Bruker Launches timsTOF Ultra Mass Spectrometer with Transformative Sensitivity, 300 Hz PASEF MS/MS, and VistaScan for Enhanced dia-PASEF 4D-Proteomics

timsTOF Ultra Further Advances Quantitative Spatial and Single-cell 4D-Proteomics and 4D-Lipidomics, Immunopeptidomics, PTM and Protein-Protein Interactions Analysis – with Speed and Robustness

• timsTOF Ultra mass spectrometer enables ID of >5000 protein groups and >55k peptides at single-cell sensitivity (0.125ng) with highest confidence at <1% False Discovery Rate
• New CSI Ultra ion source with vortex flow enhances ion formation across nanoLC (50 nL-5000nL/min) gradients, leading to dramatic sensitivity increases
• VistaScan software supports novel midia-PASEF scan for dda-like MS/MS traceability with dia-sensitivity for ‘high fidelity’ 4D-Proteomics
• timsTOF Ultra PASEF scan speed increased to 300Hz for ultra-fast MS/MS
• New microFlow emitters for capillary and analytical flow 4D-Proteomics using unique VIP-HESI ion source for high method robustness and sensitivity
• ProteoScape software now with real-time QC mode using Biognosys iRT kit
• SCiLS Lab 2024 mass spec imaging software integrates MALDI lipid and HiPlex-IHC protein expression for MALDI-guided spatial tissue biology

5 June 2023 -- Texas, US -- At the 71st ASMS meeting, Bruker Corporation announced transformative sensitivity on the 4D-Proteomics timsTOF platform with the launch of the new timsTOF Ultra mass spectrometer. It incorporates a new Captive Spray Ionisation (CSI) Ultra ion source with larger capillary and optimized vortex gas flow, a novel 4th-generation TIMS (trapped ion mobility separation) XR cell and 14bit digitiser. The timsTOF Ultra can identify over 55K peptides that map into 5000 protein groups at the single-cell level of 0.125ng protein loading, at 1% FDR, and over 4800 protein groups quantified at CVs of <20%. This breakthrough sensitivity and quantitation performance below the 1ng protein load level sets a new benchmark. Unparalleled sensitivity, with the proven robustness of the timsTOF platform, and with PASEF duty cycle now up to 300Hz for MS/MS, offers significant further performance improvements for ultra-low sample amounts, including unbiased single-cell proteomics and single-cell lipidomics, unbiased spatial proteomics, immunopeptidomics, phosphoproteomics, PTM analysis and protein-protein interaction (PPI) studies.

Dr Fabian Coscia, group leader for Spatial Proteomics at the Max Delbruck Center, Berlin, Germany, said: “The single-cell sensitivity dia-PASEF workflow on the timsTOF Ultra has brought our low-input tissue proteomics research to a new level. Using a 20-min nanoflow LC gradient combined with Bruker’s optimized dia-PASEF (3x8 window) method, we can now reproducibly quantify 1,500 – 2,000 proteins from laser micro-dissected mouse liver FFPE tissue of only 1,500µm2, regions corresponding to approximately 1-2 hepatocytes.”

These timsTOF Ultra advances have been achieved without compromising the excellent robustness for high-throughput proteomics, eg, at 50 samples per day (SPD), or even up to 398 SPD, nor the highest identification confidence of <1% peptide and <1% protein FDRs (false discovery rates), avoiding the cross-reactivity seen with targeted immune-recognition methods.

Professor Dr Karl Mechtler, proteomics head at the Innovation Hub of the Research Institute for Molecular Pathology (IMP), Gregor Mendel Institute (GMI) and the Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), added: “To truly understand cellular mechanisms and diseases, it's crucial to differentiate between the various cell types. While single-cell analysis has been game-changing, we face obstacles in maximizing its potential for throughput and proteins groups that can be analysed. It would make biological sense to detect 6000 or more proteins in a single-cell experiment. The timsTOF Ultra has overcome these barriers, allowing us to explore the proteome of individual cells at speed and unparalleled sensitivity. Thanks to the timsTOF Ultra, single-cell analysis has reached new heights, and I'm excited to see where this breakthrough will lead us next.”

Bruker also introduces VistaScan software for synchronizing TIMS ramp with the quadrupole scan to further benefit from ion mobility information at scale. This sophisticated dynamic linked-ramp supports the novel midia-PASEF mode, introduced by Stefan Tenzer.

Dr. Stefan Tenzer, professor for Quantitative Proteomics and head of MS Core Facility, Johannes Gutenberg University Mainz, commented: “Our laboratory focuses on methods for quantitative proteomics that require highest sensitivity and highest information extraction. Together with Bruker, we have developed the novel maximum information dia (midia) PASEF scanning acquisition mode which offers sensitivity of data-independent acquisition (dia), while transforming data into data-dependent acquisition (dda)-like spectra. The midia-PASEF potential for immunopeptidomics and phosphoproteomics is particularly exciting.”

Bruker has exclusively licensed midia-PASEF from Johannes Gutenberg University Mainz and plans to release midia-PASEF as a product in 2023. The timsTOF Ultra is equipped with the required VistaScan acquisition capabilities.

In addition, the timsTOF Ultra features a further improved dda-PASEF acquisition mode, increasing the speed to 300Hz for up to 18,000 collision cross-section (CCS)-enabled MS/MS spectra per minute to enable in-depth 4D-Proteomics and 4D-Lipidomics / 4D-Metabolomics with very short LC gradients of just minutes.

About Bruker Corporation
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.