title: Development of a Targeted Urine Proteome Assay for kidney diseases.
abstract: OBJECTIVE
  Since human urine is the most readily available biofluid whose proteome changes in response to disease, it is a logical sample for identifying protein biomarkers for kidney diseases.
  
  
  METHODS
  Potential biomarkers were identified by using a multiproteomics workflow to compare urine proteomes of kidney transplant patients with immediate and delayed graft function. Differentially expressed proteins were identified, and corresponding stable isotope labeled internal peptide standards were synthesized for scheduled MRM.
  
  
  RESULTS
  The Targeted Urine Proteome Assay (TUPA) was then developed by identifying those peptides for which there were at least two transitions for which interference in a urine matrix across 156 MRM runs was <30%. This resulted in an assay that monitors 224 peptides from 167 quantifiable proteins.
  
  
  CONCLUSIONS
  TUPA opens the way for using a robust mass spectrometric technology, MRM, for quantifying and validating biomarkers from among 167 urinary proteins. This approach, while developed using differentially expressed urinary proteins from patients with delayed versus immediate graft function after kidney transplant, can be expanded to include differentially expressed urinary proteins in multiple kidney diseases. Thus, TUPA could provide a single assay to help diagnose, prognose, and manage many kidney diseases.
authors.affiliation: Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA.
authors.forename: Lloyd G
authors.initials: LG
authors.lastname: Cantley
authors.affiliation: Primary Ion, Old Lyme, CT, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Colangelo
authors.affiliation: W.M. Keck Foundation Biotechnology Laboratory, School of Medicine, Yale University, New Haven, CT, USA.
authors.forename: Kathryn L
authors.initials: KL
authors.lastname: Stone
authors.affiliation: W.M. Keck Foundation Biotechnology Laboratory, School of Medicine, Yale University, New Haven, CT, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: Chung
authors.affiliation: Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Belcher
authors.affiliation: W.M. Keck Foundation Biotechnology Laboratory, School of Medicine, Yale University, New Haven, CT, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Abbott
authors.affiliation: Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Cantley
authors.affiliation: W.M. Keck Foundation Biotechnology Laboratory, School of Medicine, Yale University, New Haven, CT, USA.|Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, CT, USA.
authors.forename: Kenneth R
authors.initials: KR
authors.lastname: Williams
authors.affiliation: Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA.|Program of Applied Translational Research, Yale University School of Medicine, New Haven, CT, USA.
authors.forename: Chirag R
authors.initials: CR
authors.lastname: Parikh
mesh_terms: D015415:Biomarkers; D005260:Female; D006801:Humans; D016030:Kidney Transplantation; D008297:Male; D013058:Mass Spectrometry / Q000379:methods; D007690:Polycystic Kidney Diseases / Q000652:urine*; D011507:Proteinuria / Q000652:urine*; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D051436:Renal Insufficiency, Chronic / Q000652:urine*
chemical_list: D015415:Biomarkers; D020543:Proteome
keywords: Chronic kidney disease; Polycystic kidney disease; Targeted proteomics; Urine