ProteinCenter; a generic tool for proteomic bioinformatics analysis with comparisons across many different protein databases.

Author:Soeren Schandorff

Co-authors:Alexandre Podtelejnikov

Abstract/Description:
The generation of vast amounts of data from proteomics studies has become a common practice in many scientific laboratories. Many software tools have emerged to help process these datasets. Until now it was however unrealistic to perform comparison analysis of data sets derived from different laboratories. The proteomics community has a number of favorite protein databases. Each database has pros & cons, but the implications of searching a small and well-annotated database like Swiss-Prot as opposed to a broad database like nrdb is poorly understood, mainly because comparison of search results remains a major challenge. Comparisons are difficult because the same protein in two different data sets may appear different due to different accession codes, allelic differences, fragment vs. full length, or even sequencing errors. These issues likewise apply when dealing with data sets from other sources like literature and specialised databases. We used ProteinCenter to overcome the bottlenecks in large scale proteome comparisons and present an in-depth comparison revealing the pros and cons of searching LC MS/MS data sets against IPI, RefSeq, nrdb and Swiss-Prot.

Poster presented at:
US HUPO - 2006

Website link:http://www.proxeon.com/protein-sequence-databases-software.html