Bruker Introduces PaSER™ Software for ‘Run and Done’ 4D- ProteomicsTM and TIMS/PASEF Method Wins HUPO 2020 Award
October 19 2020 - 6:00AM
Business Wire
- HUPO 2020 Science and Technology Award for Commercialization of
TIMS Technology
- True Single Cell 1,000 Protein Group Results from Mann Lab
leverage dia-PASEF® and further improvements in ultra-low flow
Evosep chromatography and modified TIMS/PASEF set-up
- Significant Improvements in Quantitative Targeted 4D-Proteomics
with prm-PASEF®
- Licensing of PhoX cross-linker from Heck Lab enables caps-PASEF
structural proteomics
At the virtual 19th Human Proteome Organization World Congress
(hupo2020.org), Bruker Corporation (Nasdaq: BRKR) today announced
that Melvin A. Park and Oliver Raether were awarded the HUPO
Science and Technology Award for the commercialization of
Trapped Ion Mobility Spectrometry (TIMS) and the Parallel
Accumulation Serial Fragmentation (PASEF®) method. This award
recognizes innovation that changes the way scientists do
proteomics, validating the role the timsTOF Pro has on enabling
short gradients for large cohort deep 4D-Proteomics translational
studies. Bruker also takes the opportunity to recognize the
contributions of PASEF co-inventor Professor Matthias
Mann.
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Figure 1: Real-time PaSER can monitor
4D-Proteomics data acquisition (Photo: Business Wire)
A. Real-Time Database searching with PaSER™ for “Run and
Done’ 4D-Proteomics
Bruker further announced the release of PaSER, a complete
GPU-based device enabling proteomics database search in ‘real
time’, building on the recently announced acquisition of IP2
software. The term ‘PaSER’ was coined by Professor John Yates
III and Dr. Robin Park from The Scripps Research
Institute and stands for Parallel Database Search
Engine in Real-time. The unique PaSER
architecture uses a parallelized, multi-threaded search engine
running on GPUs to search proteomics results in real time at or
faster than the data acquisition. This result is ‘Run and Done’
high-throughput 4D-Proteomics where scientists have identified
peptides and protein groups as soon as the experiment is
complete.
Professor Yates will present on “The Synergies of Mass
Spectrometry and Informatics” in Bruker’s Virtual Industry Seminar
(hyperlinks to HUPO talks and events mentioned in this news release
are included below), and Dr. Robin Park will discuss IP2 and PaSER
at Bruker’s virtual proteomics user’s meeting.
Dr. Gary Kruppa, Vice President of Proteomics at Bruker
Daltonics, commented: “The timsTOF Pro enables 4D-Proteomics with
the large-scale measurement of ion mobility yielding collision
cross sections (CCS) for every measured peptide. Combined with the
timsTOF Pro speed this means that the bottleneck in proteomics has
moved from measurement to processing large amounts of data. The
speed of IP2 and the PaSER GPU-based search are an ideal match for
the timsTOF Pro, and we are thrilled to have Robin Park join us to
continue the development of IP2 and PaSER for TIMS/PASEF
methods.”
B. Ultra-high Sensitivity and True Single Cell
4D-Proteomics
The groups of Prof. Matthias Mann at the Max Planck
Institute in Martinsried, Germany, and at the Medical School of the
University of Copenhagen, with collaborators at Evosep and Bruker,
have made significant advances in high sensitivity and true single
cell proteomics. A modified timsTOF Pro allows robust measurements
of proteomes from low sample amounts and even from single cells.
Matthias Mann will present his work in “Deep Visual Proteomics for
Systems Biology” in the HUPO Connect 2020 program, while his Ph.D.
student Andreas Brunner will present at Bruker’s virtual user’s
meeting on “Ultra-high sensitivity MS on a timsTOF enables
proteomics analysis of single cells – one by one”.
Matthias Mann stated: “Making meaningful measurements of protein
expression at the true single cell level is extremely challenging
both from a sample handling and measurement perspective. We are
delighted to have Evosep and Bruker as collaborative partners to
help us implement, prove and ultimately bring to the clinic our
ideas so that true single cell proteomics can be made available to
all researchers in the near future.”
C. Targeted Quantitative 4D-Proteomics and prm-PASEF
Bruker’s prm-PASEF workflow for quantitative proteomics enables
the most highly multiplexed targeted proteomics methods available.
The additional dimension of separation provided by TIMS also
reduces interferences in MS2 quantitation. Taking advantage of the
speed and additional TIMS separation of the underlying PASEF
method, prm-PASEF can now target more than a dozen precursors in
each 100 msec TIMS separation. Professor Gunnar Dittmar of
the Luxembourg Institute of Health and Professor of Proteomics at
the University of Luxembourg will present on “New prm-PASEF Method
for Highly Multiplexed Targeted Quantitative Proteomics for
Clinical Research” at Bruker’s Virtual Industry Seminar at HUPO
Connect 2020.
D. caps-PASEF Crosslinking for Structural 4D-Proteomics and
the PhoX Crosslinker
Bruker is pleased to announce licensing PhoX cross-linking
technology (IMAC-enrichable) as result of the collaboration with
Albert Heck and Richard Scheltema at Utrecht
University. The advantage the timsTOF Pro provides for
cross-linking aided by PhoX and the novel caps-PASEF method is
described in the paper “Benefits of Collisional Cross Section
Assisted Precursor Selection for Cross-linking Mass Spectrometry”,
published in Molecular and Cellular Proteomics. The PhoX
cross-linking reagent from Bruker will be available in early
2021.
E. Software Developments for Analysis of 4D-Proteomics
Data
The third-party software ecosystem around the timsTOF Pro
continues to grow as the community takes advantage of Bruker’s
unique, open data file format. New developments include support for
dia-PASEF from Bioinformatics Solutions Inc.’s PEAKS Studio and
PEAKS Online software packages. In particular, PEAKS Online
provides an enhanced, cloud-based solution for processing of large
datasets from large sample cohorts, including further improvements
for LFQ quantitation and new workflows like SILAC. MaxQuant will
soon support dia-PASEF processing capabilities.
Biognosys announced rapid processing of timsTOF Pro 4D PASEF
data with SpectroMine, their software solution for multiplexed and
label-free quantitative DDA proteomics, built around the powerful
Pulsar search engine. Dr. Lukas Reiter, Chief Technology
Officer of Biognosys commented: “It has been a priority for us to
optimize support for timsTOF Pro in our software, resulting in fast
processing of 4D PASEF data with deep proteome coverage.
SpectroMine 2 can now be used for isobaric labeling, as well as for
label-free quantification (LFQ) workflows with timsTOF Pro
data.”
Links to Bruker events at HUPO 2020 can be found here:
https://www.bruker.com/events-records/2020/hupo-connect-2020.html.
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, please visit: www.bruker.com.
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Media Contact: Petra Scheffer Bruker Daltonics Marketing
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petra.scheffer@bruker.com
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