- New AI-powered TIMSquant™ software for CCS-enabled,
label-free quantification scalable to thousands of samples
- Early midia-PASEF® access for immunopeptidomics and PTMs on
ultra-sensitive timsTOF Ultra for DDA-like precursor traceability
in dia-PASEF
- Affordable, high-throughput ~3,500 PG plasma proteomics on
timsTOF HT with PreOmics ENRICH kit using Biognosys Spectronaut® 18
directDIA+™ software
- New PepSep™ ULTRA XL and MAX HT nano-LC columns for DDA
library creation and high-throughput proteomics,
respectively
- Novel TwinScape™ digital twin for optimal timsTOF
performance and uptime
- New partnership with Mass Dynamics for biological knowledge
generation
- Enhanced MALDI HiPLEX-IHC workflow for spatial tissue
proteomics
- New MetaboScape™ release for 4D-Lipidomics™ and
4D-Metabolomics™
At the 22nd Human Proteome Organization World Congress 2023,
Bruker Corporation (Nasdaq: BRKR) today announced advances in
instrumental methods, consumables and software for 4D-Proteomics,
MALDI HiPLEX-IHC spatial tissue proteomics, 4D-Lipidomics and
4D-Metabolomics.
This press release features multimedia. View
the full release here:
https://www.businesswire.com/news/home/20230918138030/en/
Fig. 1: TIMSquant for CCS-aware,
AI-powered quantification (Graphic: Business Wire)
A. Novel scalable AI-powered TIMSquant™ for label-free
quantification
Bruker introduces TIMSquant a scalable, CCS-enabled
AI-powered label-free quantification algorithm integrated into
Bruker ProteoScape™. TIMSquant performs accurate
quantification of peptides and proteins present in 100s or 1000s
samples by using global retention time and collision cross-section
(CCS) prediction models. Accurate, large-scale CCS data further
increases specificity and quantification consistency based on
previously identified peptides and aligned missing values.
Bruker ProteoScape is Bruker’s comprehensive GPU-powered,
TIMS DIA-NN-based proteomics software optimized for
CCS-centric informatics, and it now comes with the BPS Novor
module for de novo peptide sequencing for immunopeptidomics.
BPS Novor was co-developed with Rapid Novor Inc., a Canadian
software and CRO company. TIMS DIA-NN is a customized
version of highly regarded DIA-NN software by Demichev and
collaborators.
Dr. Kosuke Ogata, Assistant Professor at Kyoto
University, commented: "Ultra-high speed LC-MS from large-scale
clinical cohorts harnessing the high duty-cycle of timsTOF
technology is a focus of our laboratory. Analysis of
non-proteotypic peptides is critical to our research. We have
installed the BPS Novor de novo software on Bruker ProteoScape
(formerly PaSER) and we are impressed with the real-time speed and
high-quality de novo sequences produced."
Dr. Hanno Steen, Associate Professor at Harvard Medical
School & Director of Proteomics at Boston Children's Hospital,
stated: “We focus on the discovery and validation of biomarkers
from body fluids, such as plasma, serum, CSF, saliva and urine in
high throughput. We leverage the robustness of our timsTOF
instruments and real-time Bruker ProteoScape to build large
spectral libraries and analyze 1000s of clinical research samples.
We have recently expanded our bioinformatics pipeline to run on
ProteoScape, and are truly excited by the realistic potential to
apply this for the analysis of 10,000s of LC/MS runs in real time
to decipher the pathology of pediatric, immunologic, and
neurological diseases.”
B. Novel dia-PASEF scan modes
Bruker offers selected upgrades to timsControl
acquisition software with the key advances of 300 Hz PASEF
and VistaScan™ technology as downloads from the Bruker web
page (Reference 3). The 300Hz dda-PASEF acquisition now allows up
to 18,000 CCS-enabled MS/MS spectra per minute with very short LC
gradients. VistaScan allows scanning the quadrupole synchronously
with the TIMS ramp during the mobility scan to optimally cover the
ion population in the ion-mobility-mass to charge plane.
(References 1 & 2).
VistaScan enables midia-PASEF, exclusively licensed from
Johannes Gutenberg University Mainz. Bruker is initiating a limited
early-access program for midia-PASEF for immunopeptidomics and
post-translational modifications (PTMs) on the ultra-sensitive
timsTOF Ultra. These applications benefit from the
sensitivity-with-speed of midia-PASEF, as well as the DDA-like
precursor traceability that can be extracted from midia-PASEF
data.
C. PreOmics ENRICH Kit for affordable, high-throughput ~3,500
PG plasma proteomics
Bruker, together with PreOmics and Biognosys are now offering
further improved high-throughput, affordable, medium-depth plasma
proteomics kits and CRO services for reliably quantifying ~3,500
protein groups using PreOmics ENRICH-iST microbeads (SP3
technology) from minimal sample amounts and various species without
antibodies/aptamers.
D. PepSep™ ULTRA XL and PepSep™ MAX HT columns
Bruker announced the launch of the PepSep™ ULTRA XL and
PepSep™ MAX HT columns. The PepSep ULTRA XL was designed for
long LC gradients, e.g. for DDA-PASEF spectral library generation,
which can improve confidence and coverage in peptide and protein
identification during short gradients in DIA-PASEF analysis. The
PepSep MAX HT is optimized for short-gradients (<15 min
run0times) used for high throughput proteomics.
