ATLANTA, May 31, 2019 /PRNewswire/ -- At the
67th American Society for Mass Spectrometry Conference
(ASMS) being held June 2-6 in
Atlanta, Bruker is announcing
highly innovative new mass spectrometry products and workflows:
A. SpatialOMx™ Life Sciences and
Translational Mass Spectrometry Imaging
Bruker introduces the novel timsTOF
fleX™ mass spectrometer, which
includes a software-switchable MALDI source adapted to the ESI
timsTOF Pro™ platform.
This new, combined ESI/MALDI capability enables spatially-resolved
omics, SpatialOMx™, on a single
instrument. The timsTOF fleX comes with
Bruker's proprietary 10kHz
SmartBeam™ 3D laser with true pixel
fidelity for rapid, label-free MALDI imaging at high-spatial
resolution, while fully preserving the unparalleled 4D proteomics and phenomics
sensitivity of the timsTOF Pro in ESI mode.
With this unique SpatialOMx approach, researchers gain
insights into spatial molecular distributions in tissues from MALDI
imaging, to guide 4D omics molecular expression studies, e.g. on
proteins, low-level cancer antigen peptides, lipids, glycans,
metabolites, or xenobiotics, which cannot be observed by
traditional staining or labelling techniques. MALDI-guided
SpatialOMx allows for specific targeting of cell
sub-populations for subsequent ESI-TIMS/PASEF-based dda or dia 4D
proteomics or 4D lipidomics/metabolomics. Both can now be performed
on a single robust instrument, the timsTOF fleX, with
the ultra-high sensitivity needed to advance single-cell biology
research, as a perfect complement to single-cell transcriptomics by
RNA-seq.
Professor Richard Drake,
Director of the Proteomics Center at the Medical University of South Carolina, stated:
"The data from our samples using the new timsTOF
fleX system was unprecedented in terms of spatial
resolution and depth of glycan coverage. As glycans are emerging as
potential clinical markers in tissue and serum to monitor overall
immune status, and healthy or unhealthy aging, the unique
capabilities of the timsTOF flex will greatly
accelerate these efforts. The timsTOF flex allows our
cumulative approaches that we have developed for tissue and
biofluid analysis of cancers and immunotherapies to converge on one
platform. I can see unlimited applications of such an instrument in
many research areas for rapid glycan tissue imaging and biofluid 4D
omics analysis."
Dr. Rohan Thakur,
Executive Vice President at Bruker Daltonics, added: "Most tissue
proteomics studies blend cells from diverse sub-populations, with
an undesirable averaging effect that obscures a lot of important
biology and pathobiology. MALDI-guided spatialOMx on the
timsTOF fleX enables the profiling of
spatially-defined tissue regions, thereby allowing subsequent 4D
proteomics to selectively target cell-type sub-populations. The
robust, ultra-high sensitivity timsTOF fleX bridges
the divide between molecular tissue imaging and body fluids
analysis by offering nanoLC-TIMS-MS/MS on the same instrument. This
unique combination will make the timsTOF fleX an
invaluable research tool for spatially-resolved 4D proteomics and
phenomics, as well as for advancing single-cell biology,
pharmaco-proteomics, and translational 4D cross-omics workflows on
large cell numbers or patient cohorts."
Bruker is also launching
IntelliSlides™ specifically
designed to automate timsTOF fleX workflows.
The IntelliSlides come pre-inscribed with
software-readable 'teach marks' on the conductive surface to
indicate where to place the tissue sample, a bar code and tracking
number. IntelliSlides automation removes sources
of inefficiency from sample loading, as they are inherently
correctly labelled, oriented properly, and MALDI image registration
occurs at the touch of a button. With specialized software,
IntelliSlides now make MALDI Imaging even easier for
everyone. More…
Moreover, Bruker introduces SCiLS Lab 2020 MALDI
imaging software, now integrated with MetaboScape5.0
for providing automated annotations of lipids and metabolites in
tissue molecular images in spatialOMx. This unique
combination automatically matches ions measured on tissue to
molecular information in metabolomics and lipidomics workflows,
highlighting biologically relevant pathway information using MALDI
imaging.
Dr. Daniel Krug, Assistant
Professor at the Helmholtz Institute for Pharmaceutical Research
Saarland (HIPS), commented: "We use mass spectrometry in the fields
of pharmaceutical research and spatial metabolomics. This includes
in particular the analysis of myxobacterial secondary metabolomes
for novel natural products. Our lab has been using Bruker's
instrumentation and software for years, in particular SCiLS
Lab and MetaboScape. The new molecular imaging workflow
that integrates both of these software solutions greatly simplifies
and speeds up the entire MALDI imaging pipeline. It translates ion
images into molecular images with confidence in the annotated
molecules."
