The Human Urinary Proteome Fingerprint Database UPdb

Abstract

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.

Urinary Peptidomic Biomarkers in Kidney Diseases

“…Specialized scientific databases greatly help to facilitate this process [76]. In the field of nephrology, omics databases include "the Kidney and Urinary Pathway Knowledge Base" [77], the "Human Urinary Proteome Fingerprint Database" [78], and the "Chronic Kidney Disease database" [79]. More recently, a publicly available database platform that solely collects peptidomic and proteomic datasets manually extracted from published studies relative to CKD has been set up [80].…”

Integrative Systems Biology Resources and Approaches in Disease Analytics

“…In the same framework we also cover an assorted disease profiling database valuable for subtractive disease analysis studies, the Large-Scale Screening Resource (LSSR) that contains 81,980 entries, referring to 13,589 molecules. Moreover, a peak profiling database for biomarker patterns research, the Urinary Peptidomics and Peak-maps (UPdb) [63] database that comprises Human urinary fingerprints from 200 subjects analysed mainly through surface enhanced laser desorption ionisation-time of flight mass spectrometry (SELDI-TOF-MS).…”

Applying proteomics to detect early signs of chronic kidney disease: where has the magic gone?

“…Inclusion criteria were peptidomics or proteomics case-control studies relative to CKD and only studies that examined human specimens. In addition to the literature search, the authors queried several databases including the 'Chronic Kidney Disease database' [7], 'The Kidney and Urinary Pathway Knowledge Base' [8], and the 'Human Urinary Proteome Fingerprint Database' to identify proteomic data that might produce CKD biomarker candidates [9][10][11]. The authors identified 114 manuscripts in their literature mining that fit inclusion criteria.…”