New capabilities of timsTOF Pro introduced at EuPA 2019:
- DIA-PASEF work-in-progress with excellent peptide and protein ID Performance
- New workflows for intact protein analysis in biopharma on timsTOF Pro
- New workflows for next-generation 4D metabolomics, leveraging routine, accurate and large-scale collision cross section (CCS) determinations on timsTOF Pro
POTSDAM, Germany, March 25, 2019 – At the XIIIth Annual Congress of the European Proteomics Association (www.eupa.org), Bruker announces further progress in ultra-high sensitivity, high-throughput 4D proteomics using the timsTOF Pro mass spectrometer. Moreover, new intact protein analysis and next-generation 4D metabolomics workflows are being introduced, which all are available on the same, remarkably flexible timsTOF Pro platform.
The extraordinary advances in speed, sensitivity and robustness provided by the timsTOF Pro have generated tremendous interest in the proteomics community. All work performed to date has been done using Data Dependent Analysis (DDA) and the innovative parallel accumulation serial fragmentation (PASEF) method developed in collaboration with Professor Matthias Mann at the Max Planck Institute of Biochemistry in Martinsried, Germany.
In ddaPASEF, individual multiply-charged peptides are selected in real-time for MS/MS, based on the acquired ‘mobility-mass heat map’. Even with the high >100 Hz MS/MS speed of the timsTOF Pro, not all peptides can be targeted for MS/MS identification. Due to biological variation in the data from sample to sample, the same peptides may not be targeted in all runs, leading to the so-called “missing value problem” when performing quantitative proteomics.
Data Independent Analysis (DIA) is an alternative approach to fragment most of the peptides using wide selection windows, rather than selecting individual peptides in DDA. For many years, Bruker has been collaborating with the laboratories of Professor Matthias Mann to develop the timsTOF Pro for proteomics. More recently, they have teamed up with Professor Ruedi Aebersold and Dr. Ben Collins at the ETH in Zuerich, and Professor Hannes Roest at the University of Toronto, to develop a novel DIA technique on the timsTOF Pro, called diaPASEF. The speed and sensitivity of the timsTOF Pro have been shown to lead to improved throughput and better results for DIA library generation, and promise even more comprehensive proteome coverage in DIA experiments. Further progress on diaPASEF will be presented at EuPA 2019.
Professor Matthias Mann stated: “The timsTOF Pro offers very high MS/MS speed, dynamic range and an additional 4th dimension of separation by ion mobility. Due to its dual-TIMS front end, when operated with our PASEF method, the timsTOF Pro also uses ions very efficiently with nearly 100% duty cycle for highest sensitivity. The ion mobility separation provides accurate and highly reproducible collision cross section (CCS) values that allow for an additional dimension for alignment and feature matching in data processing and analysis software. The new diaPASEF method with the OpenSwath analysis software takes advantage of these attributes to provide a next-generation DIA method with superior coverage of proteins in biological samples, and with excellent quantitative performance. We are very excited about the diaPASEF work, and we look forward to continuing the collaboration with our academic collaborators and Bruker.”
About the timsTOF PRO with PASEF
The proprietary timsTOF Pro system uses PASEF, enabled by Trapped Ion Mobility Spectrometry (TIMS) to provide industry-leading data acquisition speed for shotgun proteomics. The unique dual TIMS geometry of the timsTOF Pro, combined with the time focusing of the ion packets in the TIMS device, means that the speed advantage provided by PASEF comes along with simultaneous improvements in sensitivity and quantitation. All of these gains in speed, sensitivity and quantitation maintain the advantages of Bruker’s high-performance QTOF mass spectrometers, including high mass resolution (resolving power of 50,000 FWHM even at highest data acquisition rates) in MS and MS/MS mode, ppm accurate mass, and high isotopic fidelity (True Isotopic Pattern, or TIPTM). The robust timsTOF Pro with PASEF gives scientists the tools to dig deeper into the complex cellular machinery with the potential to discover low-level, biologically significant peptides or proteins, or validate them in translational proteomics research.
About Bruker Corporation (Nasdaq: BRKR)
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