The new integrated imaging and metabolomics workflow also
supports data from Bruker's scimaX™ MRMS platform, as well
as from the new timsTOF fleX. MetaboScape's
unique T-ReX 2D algorithm performs feature extraction,
de-isotoping, and ion deconvolution on MALDI imaging datasets.
Within MetaboScape, molecular features are annotated based
on accurate mass and isotopic fidelity using
SmartFormula™ and molecular
information, e.g. from public databases such as HMDB and LipidMaps.
MetaboScape now also offers the unique ability to increase
ID scoring confidence by integrating accurate TIMS collision
cross-sections (CCS) from timsTOF analyses. Identifications flow
back to SCiLS Lab for fully annotated molecular images.
SCiLS Lab is the market-leading software for MS imaging,
while MetaboScape is the software solution of choice for
identification of metabolite markers and pathway
mapping... More…
B. 4D Proteomics and 4D Phenomics
Innovations
DiaPASEF and MBR-ddaPASEF Advances in 4D Proteomics
Bruker's revolutionary timsTOF™ Pro for
next-generation nLC-TIMS-MS/MS 4D proteomics has been further
enhanced by combining PASEF with data-independent (DIA) acquisition, in diaPASEF
for ultra-high sensitivity bottom-up proteomics. While the
unmatched duty-cycle of data-dependent acquisition (DDA) PASEF dramatically
improved sensitivity and depth of coverage using short nanoLC
runtimes, the stochastic nature of DDA results in missing values,
an issue significantly improved by diaPASEF worflows, or by
match-between-runs (MBR) for ddaPASEF.
The novel diaPASEF1 workflow, shown at ASMS 2019 as
work-in-progress available to methods development customers,
uses overlapping windows in the ion mobility domain to trigger
MS/MS, efficiently using the quadrupole to transmit the precursor
ions at high sensitivity. By using the inherent duty-cycle
advantage of PASEF, the new diaPASEF workflow typically results in
a 30% improvement, now with over 7,000 proteins identified in a 120
minute single-shot experiments with 200 ng of HeLa digest injected.
Data analysis, including 4D feature alignment in mass,
retention time, ion mobility and intensity, is performed using the
new Mobi-DIK software, which is based on the OpenMS
software developed in the group of Professor Hannes Roest at the University of Toronto.
Dr. Gary Kruppa, Bruker's
Vice President of Proteomics, explained: "Adding the diaPASEF
workflow is a major step forward in addressing the missing values
problem in bottom-up proteomics, and in improving label free
quantification (LFQ). The timsTOF Pro is fast gaining
a reputation of delivering increased depth of coverage using short
gradients, and for providing industry-leading robustness due to its
orthogonal source and dual-TIMS funnel design. Furthermore, peptide
CCS values obtained on the timsTOF Pro are proving
fundamental to increasing protein ID numbers in diaPASEF workflows,
and also in using CCS for match-between-runs (MBR) in ddaPASEF, in
order to further improve data completeness and LFQ performance at
low protein abundance. We would like to thank our scientific
partners Drs. Matthias Mann,
Ruedi Aebersold, Ben Collins and Hannes
Roest for the most fruitful diaPASEF collaboration, and Dr.
Juergen Cox for the excellent
further progress with MBR-ddaPASEF."
Dr. Juergen Cox, Group
Leader of Computational Systems Biochemistry at the Max-Planck
Institute of Biochemistry in Martinsried, stated: "We have
developed a highly parallelizable 4D feature detection algorithm
for timsTOF Pro datasets that extracts peaks which are
assembled to isotope patterns, followed by mass re-calibration
using non-linear fitting of m/z, and also alignment in retention
time, ion mobility and signal intensity. The missing value problem
in label-free protein quantification over many samples can now be
greatly reduced by MS1-level CCS-aware match-between-runs
(MBR)2, resulting in significantly improved assay
precision and accuracy using a benchmark."
New Consumables and Software for 4D Proteomics
Bruker and PreOmics GmbH announced a co-development and
co-marketing agreement, which will
focus on PreOmics iST sample preparation technology on the
timsTOF Pro. The inStageTip (iST) technology removes
detergents, polymers, salts, lipids and other contaminants, and has
exceptional peptide recovery. New iST protocols enable
robust and reproducible sample preparation with a significant time
advantage (over 40 hrs saved) compared to common protocols, and
iST is suitable for integration in semi-automated,
high-throughput sample prep.
Drs. Nils Kulak and
Garwin Pichler, Managing
Directors at PreOmics, commented: "We are very excited to work with
Bruker on end-to-end workflows that make protein analysis simply
better, and to share these improvements with our highly valued
academic and biopharma customers around the world. We are convinced
that the power of the timsTOF Pro for 4D
proteomics is a perfect match for our iST sample processing
technology."
