ADELAIDE, Australia, Sept.
16, 2019 /PRNewswire/ -- At the 18th Human Proteome
Organization World Congress (www.hupo2019.org), Bruker (Nasdaq:
BRKR) today announced the release of the diaPASEF
workflow, a novel data-independent acquisition (DIA) method on the
timsTOF Pro platform. The timsTOF Pro
leverages trapped ion mobility spectrometry (TIMS) and 'parallel
accumulation - serial fragmentation' (PASEF),
developed in an intensive collaboration over several years with the
group of Professor Matthias Mann at
the Max Planck Institute in Martinsried1,2, for
unmatched duty cycle, sensitivity and speed.
The new diaPASEF3 workflow, shown as
work-in-progress at ASMS 2019, uses overlapping windows in the ion
mobility domain to trigger MS/MS, efficiently using the quadrupole
to transmit precursor ions at high sensitivity. Using the inherent
duty-cycle advantage of PASEF, diaPASEF typically
results in a further 30% improvement in protein identifications,
now with over 7,500 proteins identified in a 120 minute single-shot
experiment on 200 ng of HeLa digest. diaPASEF also
alleviates the so-called 'missing value problem' in stochastic,
data-dependent acquisition (DDA) methods, and thereby improves data
completeness and sensitivity.
Data analysis, including 4D feature alignment in retention time,
ion mobility, mass and intensity, was originally performed using
the new Mobi-DIK software developed in the group of
Professor Hannes Röst at the
University of Toronto. The breakthrough diaPASEF
method is the result of a collaboration with our scientific
partners Professors Matthias Mann
(Max Planck Institute, Martinsried), Ruedi
Aebersold (IMSB at ETH Zuerich), Ben
Collins (Queen's University Belfast), and Hannes Röst
(University of Toronto).
Bruker also has worked with several additional partners to
develop user-friendly and fast solutions for
diaPASEF data analysis. At HUPO 2019, the
following beta releases or release versions are available for
diaPASEF processing:
Mobi-DIK (U. Toronto),
PEAKS (Bioinformatics Solutions Inc.),
Spectronaut (Biognosys
AG), MaxQuant (Max Planck Institute,
Martinsried), and Skyline (MacCoss Lab
Software). In addition to the much more efficient ion usage in
diaPASEF, when compared to traditional DIA methods,
the timsTOF Pro provides the additional
dimension of ion mobility, or collision cross sections (CCS), which
all CCS-aware proteomics software solutions now take advantage of.
Besides retention time alignment, the timsTOF
Pro also allows simultaneous ion mobility alignment of
precursors and fragments in diaPASEF, improving the
reliability and specificity of the assignments even further.
More exciting results on the quantitative performance of
diaPASEF will be presented at HUPO 2019: Using
label-free quantification (LFQ) on a mixture of three proteomes
(HeLa, Yeast, E.coli) and Spectronaut software, more than 8,000
proteins could be reliably identified and quantified with at least
two peptides at a false discovery rate of 1%.
Dr. Lukas Reiter, Chief
Technology Officer at Biognosys, commented: "We are very interested
in and excited by the possibilities of enhancing DIA experiments
with the 4D capabilities of the timsTOF Pro and diaPASEF. Our
initial evaluation of the performance of the diaPASEF method on the
timsTOF Pro, based on our newly released diaPASEF data processing
in Spectronaut, has already shown industry-leading performance in
terms of speed, sensitivity and quantitative results. We look
forward to following Bruker's developments on further applications
of the diaPASEF method."
Dr. Roman Fischer,
Principal Investigator at the Nuffield Department of Medicine,
Target Discovery Institute at University of
Oxford, stated: "The arrival of the timsTOF Pro with PASEF
has completely changed the game for clinical proteomics. Suddenly
we can scale up clinical studies by a factor of 10x or more, and
even improve on robustness, data depth and completeness. We are
excited about the prospects for diaPASEF with short gradients for
our clinical research."
Work-in-Progress Novel 3D-targeted PRM workflow
with additional ion mobility targeting
For targeted quantitative proteomics, Bruker also introduces a
novel 3D-targeted Parallel Reaction Monitoring (PRM) method on the
timsTOF Pro as work-in-progress at HUPO 2019.
