POTSDAM, Germany, March 25, 2019 /PRNewswire/ -- At the XIIIth
Annual Congress of the European Proteomics Association
(www.eupa.org), Bruker announces further progress in ultra-high
sensitivity, high-throughput 4D proteomics using the timsTOF
Pro mass spectrometer. Moreover, new intact protein
analysis and next-generation 4D metabolomics workflows are being
introduced, which all are available on the same, remarkably
flexible timsTOF Pro platform.
The extraordinary advances in speed, sensitivity and robustness
provided by the timsTOF Pro have generated tremendous
interest in the proteomics community. All work performed to date
has been done using Data Dependent Analysis (DDA) and the
innovative parallel accumulation serial fragmentation (PASEF)
method developed in collaboration with Professor Matthias Mann at the Max Planck Institute of
Biochemistry in Martinsried, Germany.
In ddaPASEF, individual multiply-charged peptides
are selected in real-time for MS/MS, based on the acquired
'mobility-mass heat map'. Even with the high >100 Hz MS/MS speed
of the timsTOF Pro, not all peptides can be targeted
for MS/MS identification. Due to biological variation in the data
from sample to sample, the same peptides may not be targeted in all
runs, leading to the so-called "missing value problem" when
performing quantitative proteomics.
Data Independent Analysis (DIA) is an alternative approach to
fragment most of the peptides using wide selection windows, rather
than selecting individual peptides in DDA. For many years, Bruker
has been collaborating with the laboratories of Professor
Matthias Mann to develop the
timsTOF Pro for proteomics. More recently, they have
teamed up with Professor Ruedi
Aebersold and Dr. Ben Collins
at the ETH in Zuerich, and
Professor Hannes Roest at the
University of Toronto, to develop a
novel DIA technique on the timsTOF Pro, called
diaPASEF. The speed and sensitivity of the
timsTOF Pro have been shown to lead to improved
throughput and better results for DIA library generation, and
promise even more comprehensive proteome coverage in DIA
experiments. Further progress on diaPASEF will be
presented at EuPA 2019.
Professor Matthias Mann stated:
"The timsTOF Pro offers very high MS/MS speed, dynamic range
and an additional 4th dimension of separation by ion
mobility. Due to its dual-TIMS front end, when operated with our
PASEF method, the timsTOF Pro also uses ions very
efficiently with nearly 100% duty cycle for highest sensitivity.
The ion mobility separation provides accurate and highly
reproducible collision cross section (CCS) values that allow for an
additional dimension for alignment and feature matching in data
processing and analysis software. The new diaPASEF method with the
OpenSwath analysis software takes advantage of these attributes to
provide a next-generation DIA method with superior coverage of
proteins in biological samples, and with excellent quantitative
performance. We are very excited about the diaPASEF work, and we
look forward to continuing the collaboration with our academic
collaborators and Bruker."
Rohan Thakur, Ph.D., and Bruker
Executive Vice President for Life-Science Mass Spectrometry,
commented further: "With both ddaPASEF and soon also diaPASEF
workflows, the timsTOF Pro represents a major advance in
robust, ultra-high sensitivity and high-throughput quantitative
proteomics. Its unique 4D nanoLC-TIMS-MS-MS analysis capabilities
deliver ultra-high sensitivity and speed due to its unique
time-focusing advantages inherent in the combination of dual TIMS
technology and the breakthrough PASEF method. In addition, we have
recently demonstrated that the timsTOF Pro is also an
excellent system for intact protein analysis for biopharma
applications, using appropriate LC separations, but all on the
exact same mass spectrometer.ˮ
Dr. Thakur continued: "Beyond 4D proteomics, we have now also
introduced novel 4D workflows that could revolutionize
next-generation lipidomics and metabolomics. Both of these
phenomics methods greatly benefit from the additional, large-scale
and accurate CCS information for every known and unknown compound
measured. We are very pleased that Professor Jeremy Nicholson will explore and further
develop novel 4D phenomics methods on the timsTOF Pro
platform at his new, world-class phenomics laboratories at Murdoch
University and at the Australian National Phenome Center.ˮ
Bruker had previously introduced the timsTOF Pro for
4D lipidomics with MetaboScape software at HUPO 2018.
This combination enables molecule-specific and accurate collision
cross section prediction for most classes of lipids using machine
learning with the CCSPredict™ algorithm.
The additional innovations introduced at EuPA 2019 follow just
three weeks after Bruker announced the following new timsTOF®
Pro-based solutions and capabilities at US HUPO 2019 (see
separate press release, dated March 4,
2019):
- High-throughput clinical plasmaproteomics research: 192
depleted plasma samples from septic shock patients measured in 2
days, with 11.5 minute gradients using the Evosep One HPLC system
with only 100 ng/run
- Enhanced proteomics data completeness: MaxQuant
'match-between-runs' with large-scale CCS values for dramatic
improvements in peptide and protein data completeness
- Host cell protein (HCP) analysis for biologics: Protein
Metrics adds large-scale, accurate CCS to Byonic 4D database search
engine for biopharmaceutical companies
About the timsTOF PRO with PASEF
The proprietary timsTOF Pro system uses
PASEF, enabled by Trapped Ion Mobility Spectrometry (TIMS) to
provide industry-leading data acquisition speed for shotgun
proteomics. The unique dual TIMS geometry of the timsTOF
Pro, combined with the time focusing of the ion packets in
the TIMS device, means that the speed advantage provided by PASEF
comes along with simultaneous improvements in sensitivity and
quantitation. All of these gains in speed, sensitivity and
quantitation maintain the advantages of Bruker's high-performance
QTOF mass spectrometers, including high mass resolution (resolving
power of 50,000 FWHM even at highest data acquisition rates) in MS
and MS/MS mode, ppm accurate mass, and high isotopic fidelity (True
Isotopic Pattern, or TIP™). The robust timsTOF Pro
with PASEF gives scientists the tools to dig deeper into the
complex cellular machinery with the potential to discover
low-level, biologically significant peptides or proteins, or
validate them in translational proteomics research.
About Bruker Corporation (Nasdaq: BRKR)
Bruker is enabling scientists to make breakthrough discoveries
and develop new applications that improve the quality of human
life. Bruker's high-performance scientific instruments and
high-value analytical and diagnostic solutions enable scientists to
explore life and materials at molecular, cellular and microscopic
levels. In close cooperation with our customers, Bruker is enabling
innovation, improved productivity and customer success in life
science molecular research, in applied and pharma applications, in
microscopy and nanoanalysis, and in industrial applications, as
well as in cell biology, preclinical imaging, clinical phenomics
and proteomics research and clinical microbiology. For more
information: www.bruker.com.
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Director, Investor
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Bruker
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Corporate
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T: +49 (421)
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Bruker
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E:
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T: +1 (978) 663-3660,
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