%0 Journal Article
%T The Human Urinary Proteome Fingerprint Database UPdb
%A Holger Husi
%A Janice B. Barr
%A Richard J. E. Skipworth
%A Nathan A. Stephens
%A Carolyn A. Greig
%A Henning Wackerhage
%A Rona Barron
%A Kenneth C. H. Fearon
%A James A. Ross
%J International Journal of Proteomics
%D 2013
%I Hindawi Publishing Corporation
%R 10.1155/2013/760208
%X The use of human urine as a diagnostic tool has many advantages, such as ease of sample acquisition and noninvasiveness. However, the discovery of novel biomarkers, as well as biomarker patterns, in urine is hindered mainly by a lack of comparable datasets. To fill this gap, we assembled a new urinary fingerprint database. Here, we report the establishment of a human urinary proteomic fingerprint database using urine from 200 individuals analysed by SELDI-TOF (surface enhanced laser desorption ionisation-time of flight) mass spectrometry (MS) on several chip surfaces (SEND, HP50, NP20, Q10, CM10, and IMAC30). The database currently lists 2490 unique peaks/ion species from 1172 nonredundant SELDI analyses in the mass range of 1500 to 150000. All unprocessed mass spectrometric scans are available as ¡°.xml¡± data files. Additionally, 1384 peaks were included from external studies using CE (capillary electrophoresis)-MS, MALDI (matrix assisted laser desorption/ionisation), and CE-MALDI hybrids. We propose to use this platform as a global resource to share and exchange primary data derived from MS analyses in urinary research. 1. Introduction Screening of human tissues and biofluids for disease biomarkers is an important task in healthcare and disease prevention but is often hindered by the complexity of the system studied, for example, plasma. A substantially less complex system such as urine, which contains approximately 3000 proteins [1, 2], would be a preferred medium to screen for protein or peptide biomarkers as sampling is both simple and noninvasive, and unrestricted quantities are obtainable. Urine is relatively stable in terms of protein/peptide composition and fragmentation state compared with other body fluids such as serum, where proteolytic degradation by endogenous proteases has been shown to occur during or after sample collection [3]. Several investigations have been published describing the urinary peptidome and proteome [4, 5], including biomarker discoveries for several disease processes [6¨C10]. These studies have used methodologies ranging from traditional 2D gel electrophoresis alone [11] or coupled with mass spectrometry (2-DE-MS) [12], immunohistochemistry [13], liquid chromatography mass spectrometry (LC-MS) [14], and surface enhanced laser desorption ionisation-time of flight mass spectrometry (SELDI-TOF-MS) [15¨C17]. In complex disease processes, the identification of biomarkers is key to developing novel therapeutic target molecules. Identification of the most robust urinary biomarkers will be enhanced by collating and correlating
%U http://www.hindawi.com/journals/ijpro/2013/760208/