For proteomics software, Bruker and Genedata announced a
partnership for the Genedata Expressionist software
platform, which now supports the timsTOF Pro 4D omics
format. Native support of the latest timsTOF Pro data file
format opens new opportunities for streamlining and automating the
most complex proteomics, metabolomics and biotherapeutics
characterization studies. The power of intelligent precursor
selection for deep proteome coverage with fast gradients of the
timsTOF Pro in combination with the scalability and speed of
Genedata Expressionist enables the implementation of a
next-generation host cell protein (HCP) analysis platform.
Dr. Peter Hufnagel, Life
Sciences Software Manager at Bruker, expanded: "Our API-driven open
data file format philosophy is helping to accelerate the adoption
of timsTOF data into many important third party software
solutions. Incorporation into Genedata Expressionist
is an important further step requested by mutual biopharma
customers for HCP analysis, and this was rapidly accomplished by
Genedata due to our open file format architecture."
Dr. Markus Brosch,
Business Unit Head for Genedata Expressionist, said:
"Genedata Expressionist® builds on its proven
proteomics capabilities to identify and quantify host cell proteins
(HCPs) right down to the detection limit. It uniquely supports a
wide range of HCP search and analysis strategies leveraging a
high-performance enterprise architecture, offering unprecedented
speed and scalability required to process large volumes of complex
proteomics data. Our joint customers can now not only automate and
accelerate HCP analysis, but utilize one software platform for all
their needs across proteomics, metabolomics and biotherapeutics
characterization."
Novel Ultra-high Sensitivity 4D Lipidomics Workflow
Building on the success of MetaboScape® and
CCSPredict™, Bruker announces advances to ultra-high
sensitivity 4D lipidomics workflows on the timsTOF
Pro and timsTOF fleX platforms, demonstrating
high-throughput and high-sensitivity measurements using
LC-TIMS-MS/MS. Optimization of novel PASEF 4D lipidomics methods
now enables the number of identified lipids in single-shot analysis
to be almost doubled, whilst obtaining attomole sensitivity.
This innovative workflow uses nanoLC-TIMS-PASEF to quantify
approximately 500 lipids with very high quantitative accuracy and
reproducibility from just a few thousand cells, in addition to
building a library of more than 1,000 accurate CCS values from
human plasma, mouse liver and human cancer cells.
Dr. Florian Meier,
postdoctoral fellow at Max-Planck Institute of Biochemistry and
senior author of the study3, added: "Our study
establishes 4D lipidomics and paves the way for more sensitive
lipidomics using PASEF. The precision and accuracy obtained using
TIMS can be leveraged to facilitate lipid assignment, in addition
to the comprehensive MS/MS information generated by PASEF.
Additionally, high-precision CCS values provide a basis for machine
learning techniques to predict CCS values more accurately and for a
broader range of lipid classes."
Please join us on Sunday, June
2nd, from 7:30 am to 12:30
pm for our eXceed Symposium at the Marriott Marquis Atlanta
to listen to Prof. Vicki Wysocki
speak about results obtained in her
laboratory with the timsTOF Pro. Moreover, Prof.
Jeff Spraggins and Prof.
Nathalie Agar will share their
experience and initial results on the new timsTOF
fleX. Two parallel sessions follow on 4D
Proteomics/Biopharma and MS Imaging/SpatialOMx.
Bruker will host a scientific press conference on Monday, June 3, 2019, at 9:30 am EDT at the Omni Hotel, Grand Ballroom D,
North Tower M4, including Bruker management and guest speaker Prof.
Vicki Wysocki .
Customers are invited to visit the Bruker's ASMS booth #515
throughout the conference.
For more information: www.bruker.com/events/2019/asms-2019
- Parallel accumulation serial fragmentation combined with
data independent acquisition (diaPASEF): Bottom up proteomics with
near optimal ion usage, by Florian
Meier, Andreas-David Brunner,
Max Frank, Annie Ha, Eugenia
Voytik, Stephanie
Kaspar-Schoenefeld, Markus
Lubeck, Oliver Raether,
Ruedi Aebersold, Ben C Collins,
Hannes L Rost, and Matthias Mann.
www.biorxiv.org/content/10.1101/656207v1
- MaxQuant software for ion mobility enhanced shotgun
proteomics, by Nikita Prianichnikov, Heiner Koch, Scarlet
Koch, Markus Lubeck,
Raphael Heilig, Sven Brehmer, Roman
Fischer, Jürgen Cox.
www.biorxiv.org/content/10.1101/651760v1
- Trapped ion mobility spectrometry (TIMS) and parallel
accumulation - serial fragmentation (PASEF) enable in-depth
lipidomics from minimal sample amounts, by Catherine G
Vasilopoulou, Karolina Sulek,
Andreas-David Brunner, Ningombam
Sanjib Meitei, Ulrike
Schweiger-Hufnagel, Sven W.
Meyer, Aiko Barsch,
Matthias Mann, and Florian Meier.
www.biorxiv.org/content/10.1101/654491v1
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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