Comprehensive human urine standards for comparability and standardization in clinical proteome analysis

Purpose: Urine proteomics is emerging as a powerful tool for biomarker discovery. The purpose of this study is the development of a well-characterized "real life" sample that can be used as reference standard in urine clinical proteomics studies. Experimental design: We report on the generation of male and female urine samples that are extensively characterized by different platforms and methods (CE-MS, LC-MS, LC-MS/MS, 1-D gel analysis in combination with nano-LC MS/MS (using LTQ-FT ultra), and 2-DE-MS) for their proteome and peptidome. In several cases analysis involved a definition of the actual biochemical entities, i.e. proteins/peptides associated with molecular mass and detected PTMs and the relative abundance of these compounds. Results: The combination of different technologies allowed coverage of a wide mass range revealing the advantages and complementarities of the different technologies. Application of these samples in "inter-laboratory" and "inter-platform" data comparison is also demonstrated. Conclusions and clinical relevance: These well-characterized urine samples are freely available upon request to enable data comparison especially in the context of biomarker discovery and validation studies. It is also expected that they will provide the basis for the comprehensive characterization of the urinary proteome.

Kolch, Walter (author)
Aivaliotis, Michalis (author)
Bouyssie, David (author)
Court, Magali (author)
Dihazi, Hassan (author)
Dihazi, Gry H. (author)
Franke, Julia (author)
Garin, Jerome (author)
de Peredo, Anne Gonzalez (author)
Iphoefer, Alexander (author)
Jaensch, Lothar (author)
Lacroix, Chrystelle (author)
Makridakis, Manousos (author)
Masselon, Christophe (author)
Metzger, Jochen (author)
Monsarrat, Bernard (author)
Mrug, Michal (author)
Norling, MartinSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Uppsala universitet,Centrum för bioinformatik,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics(Swepub:slu)49319 (author)
Novak, Jan (author)
Pich, Andreas (author)
Pitt, Andrew (author)
Bongcam-Rudloff, ErikSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Uppsala universitet,Centrum för bioinformatik,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics(Swepub:slu)50410 (author)
Siwy, Justyna (author)
Suzuki, Hitoshi (author)
Thongboonkerd, Visith (author)
Wang, Li-Shun (author)
Zoidakis, Jerome (author)
Zuerbig, Petra (author)
Schanstra, Joost P. (author)
Vlahou, Antonia (author)
Uppsala universitetCentrum för bioinformatik (creator_code:org_t)
Sveriges lantbruksuniversitet

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Bioinformatics

By the university: Uppsala University; Swedish University of Agricultural Sciences

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