Label-free proteomic methodology for the analysis of human kidney stone matrix composition

Frank A. Witzmann, Andrew P. Evan, Fredric L. Coe, Elaine M. Worcester, James E. Lingeman, James C. Williams

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


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. Conclusion: 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.

Original languageEnglish (US)
Article number4
JournalProteome Science
Issue number1
StatePublished - 2016


  • Calcium oxalate
  • Kidney stone
  • Label-free quantitative liquid chromatography-tandem mass spectrometry
  • Matrix protein
  • Nephrolithiasis
  • Proteomics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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