- Bruker PaSER™ software now incorporates transformative
CCS-enabled DIA-NN deep neural network learning with breakthrough
dia-PASEF capabilities to identify:
- >8000 quantified cell lysate proteins with 40-minute
gradients
- >5000 quantified cell lysate proteins with 4.8-minute
separations on Evosep One
- >5000 quantified proteins in just 10 ng of cell lysate
digest with 95-minute gradients
- Work-in-progress CCS-enabled ‘prm Live’ on timsTOF Pro
enables low-cost, targeted proteomics with >1800 peptides
quantified with highest sensitivity and excellent CVs
- Advances in CCS-enabled TIMScore™ algorithm yield
significantly greater phosphopeptide and protein coverage with more
confident peptide identifications
- Novel OligoQuest™ software and workflow for high confidence
sequence verification in support of RNA and modified
oligonucleotide therapeutics development
- SCiLS™ autopilot software for automated Mass Spectrometry
Imaging (MSI) acquisition on the timsTOF fleX and rapifleX® MALDI
platforms using Bruker IntelliSlides™
- Showcasing two novel systems launched already in June
2021:
- timsTOF SCP for unbiased single cell proteomics (SCP), e.g., to
study cell-type specific proteomes in spatial cancer biology and
correlate them with sc-RNA-seq transcriptomes
- next-generation timsTOF Pro 2 with unprecedented proteomic
depth and throughput
At the 69th ASMS meeting in Philadelphia, Bruker Corporation
(Nasdaq: BRKR) announced novel CCS-enabled 4D proteomics for major
capability enhancements for timsTOF Pro 2, timsTOF fleX and timsTOF
SCP mass spectrometers.
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Graphical representation of dia-PASEF
scan function (Graphic: Business Wire)
Dr. Rohan Thakur, Bruker’s EVP for Life Sciences Mass
Spectrometry explained: “TIMScore developed by the Yates Lab at
Scripps reduces peptide candidate ambiguity by evaluating predicted
against experimental CCS, for forward and decoy/reverse peptides.
The utility of CCS values augments DIA-NN in our collaboration with
the Ralser Lab at Charité, and it also enhances the detection of
PhoX™ crosslinked peptides in our collaboration with the Scheltema
Lab at Utrecht University. Finally, the Marto Lab at Dana Farber
Cancer Institute just published CCS-enabled prm Live with real-time
retention time corrections for parallel targeted high-sensitivity,
low CV quantitation of over 1800 peptides.”
A. PaSER powered by CCS-enabled DIA-NN for dia-PASEF
workflows
Translational proteomics, requiring high-throughput, short
gradients and uncompromised proteome depth is achieved using
dia-PASEF, published in Nature Methods [Mann, Nat Meth 2020], and
supported by various proteomics software packages including DIA-NN,
Spectronaut, MaxQuant and PEAKS Online. The DIA-NN software
[Demichev, Nat Methods. 2020] version 1.8 incorporates a novel CCS
module for deep neural network learning to score peptide spectrum
matches [Demichev, bioRxiv 2021] in dia-PASEF.
In collaboration with Drs. Vadim Demichev and Markus Ralser at
the Charité – Universitätsmedizin Berlin, Bruker is now integrating
CCS-enabled DIA-NN into PaSER GPU-powered proteomics software for
the timsTOF platform for enhanced identification and
quantification. Professor Ralser and co-workers work accelerates
translational proteomics in large sample cohorts and is
transformative by identifying >5000 quantified proteins in
5-minute acquisition times with dia-PASEF.
Dr. Markus Ralser, Einstein Professor of Biochemistry at
Charité, commented: “We’ve been very impressed with the performance
of the timsTOF Pro in our laboratories. We’re also pleased to see
Bruker incorporating the open-source version of Vadim Demichev’s
DIA-NN in its PaSER real-time proteomics workflows and look forward
to working with Bruker to further improve 4D-Proteomics
workflows.”
B. prm-PASEF Live increases number of targeted peptides for
high-sensitivity quantification
prm-PASEF workflows for parallelization of targeted compound
acquisition maintains very high sensitivity while targeting more
compounds than traditional PRM approaches. A new prm-PASEF editor
can now be used independently or when Skyline™ is used to create
prm methods. A recent paper by Professor Jarrod Marto et al.
