The need for an efficient and reliable data interpretation tool was highlighted in a recent publication in which the authors concluded: “Most notably, we found generic problems in databases to be the major hurdle for the correct characterization of proteins in the test sample.” [A HUPO test sample study reveals common problems in mass spectrometry-based proteomics, Nature Methods (6, 423-430 2009)]
However, to help overcome this challenge and ‘bridge the gap’ between search engine and publication, key proteomics centers in Europe and the U.S.A. are already using ProteinCenter, a web-based, data interpretation tool from Proxeon.
ProteinCenter can quickly compare and interpret proteomics data sets to overcome the hurdle of proteins existing under different names and accession keys in the protein databases, allowing confidence in our protein characterization results.
ProteinCenter contains a consolidated, biologically annotated, protein sequence database, derived and regularly updated, from all major protein databases to enable filtering, clustering and statistical bioinformatic analysis from single, combined or comparison datasets.
During the forthcoming HUPO 2009 in Toronto, Proxeon will be previewing new functionalities in the latest version, ProteinCenter v.3.0. These include the ability to discover more about underlying biology by grouping proteins and peptides according to their quantitative profiles and finding differences in the hydrophobicity and iso-electric points of peptides across multiple data sets for method optimization.
Scientists can request an online analysis of their own data or listen to web seminars from other users at www.proxeon.com.