At the Human Proteome Organization (HUPO) 4th Annual World Congress, Bruker Daltonics, has announced that the HUPO Brain Proteome Project (BPP) Bioinformatics Committee has decided to include key features of Bruker Daltonics' ProteinScape™ database solution for proteomics project management in HUPO BPP's standard data reprocessing guidelines.
These capabilities include the ScoreBooster™, Metascore™ and ProteinExtractor™, which together are expected to further improve the quality and validation of information and knowledge gained from proteomics projects.
ProteinScape is designed to generate high quality information via optimization and validation strategies in every step in the mass spectrometry data interpretation process.
Peptide mass fingerprint (PMF) spectra are pre-processed with ScoreBooster, an algorithm that is designed to combine the steps of data calibration, removing calibrant signals and protein searches in an iterative manner, resulting in significant improvement of the protein identification rate.
ProteinScape is designed to integrate several different search engines including Mascot, Phenyx and Profound to allow cross-validation and consolidation of the identification results through the complementary use of several search engines using the MetaScore algorithm to provide enhanced reliability and to increase confidence by intelligent combination of scoring schemes from these different search engines.
The evaluation of proteins based on the peptides identified by these search engines is performed by the ProteinExtractor algorithm which generates true non-redundant protein lists from LC-MS/MS search results.
ProteinExtractor decreases redundancies in the protein results, reducing manual validation efforts significantly.
"These are the key features for our automated approach in analyzing the HUPO BPP pilot study data," stated Dr. Christian Stephan of the BPP Bioinformatics Committee, who conducts brain proteomics research at the Ruhr University Medical Proteomics Center.
The aim of HUPO's Brain Proteome Project (BPP) pilot studies is to derive in-depth knowledge from samples which are analyzed in laboratories worldwide using different separation and MS techniques.
The HUPO BPP data were collected, stored and submitted in ProteinScape, the chosen database system for all of BPP's proteomics project management. ProteinScape remains fully in compliance with all applicable HUPO Proteomics Standards Initiative (PSI) standards.
Professor Helmut E. Meyer, Director of the HUPO Brain Proteome Project, pointed out: "In particular, the new features of ProteinScape allow us to store, handle and analyze the huge amount of data in a very effective way."
With Bruker Daltonics' addition of the mzData standard format to ProteinScape, mass spectrometry data comparison, exchange and verification have been facilitated. The mzData format was established as a standard data exchange format by the HUPO PSI.
"The use of a sophisticated bioinformatics database system is a requirement for the successful management of the vast amount of heterogeneous data resulting from the great variety of workflow approaches used in proteomics today," said Professor Herbert Thiele, Director of Bioinformatics at Bruker Daltonics.
He adds, "The HUPO BPP reprocessing effort clearly indicates the need for advanced algorithms for data evaluation and validation. More quality results generate more confidence and produce much more relevant knowledge."