Bruker Launches de novo Sequencing for Immunopeptidomics, Library-Free dia-PASEF, Mass Dynamics Knowledge Visualization
March 06 2023 - 10:30AM
Business Wire
- PaSER™ Novor faster, real-time de novo sequencing for
immunopeptidomics
- Library-free dia-PASEF® analysis with PaSER 2023b proteomics
software
- Partnership with Mass Dynamics for 4D-Proteomics™ knowledge
visualization
At the 19th US HUPO, Bruker Corporation (Nasdaq: BRKR) announced
important bioinformatics launches for 4D-Proteomics on the timsTOF
platform: A novel de novo sequencing algorithm was developed in
collaboration with Rapid Novor Inc., using over 1.7 million PASEF
data-points to improve accuracy and speed for immunopeptidomics in
real-time. The unmatched sensitivity of the timsTOF SCP
system coupled to the new PaSER Novor algorithm delivers a
significant performance boost for immunopeptidomics, especially for
small tumor biopsy samples.
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timsTOF SCP ultra-high sensitivity MS
(Photo: Business Wire)
dia-PASEF data analysis using library-free TIMS DIA-NN software
now features further improved quantification accuracy, while Mass
Dynamics graphical visualization and statistical cloud software now
seamlessly integrates with 4D-Proteomics dia-PASEF data.
A. PaSER Novor for Immunopeptide Sequencing
With PaSER Novor, Bruker launches advanced capabilities
for immunopeptidomics, developed in collaboration with Rapid
Novor Inc., a Canadian software and CRO services company for
antibody sequencing.
Immunopeptidomics requires the sequencing of peptides that are
not proteolytic in nature from small tumor biopsy samples on the
timsTOF SCP ultra-high sensitivity platform. The search space for
proteomics database algorithms can become too big for accurate
searches, resulting in low reproducibility and long search times.
PaSER Novor derives the peptide sequence from fragment ion
spectra de novo after training with over 1.7 million timsTOF data
points for real-time results using the GPU-enabled Bruker
PaSER proteomics software platform.
Professor Tony Purcell, Head Immunoproteomics Laboratory at
Monash University, said: “De novo searches have been a critical
aspect in my lab’s research for many years. This novel algorithm
delivers results with accuracy at the speed of data acquisition and
enables immunopeptidomics at scale and in real time. This has major
implications in how fast my group can translate research into
actionable information, and it pushes this workflow even closer to
delivering clinical patient impact on an unprecedented
timescale.”
B. TIMS-DIA-NN 2.0 Enables Library-free dia-PASEF
TIMS DIA-NN is a CCS-centric version of DIA-NN [1] with
significant enhancements. TIMS DIA-NN 2.0 can now process dia-PASEF
data in a library free approach with further improved
quantification accuracy through novel machine learning
capabilities.
Dr. Brett Phinney, Director UC Davis Proteomics Core facility,
commented: “Proteomics has come a long way, but chromatography and
data analysis are just as important as the mass spectrometry
instruments. Stable chromatography over large sample cohorts,
coupled with real-time search for DDA and DIA have brought the
efficiency of my lab to new levels, and this only gets better with
library-free search capabilities of TIMS DIA-NN.”
C. Graphical Knowledge Visualization by Mass Dynamics for
4D-Proteomics
Through Bruker’s collaboration with Prof. Andrew Webb at WEHI,
co-founder of Mass Dynamics Pty Ltd - a software company in
Australia, timsTOF 4D-Proteomics can now leverage Mass Dynamics
statistical analyses, interactive and intuitive visualizations for
knowledge extraction in proteomics. Beyond lists of protein groups,
volcano plots, protein-protein interactions, PCA plots and a myriad
of other visualizations facilitate biological and disease
insights.
Co-founder and CEO of Mass Dynamics Paula Burton stated: “The
integration of PaSER’s real-time search and Mass Dynamics’
discovery service is a formidable alliance. Life scientists can now
focus on biological questions and leverage proteomics for
answers.”
Dr. Dennis Trede, Director of Informatics, Bruker Life Sciences
Mass Spectrometry, commented: “We are pleased that our partnerships
with Rapid Novor and Mass Dynamics are resulting in
meaningful proteomics advances. The ultra-high sensitivity of the
timsTOF SCP with Rapid Novor now enable at scale
immunopeptidomics from small tumor biopsies.”
All Bruker software solutions announced at US HUPO can be used
with all models of the timsTOF platform: timsTOF Pro 2, timsTOF HT,
timsTOF SCP, and timsTOF fleX. The Biognosys Spectronaut® 17
software, with its novel Direct DIA+ capability, launched at the
International HUPO Cancun meeting, and also fully supports
dia-PASEF timsTOF data.
References:
- Nat Commun. 2022 Jul 8;13(1):3944.
https://doi.org/10.1038/s41467-022-31492-0.
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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