“PRM-LIVE with Trapped Ion Mobility Spectrometry and Its
Application in Selectivity Profiling of Kinase Inhibitors”
dynamically adjusts retention time windows for reproducible target
scheduling using iRT peptides as retention time standards to
quantify 1857 tryptic peptides from cell lysate in a 60 min
acquisition. This innovative prm-PASEF Live concept overcomes
chromatographic drift in retention time and improves quantitative
precision and reproducibility of multiplexing targets. Dr. Marto
will present at the Bruker Press Conference at ASMS on November 2nd
at 11 am EDT.
C. TIMScore for CCS-enabled database search engines
CCS values in 4D-Proteomics applications are used in post
processing for ‘match between runs’ for label-free quantitation
[Cox, MCP 2020]. TIMScore now harnesses machine learning for a
CCS-enabled algorithm enabling search engines to provide greater
peptide and protein identification while retaining stringent false
discovery rates (FDR). Hundreds of thousands of experimental data
points were used to train a ML algorithm that can accurately
predict CCS value of tryptic and phosphorylated peptides.
Phosphorylation plays a critical role in cell signaling and
biology, but phosphorylated peptides are more difficult to
identify. TIMScore increased the number of phosphorylated peptides
by >10% in unenriched leukemia cell line samples provided by
Professor Eric Fischer at the Dana Farber Cancer Institute.
Professor Stanley Stevens at the University of South Florida
added: “TIMScore increased the identification of phosphorylated
peptides enriched from mouse microglia cell line by 11%. CCS values
and 4D-Proteomics have become indispensable in our application of
mass spectrometry-based proteomics. TIMScore shows promise to
transform how DDA searches are performed, identifying many more
meaningful peptides and proteins allowing us to go deeper into the
proteome using CCS.”
D. Launch of OligoQuest™
Bruker’s new OligoQuest software in the GLP-ready BioPharma
Compass suite offers enhanced RNA and oligonucleotide
characterization. OligoQuest leverages high isotopic fidelity from
maXis II and timsTOF Pro to characterize nucleic acid
macromolecules, such as single-guide RNA as well as their
impurities. Furthermore, fast PASEF acquisition maps complex
mixtures derived from digested mRNA samples.
Co-developed with RiboDynamics, LLC, OligoQuest offers
algorithms and workflows to annotate tandem MS data from
oligonucleotide sequences >100 nucleotides. Dan Fabris, CEO of
RiboDynamics and Harold S. Schwenk Sr. Professor at the University
of Connecticut, explained: “Isotopic fidelity combined with
ultra-high resolution mass spectrometry has shown tremendous
promise for the analysis of highly modified RNA, but commercial
software tools have been unavailable. Simplifying this analysis
with OligoQuest will dramatically accelerate research and
development in the RNA space.”
E. SCiLS autopilot for automating MALDI Mass Spectrometry
Imaging (MSI)
Bruker introduces the automated setup of MALDI Imaging with
SCiLS™ autopilot enabled by IntelliSlides™. SCiLS autopilot
automatically conducts six key performance optimizations to quickly
move from a prepared slide to acquisition of data. The scanned
sample image is registered with on the barcode on the IntelliSlide,
tissue margins are automatically detected, followed by automated
multi-step optimization to decrease the time and expertise needed
for MALDI Imaging, and to ensure reproducibility and image quality.
Through SCiLS autopilot automation, MALDI Imaging can be easily
integrated by non-expert users to add physiological tissue context
to their 4D-Omics studies.
Dr. Michael Easterling, Bruker Director of MALDI Imaging,
stated: “With market adoption of MALDI Imaging in biopharma,
intelligent automation is important to ensure seamless integration
of imaging and a driver of robust results. Deep platform
integration of acquisition and processing software with
imaging-optimized platforms, such as the timsTOF fleX, provides
spatial physiological context to multiomics.”
References:
[Mann, Nat Methods 2020]:
https://doi.org/10.1038/s41592-020-00998-0 [Demichev, Nat Methods.
2020]: https://dx.doi.org/10.1038%2Fs41592-019-0638-x [Demichev,
bioRxiv 2021]: https://doi.org/10.1101/2021.03.08.434385 [Cox, MCP
2020]: https://doi.org/10.1074/mcp.tir119.001720 [Marto, Anal.
Chem. 2021]: https://doi.org/10.1021/acs.analchem.1c02349
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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