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Molecular & Cellular Proteomics 8:1658-1673, 2009.
© 2009 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Application of Label-free Quantitative Peptidomics for the Identification of Urinary Biomarkers of Kidney Chronic Allograft Dysfunction^*,

Luis F. Quintana^,,¶, Josep M. Campistol^,, Maria P. Alcolea^||, Elisenda Bañon-Maneus, Amandaé Sol-González and Pedro R. Cutillas^||,**

From the Servicio de Nefrología y Trasplante renal and
Laboratorio Experimental de Nefrología y Trasplante renal (LENIT), Hospital Clinic, Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Universidad de Barcelona 08036 Barcelona, Spain and
||Analytical Signalling Group, Centre for Cell Signalling, Institute of Cancer, Barts and the London and Queen Mary Medical School, Queen Mary University of London, London EC1M 6BQ, United Kingdom

The advent of quantitative proteomics opens new opportunities in biomedical and clinical research. Although quantitative proteomics methods based on stable isotope labeling are in general preferred for biomolecular research, biomarker discovery is a case example of a biomedical problem that may be better addressed by using label-free MS techniques. As a proof of concept of this paradigm, we report the use of label-free quantitative LC-MS to profile the urinary peptidome of kidney chronic allograft dysfunction (CAD). The aim was to identify predictive biomarkers that could be used to personalize immunosuppressive therapies for kidney transplant patients. We detected (by LC-M/MS) and quantified (by LC-MS) 6000 polypeptide ions in undigested urine specimens across 39 CAD patients and 32 control individuals. Although unsupervised hierarchical clustering differentiated between the groups when including all the identified peptides, specific peptides derived from uromodulin and kininogen were found to be significantly more abundant in control than in CAD patients and correctly identified the two groups. These peptides are therefore potential biomarkers that might be used for the diagnosis of CAD. In addition, ions at m/z 645.59 and m/z 642.61 were able to differentiate between patients with different forms of CAD with specificities and sensitivities of 90% in a training set and, significantly, of 70% in an independent validation set of samples. Interestingly low expression of uromodulin at m/z 638.03 coupled with high expression of m/z 642.61 diagnosed CAD in virtually all cases. Multiple reaction monitoring experiments further validated the results, illustrating the power of our label-free quantitative LC-MS approach for obtaining quantitative profiles of urinary polypeptides in a rapid, comprehensive, and precise fashion and for biomarker discovery.

** To whom correspondence regarding biotechnological questions should be addressed. E-mail: p.cutillas{at}qmul.ac.uk.

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