In traditional 2D PRM experiments, retention times and masses are
used to target and quantify lists of targeted protein biomarkers. A
problem in 2D PRM is that interfering peptides that co-elute with
similar precursor masses can be co-fragmented, which can reduce
quantitative performance, especially near the lower limits of
quantitation in complex matrices, like plasma.
The timsTOF Pro with its unique 4D proteomics
capabilities now can target proteins in three dimensions, namely
retention time and mass, plus by universal, molecule-specific and
precise CCS values. This additional 3D-targeting for PRM in ion
mobility, combined with the sensitivity enhancement provided by
TIMS/PASEF, and the >100 Hz MS/MS speed at 50,000 mass
resolution of the timsTOF Pro, means that more
proteins can be '3D-targeted' by PRM with better sensitivity and
quantitation.
Dr. Gary Kruppa, Bruker's
Vice President of Proteomics, said: "With diaPASEF we expect
accelerated development of new applications and more exciting
results. The development of fast and user-friendly software for
library generation and results analysis also is key to the adoption
of diaPASEF. We are very pleased to have such widespread support
for diaPASEF software from our collaboration partners. Combined
with new developments in 3D-targeted PRM for proteomics, the
timsTOF Pro covers ever more CCS-aware 4D proteomics
workflows in a unique way.ˮ
Bruker has begun collaborating with early adopters on
3D-targeted PRM quantitation for proteomics with new beta-software
to evaluate performance and obtain user input:
Dr. Jarrod Marto,
Associate Professor at the Dana-Farber Cancer Institute, Harvard
Medical Center, and Brigham and
Women's Hospital stated: "We are excited to be working with Bruker
on combining first-in-class acquisition speed with ion mobility to
drive new 3D-targeted PRM workflows on the timsTOF Pro. Our initial
results are very promising, and we are very pleased with the
collaborative effort to push PRM to new levels of performance."
Please join us at Bruker's booth #37-40 throughout the HUPO
conference. Bruker-sponsored lunch seminars will be held on
Monday, Sept. 16th, and Tuesday, Sept. 17th, and our breakfast
seminar is on Tuesday, Sept.
17th, all at the Adelaide convention center. For a complete
list of our seminars with guest speakers and other events, please
visit: https://www.bruker.com/events/2019/hupo.html
- Parallel accumulation – serial fragmentation (PASEF):
Multiplying sequencing speed and sensitivity by synchronized scans
in a trapped ion mobility device; F. Meier, S. Beck, N. Grassl, M.
Lubeck, M. A. Park, O. Raether, and M. Mann; J Proteome Res. 2015
Dec 4;14(12):5378-87.
- Online Parallel Accumulation-Serial Fragmentation (PASEF) with
a Novel Trapped Ion Mobility Mass Spectrometer. Meier F, Brunner
AD, Koch S, Koch H, Lubeck M, Krause M, Goedecke N, Decker J,
Kosinski T, Park MA, Bache N, Hoerning O, Cox J, Räther O, Mann M.;
Mol Cell Proteomics. 2018 Dec;17(12):2534-2545.
- Parallel accumulation – serial fragmentation combined with
data-independent acquisition (diaPASEF): Bottom-up proteomics with
near optimal ion usage; F. Meier, A. Brunner, M. Frank, A. Ha, E. Voytik, S.
Kaspar-Schoenefeld, M. Lubeck, O. Raether, R. Aebersold, B. C.
Collins, H. L. Röst, M. Mann; bioRxiv 656207; doi:
https://doi.org/10.1101/656207.
About the timsTOF Pro with PASEF
The timsTOF Pro system uses PASEF, enabled
by Trapped Ion Mobility Spectrometry (TIMS), to provide
industry-leading speed for shotgun proteomics. Its unique dual TIMS
geometry, combined with the time focusing of the ions in the TIMS
device, means that the speed advantage provided by PASEF comes
along with simultaneous improvements in sensitivity and
quantitation. These gains in speed, sensitivity and quantitation
maintain the advantages of Bruker's high-performance QTOF mass
spectrometers, including resolving power of 50,000 FWHM even at
highest acquisition rates in MS and MS/MS mode, ppm accurate mass,
and high isotopic fidelity (True Isotopic Pattern, or
TIPTM).
The exceptionally 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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