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Bruker collaborates with Utrecht University on mass spectrometry methods

Crosslinking mass spectrometry (XL-MS) can leverage the PhoX Crosslinker and TIMS/PASEF methods with the large-scale use of accurate collision cross sections

9 Aug 2020
Diane Li
Assistant Editor

Industry news

Bruker Corporation has announced a collaboration with Utrecht University to advance the study of the 3-D structures and interactions of proteins by mass spectrometry. The laboratory of Albert Heck at Utrecht University has been a leader in proteomics and the study of protein structure and interactions by mass spectrometry for over two decades. Richard Scheltema recently joined Utrecht University as group leader to focus on crosslinking mass spectrometry (XL-MS) for structural and interaction proteomics.

The collaborative work will focus on the development of TIMS (Trapped Ion Mobility Spectrometry) and PASEF (Parallel Accumulation Serial Fragmentation) methods, along with crosslinkers and XL-MS software for the timsTOF Pro 4D-Proteomics mass spectrometer, in order to take advantage of its unique large-scale, accurate CCS workflows. These have been described in the foundational paper “Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry“, just published in a breakthrough paper in Molecular and Cellular Proteomics.

Bruker plans to commercialize the results of the collaboration as integrated solutions for the study of protein structures and interactions using XL-MS. Combining the novel, enrichable PhoX crosslinker, developed by Heck and Scheltema, with the extreme speed and sensitivity of PASEF methods on the timsTOF Pro platform, enables the discovery of more crosslinked products which yield more information about protein structures and interactions. Advanced analysis software is key, as XL-MS data is more complex and even more information-rich than typical shot-gun proteomics experiments. Scheltema is working on enabling the innovative XlinkX software to process TIMS/PASEF data and making it available to the community of timsTOF Pro users.

Albert Heck of Utrecht University commented: “We are delighted to work with Bruker on the further development of workflows for XL-MS that take advantage of the speed of PASEF and the unique large-scale, accurate CCS data to enhance the detection of crosslinks in XL-MS. We are excited by the initial results published in Molecular and Cellular Proteomics and look forward to advancing XL-MS even further. We are also interested in other applications of ion mobility separation and CCS on the timsTOF Pro to glycoproteomics and top-down proteomics.”

Dr. Gary Kruppa, the Vice President of Proteomics at Bruker, said: “Having personally been involved in some of the conceptual work in XL-MS in 2001 at Sandia National Laboratory, I believe the advances made by Heck’s group will make this technique more routinely available for structural biology studies using the timsTOF Pro. Our collaboration with Utrecht University will accelerate adoption of XL-MS within the broader structural and interaction proteomics community.”

Richard Scheltema of Utrecht University stated: “My group intends to push the boundaries of PASEF to enhance XL-MS workflows by making them CCS-aware. We have a significant ongoing effort in bioinformatics applied to analyzing XL-MS data using our XlinkX software. We are excited to work with the open data-format architecture of the timsTOF Pro in XlinkX to develop code that can use large-scale, accurate CCS values for the identification of crosslinks and to further improve false discovery rate (FDR) calculations.”

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Mass SpectrometryMass spectrometry (MS) is a powerful analytical technique used to identify and quantify molecules based on the mass-to-charge ratio of gas-phase ions. It provides detailed information about the structure, composition, and properties of compounds and is widely used across fields such as environmental monitoring, materials science, drug discovery and development, food and beverage testing, and wider chemical research. Key MS techniques include tandem mass spectrometry (MS/MS), liquid chromatography–mass spectrometry (LS-MS) and inductively coupled plasma (ICP-MS). Choosing from these wide range of techniques and technologies can be a daunting task, so keep up to date with scientific applications, performance expectations, and customer reviews here all in one place. Visit our product directory to receive quotes direct from the manufacturer. Protein PurificationProtein purification is a vital step in drug discovery, therapeutics, biotech and life science research. The purification process typically involves subcellular or membrane protein extraction with cell lysis kits, separation of proteins from cell debris by filtration or spin columns, and the isolation of proteins of interest from other proteins and impurities with affinity purification (including fusion protein tags and antibody binding proteins A, G and L), immunoprecipitation or chromatographic methods, such as ion exchange, size exclusion and immobilized metal affinity chromatography. All purification methods come in multiple formats for your laboratory needs, including agarose or magnetic beads, resins, columns and filter plates. Find the best protein purification equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Protein CrystallographyProtein crystallization is the process of crystallizing purified proteins for 3D structure analysis by x-ray crystallography. The main methods of protein crystallization include sitting drop, hanging drop and microbatch. It is important to control parameters such as pH, temperature and concentration. Following crystallization, detectors and software are used for data collection and analysis.Clinical ChemistryBiochemistry (or clinical chemistry) involves the analysis of bodily fluids using chemical tests. Techniques used include HPLC, chromatography, spectroscopy, mass spectrometry, immunochemical, electrophoresis, turbidometric / spectrophotometric assay, MRI and ISE analysis. Tests are often carried out on plasma or serum but urine (urinalysis) and fecal specimens are also processed.Protein QuantificationThe detection and quantification of proteins in a sample is vital across life sciences, pharmaceutical research and clinical diagnostics, and a variety of equipment is available to scientists to simplify the workflow. Proteins of interest can be easily labeled and detected on light-based detection instruments. Immunoassay kits allow you to identify a specific protein of interest and protein detection beads or antibody microarrays allow you to identify multiple specific proteins at once. Protein interactions and enzyme activity can also be monitored with protein-protein interaction assays. Additionally, the biophysical characterization of proteins is made easy with biokinetic analyzers. Find the best protein detection and quantification products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Protein ExpressionProtein expression is the utilization of cell machinery for the synthesis of proteins and has become a critical tool in biotherapeutic, genomic, and proteomic research. Produce recombinant proteins with expression vectors in combination with a host cell suitable for high-level protein expression. For production of toxic proteins, consider cell-free expression vectors. Create and monitor post-translational modifications with protein modification kits. Find the best protein expression products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Protein InteractionsProtein interactions are essential for understanding cellular processes, as proteins work together to carry out biological functions. Studying protein interactions can provide insights into disease mechanisms, drug development, and cell signaling pathways. Explore the best tools for protein interaction research in our peer-reviewed product directory; compare products, check reviews, and get pricing directly from manufacturers.Protein BiologyThe analysis of protein expression, identity and function is vital for many areas of life science research and drug discovery. Some of the most commonly used techniques in protein analysis include Western blotting, electrophoresis and mass spectrometry.

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Bruker collaborates with Utrecht University on mass spectrometry methods