with label-free quantitative mass spectrometry to generate a comprehensive profile of their proteomes, including physicochemical and bioinformatic analysis.`.
  
  
  RESULTS
  We identified and quantified 1,059 unique protein database entries in the two human kidney stone samples, revealing a more complex proteome than previously reported. Protein composition reflects a common range of proteins related to immune response, inflammation, injury, and tissue repair, along with a more diverse set of proteins unique to each stone.
  
  
  CONCLUSIONS
  The use of a simple chaotropic reducing solution and moderate sonication for extraction and solubilization of kidney stone powders combined with label-free quantitative mass spectrometry has yielded the most comprehensive list to date of the proteins that constitute the human kidney stone proteome.
authors.affiliation: Department of Cellular and Integrative Physiology, Indiana University School of Medicine, 635 Barnhill Drive, Room 362A, Indianapolis, IN 46202-5120 USA.
authors.forename: Frank A
authors.initials: FA
authors.lastname: Witzmann
authors.affiliation: Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN USA.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Evan
authors.affiliation: Department of Medicine, Nephrology Section, University of Chicago, Chicago, IL USA.
authors.forename: Fredric L
authors.initials: FL
authors.lastname: Coe
authors.affiliation: Department of Medicine, Nephrology Section, University of Chicago, Chicago, IL USA.
authors.forename: Elaine M
authors.initials: EM
authors.lastname: Worcester
authors.affiliation: International Kidney Stone Institute, Methodist Hospital, Indianapolis, IN USA.
authors.forename: James E
authors.initials: JE
authors.lastname: Lingeman
authors.affiliation: Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Williams
keywords: Calcium oxalate; Kidney stone; Label-free quantitative liquid chromatography–tandem mass spectrometry; Matrix protein; Nephrolithiasis; Proteomics