HUPO Brain Proteome Project Uses Bruker Daltonics' Enhanced ProteinScape(TM) Capabilities for Standard Data Reprocessing

     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
www.bruker-biosciences.com

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