Bruker Introduces Novel 4D-Proteomics™ timsTOF® Capabilities

1. New AI-powered TIMSquant™ software for CCS-enabled, label-free quantification scalable to thousands of samples
2. Early midia-PASEF® access for immunopeptidomics and PTMs on ultra-sensitive timsTOF Ultra for DDA-like precursor traceability in dia-PASEF
3. Affordable, high-throughput ~3,500 PG plasma proteomics on timsTOF HT with PreOmics ENRICH kit using Biognosys Spectronaut® 18 directDIA+™ software
4. New PepSep™ ULTRA XL and MAX HT nano-LC columns for DDA library creation and high-throughput proteomics, respectively
5. Novel TwinScape™ digital twin for optimal timsTOF performance and uptime
6. New partnership with Mass Dynamics for biological knowledge generation
7. Enhanced MALDI HiPLEX-IHC workflow for spatial tissue proteomics
8. New MetaboScape™ release for 4D-Lipidomics™ and 4D-Metabolomics™

BUSAN, South Korea--(BUSINESS WIRE)-- 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.

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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 (