READ MORE ABOUT DIAGNOSTIC PRODUCTS
||

HUMAN URINARY PROTEOME DATABASE

A database of naturally occurring human urinary peptides and proteins for use in clinical applications

Owing to its availability, ease of collection, and correlation with pathophysiology of diseases, urine is an attractive source for clinical proteomics. However, many proteomic studies have had only limited clinical impact, due to factors such as modest numbers of subjects, absence of disease controls, small numbers of defined biomarkers, and diversity of analytical platforms. Therefore, it is difficult to merge biomarkers from different studies into a broadly applicable human urinary proteome database. Ideally, the methodology for defining the biomarkers should combine a reasonable analysis time with high resolution, thereby enabling the profiling of adequate samples and recognition of sufficient features to yield robust diagnostic panels. CE/MS, which was used to analyze urine samples from healthy subjects and patients with various diseases, is a suitable approach for this task. The database of these datasets compiled from the urinary peptides enables the diagnosis, classification, and monitoring of a wide range of diseases. CE/MS exhibits excellent performance for biomarker discovery and allows subsequent biomarker sequencing independent of the separation platform. This approach may elucidate the pathogenesis of many diseases, and better define especially renal and urological disorders at the molecular level.

To further promote and enable research and development in the area of urinary proteomics, we are making a fraction of this database, which currently contains over 25000 entries from independent samples, publicly available. By using this large collection of data, scientists worldwide are enabled to evaluate urinary biomarkers "in silico". As this database is a continuously growing project, we will update it on a monthly basis, which will result in the addition of further datasets and sequences. We hope that additional research groups will make their data available through this site and we welcome any contribution of additional datasets.

 

Figure: Disease conditions currently represented in the human urinary proteome database.
 

Parts of the Human Urinary Database are published in:
PROTEOMICS - Clinical Applications 2008, 2(7-8): 964-973

View Abstract
 

and
Proteomics Clin Appl. 2011 Jun;5(5-6):367-74. doi:10.1002/prca.201000155.

For details, please contact:

Prof. Dr. Dr. Harald Mischak
Email: mischak@mosaiques-diagnostics.com
        

or
Dr. Petra Zurbig
Email: zuerbig@mosaiques-diagnostics.com

 

 


Human Urinary Database

Legend: Table consists of 3 different spreadsheets called (1) polypeptides, (2) disease conditions, and (3) patients’ raw data.

(1): Polypeptides. Table listing all peptides/proteins (Protein ID) detected, their calibrated molecular mass [Da], normalized CE migration time [min], mean amplitide [counts], and frequency.
(2): Disease conditions. Table includes all 13,027 patients. Sample ID is correlated to their specific indication of diseases.

(3-16): Patients raw data. Tables in pivot format show the CE/MS data of the 13,027 samples in the database. The protein IDs of all peptides are given in the first column named “Protein ID”; the unique Sample IDs constitute the first row. The MS data from each sample are arranged in one column. The number in each cell represents the calibrated amplitude of the mass spectrometric signal of each peptide/protein detected in the sample.

 
View HUMAN URINARY DATABASE v3.0  
(pivot table, 269 MB, update February 11, 2011)


Legend: Table consists of 20 different spreadsheets called (1) polypeptides, (2) disease conditions, and (3‑19) patients’ raw data part 1 to 18.

(1): Polypeptides. Table listing all peptides/proteins (Protein ID) detected, their calibrated molecular mass [Da], and normalized CE migration time [min].
(2): Disease conditions. Table includes all 3,926 patients. Sample ID is correlated to their specific indication of diseases.

(3-16): Patients raw data part 1 to 18. Tables in pivot format show the CE/MS data of the 3,926 samples in the database. The protein IDs of all peptides are given in the first column named “Protein ID”; the unique Sample IDs constitute the first row. The MS data from each sample are arranged in one column. The number in each cell represents the calibrated amplitude of the mass spectrometric signal of each peptide/protein detected in the sample. The table is divided into 18 spreadsheets, since Microsoft Excel limits the maximal number of columns to 256.

 
View HUMAN URINARY DATABASE v1.0 *
(pivot table, 161 MB)

View HUMAN URINARY DATABASE v2.0 *
(pivot table, 171 MB, update December 7, 2007)

View HUMAN URINARY DATABASE v2.0 *
(pivot table, self-extracting archive 14 MB, update December 7, 2007)

View HUMAN URINARY DATABASE v2.0
(for import, self-extracting archive 62.5 MB, update December 7, 2007)

 

Human Urinary Peptide Sequences

Urinary peptide sequences obtained with MS/MS sequencing. The table contains (from left to right) the number of the data base entry (Protein ID), the associated mass, the CE migration time, and the amplitude of the peptide signal. The additional information after sequence analysis is the peptide sequence, the name of the protein fragment, the SwissProt entry, the accession number, the calculated monoisotopic mass, and the deviation between observed and expected mass.

View HUMAN URINARY PEPTIDE SEQUENCES v1.0 *

View HUMAN URINARY PEPTIDE SEQUENCES v2.0
(update December 7, 2007)

View HUMAN URINARY PEPTIDE SEQUENCES v3.0 * 
(update February 14, 2011)


(*) These downloads are password-protected. Password: Mosa573X