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Clinical Chemistry and Laboratory Medicine (CCLM)

Published in Association with the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM)

Editor-in-Chief: Plebani, Mario

Ed. by Gillery, Philippe / Greaves, Ronda / Lackner, Karl J. / Lippi, Giuseppe / Melichar, Bohuslav / Payne, Deborah A. / Schlattmann, Peter


IMPACT FACTOR 2018: 3.638

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Volume 55, Issue 2

Issues

An integrated proteomic and peptidomic assessment of the normal human urinome

Ashley Di Meo
  • Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, Canada
  • Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
  • Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Ihor Batruch / Arsani G. Yousef / Maria D. Pasic
  • Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
  • Department of Laboratory Medicine, St. Joseph’s Health Centre, Toronto, ON, Canada
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Eleftherios P. Diamandis
  • Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
  • Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
  • Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ George M. Yousef
  • Corresponding author
  • Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, ON, Canada
  • Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-07-09 | DOI: https://doi.org/10.1515/cclm-2016-0390

Abstract

Background:

Urine represents an ideal source of clinically relevant biomarkers as it contains a large number of proteins and low molecular weight peptides. The comprehensive characterization of the normal urinary proteome and peptidome can serve as a reference for future biomarker discovery. Proteomic and peptidomic analysis of urine can also provide insight into normal physiology and disease pathology, especially for urogenital diseases.

Methods:

We developed an integrated proteomic and peptidomic analytical protocol in normal urine. We employed ultrafiltration to separate protein and peptide fractions, which were analyzed separately using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) on the Q-Exactive mass spectrometer.

Results:

By analyzing six urines from healthy individuals with advanced age, we identified 1754 proteins by proteomic analysis and 4543 endogenous peptides, arising from 566 proteins by peptidomic analysis. Overall, we identified 2091 non-redundant proteins by this integrated approach. In silico protease activity analysis indicated that metalloproteases are predominantly involved in the generation of the endogenous peptide signature. In addition, a number of proteins that were detected in normal urine have previously been implicated in various urological malignancies, including bladder cancer and renal cell carcinoma (RCC).

Conclusions:

We utilized a highly sensitive proteomics approach that enabled us to identify one of the largest sets of protein identifications documented in normal human urine. The raw proteomics and peptidomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD003595.

This article offers supplementary material which is provided at the end of the article.

Keywords: mass spectrometry; peptide sequence alignment; protease activity analysis; urinary peptidome; urinary proteome

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About the article

Corresponding author: George M. Yousef, MD, PhD, FRCPC (Path), Department of Laboratory Medicine, and the Keenan Research Centre for Biomedical Science at the Li Ka Shing Knowledge Institute, St. Michael's Hospital, 30 Bond Street, Toronto, ON, M5B 1W8, Canada, Phone: +1-416-864-6060, Ext: 77605, Fax: +416-864-5648


Received: 2016-05-03

Accepted: 2016-06-09

Published Online: 2016-07-09

Published in Print: 2017-02-01


Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

Research funding: This work was supported by grants from the Canadian Institute of Health Research (MOP 119606), Kidney Foundation of Canada (KFOC130030), Kidney Cancer Research Network of Canada and Prostate Cancer Canada Movember Discovery Grants (D2013-39).

Employment or leadership: None declared.

Honorarium: None declared.

Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.


Citation Information: Clinical Chemistry and Laboratory Medicine (CCLM), Volume 55, Issue 2, Pages 237–247, ISSN (Online) 1437-4331, ISSN (Print) 1434-6621, DOI: https://doi.org/10.1515/cclm-2016-0390.

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