HUPO Brain Proteome Project Uses Bruker Daltonics' Enhanced ProteinScape(TM) Capabilities for Standard Data Reprocessing
29 August 2005 - 3:00PM
Business Wire
New ProteinScape algorithms, features and functionality boost
proteomics research results being presented at 4th HUPO World
Congress At the Human Proteome Organization (HUPO) 4th Annual World
Congress, Bruker Daltonics, an operating company of Bruker
BioSciences Corporation (NASDAQ: BRKR), announces today that the
HUPO Brain Proteome Project (BPP) Bioinformatics Committee has
decided to include key new features of Bruker Daltonics'
ProteinScape(TM) database solution for proteomics project
management in HUPO BPP's standard data reprocessing guidelines.
These novel capabilities include the pioneering ScoreBooster(TM),
Metascore(TM) and ProteinExtractor(TM), which together are expected
to further improve the quality and validation of information and
knowledge gained from proteomics projects. ProteinScape generates
high quality information via optimization and validation strategies
in every step in the mass spectrometry (MS) data interpretation
process. Peptide mass fingerprint (PMF) spectra are pre-processed
with ScoreBooster, an algorithm that combines 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 integrates 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 novel 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 unique 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.
Importantly, ProteinScape remains fully in compliance with all
applicable HUPO Proteomics Standards Initiative (PSI) standards. To
produce reliable, reproducible and comparable results, reprocessing
of all proteomics data is currently performed with ProteinScape at
the Data Collection Center in Bochum, Germany, in collaboration
with the European Bioinformatics Institute in Hinxton, UK, and
other collaborators. 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." He will present BPP
data during the Congress. 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. Research scientists get extraordinary flexibility in
sharing these data more easily, greatly accelerating the process of
extracting knowledge from the experimental data. "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. "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." Bruker
Daltonics scientists will make various presentations at the HUPO
World Congress. For information about the Congress, please see
www.hupo2005.com. ProteinScape is a co-development of Bruker
Daltonics and Protagen AG of Dortmund, Germany, and is distributed
exclusively by Bruker Daltonics. ABOUT BRUKER BIOSCIENCES Bruker
BioSciences Corporation (NASDAQ: BRKR), headquartered in Billerica,
Massachusetts, is the publicly traded parent company of Bruker AXS
Inc. and Bruker Daltonics Inc. Bruker AXS is a leading developer
and provider of life science and advanced materials research tools
based on X-ray technology. Bruker Daltonics is a leading developer
and provider of innovative life science tools based on mass
spectrometry. For more information, please visit www.bdal.com and
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