Dr. Byoung-Kyu Cho, Assistant Professor at Washington
University School of Medicine and Proteomics Lead at Mass
Spectrometry Technology Access Center (MTAC) commented: “PepSep MAX
HT columns have brought a remarkable transformation to our mass
spectrometry endeavors. This compact column stands out with
superior throughput, enduring robustness, and an interface that is
user-friendly, making it easy to operate. To all colleagues in
search of top-tier high-throughput data, I endorse the PepSep MAX
HT.”
E. TwinScape digital twin functionality in Bruker ProteoScape
software
To ensure optimal run conditions for every sample, Bruker
introduces TwinScape™, a digital twin for the timsTOF
platform, using Bruker ProteoScape software and the
Biognosys iRT kit. TwinScape continuously monitors key parameters
to ensure that complex assays and large studies are run under
optimal conditions, supporting real-time QC with the iRT kit, which
contains eleven non-naturally occurring synthetic peptides. The iRT
kit peptides have been optimized for stability, sensitivity, rt
spacing and peptide CCS.
Dr. Roman Fischer, Associate Professor at University of
Oxford, commented: “At the Centre for Translational Proteomics
(CTP), we provide services for clients interested in deep proteomes
from small sample amounts. Clinical proteomics and spatial
proteomics both of require characterization of large sample cohorts
at high throughput. Bruker ProteoScape monitors the sample and data
quality in real-time, exploiting the outstanding robustness of the
timsTOF platforms for high-throughput deep proteomics.”
F. Biological knowledge generation from 4D-Proteomics with
Mass Dynamics
Bruker’s collaboration with Prof. Andrew Webb at WEHI,
co-founder of Mass Dynamics Pty Ltd, has led to the integration of
data from Bruker ProteoScape™ and now Spectronaut®
with Mass Dynamics interactive visualization tools for knowledge
extraction to allow scientists to answer more biological
questions.
G. Novel SpatialOMx workflows enhancing 4D-Proteomics
In collaboration with AmberGen, Bruker further advances the
novel MALDI HiPLEX-IHC workflow for spatial proteomics based
on antibody-based localization of target proteins with a
significantly enhanced probe selection and robust workflows similar
to IHC protocols, adapting HiPLEX-IHC to a variety of areas from
immunooncology to neuropathology.
Dr. Bernd Bodenmiller, Professor University of Zuerich
and ETH Zuerich, and Director of the Department of Quantitative
Biomedicine, noted: “Recent research shows that spatial proteomics
provides biological context about tissue neighborhoods by providing
spatially defined biomarkers. The cellular arrangements and
location of proteins in the tissue microenvironment elucidates
biological mechanisms in disease or homeostasis, supporting novel
precision medicine applications. Using HiPLEX-IHC tissue imaging on
our timsTOF fleX enhances our multiomic spatial view of tissue
ecosystems.”
H. Novel MetaboScape software for 4D multiomic
research
In the new release of MetaboScape®, CCS-enabled
4D-Lipidomics is complemented by integrating semi-quantitative
analysis utilizing stable isotopically labeled lipid standards.
Dr. Heiko Hayen, Institute of Inorganic and Analytical
Chemistry, University of Münster, Germany, said: “The new
CCS-enabled workflow with T-ReX 4D in MetaboScape allows us to
accurately normalize our lipid class concentrations with labelled
internal standards. By adopting this solution, we observed a
noticeable improvement in standard deviations among covered lipids,
enhancing reproducibility in our lipidomics research.”
Dr. Viswa Colluru, CEO and Founder of Enveda Biosciences,
said: “The open software ecosystem provided by Bruker is at the
foundation of our discovery platform. Their CCS-enabled workflows
give us an edge in discerning compounds from nature with better
resolution. Bruker’s commitment to innovation and customer support
makes them a great partner and helps achieve our mission of
translating nature into medicine."
References:
- Distler et al., bioRxiv 2023.01.30.526204,
https://doi.org/10.1101/2023.01.30.526204
- Skowronek et al., Molecular & Cellular Proteomics, Feb
2023; 22(2):100489-100489,
https://doi.org/10.1016/j.mcpro.2022.100489
-
https://www.bruker.com/protected/de/services/software-downloads/mass-spectrometry/acquisition-software.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 and cell biology research, in applied and pharma
applications, in microscopy and nanoanalysis, as well as in
industrial applications. Bruker offers differentiated, high-value
life science and diagnostics systems and solutions in preclinical
imaging, clinical phenomics research, proteomics and multiomics,
spatial and single-cell biology, functional structural and
condensate biology, as well as in clinical microbiology and
molecular diagnostics. Please visit www.bruker.com.
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Media Petra Scheffer Bruker Daltonics Marketing
Communications T: +49 (421) 2205-2843 E:
petra.scheffer@bruker.com
Investor Relations Justin Ward Sr. Director Investor
Relations & Corp Development T: +1 (978) 663–3660, ext. 1479 E:
Investor.Relations@bruker.com
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