New Nature Communications Publication by Mann & Theis Groups Harnesses the Benefits of Large-scale Peptide Collisional Cross Section (CCS) Measurements and Deep Learning for 4D Proteomics

Bruker Corporation (Nasdaq: BRKR) today announces a seminal publication from the groups of Professors Matthias Mann and Fabian Theis in the journal Nature Communications with the title ‘Deep learning the collisional cross sections of the peptide universe from a million experimental values’ by Florian Meier et al. (doi.org/10.1038/s41467-021-21352-8)¹.

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Fig. 1: Large-scale peptide collisional cross section (CCS) measurement with TIMS and PASEF. From "Deep learning the collisional cross sections of the peptide universe from a million experimental values". (a) Workflow from extraction of whole-cell proteomes through digestion, fractionation, and chromatographic separation of each fraction. The TIMS-quadrupole TOF mass spectrometer was operated in PASEF mode. (b) Overview of the CCS dataset in this study by organism. (c) Frequency of peptide C-terminal amino acids. (d) Frequency of peptide N-terminal amino acids. (e) Distribution of 559,979 unique data points, including modified sequence and charge state, in the CCS vs. m/z space color-coded by charge state. Density distributions for m/z and CCS are projected on the top and right axes, respectively. Source data are provided as a Source Data file. (Graphic: Business Wire)

The Nature Communications paper describes CCS values measured on the timsTOF pro as an essentially intrinsic property of the peptide ions, which can be used to improve confidence in peptide and protein group identification in 4D shotgun proteomics. Since mass spectrometry-based proteomics relies on accurate matching of acquired spectra against a database of protein sequences, accurate CCS values offer the benefit of narrowing down the list of candidates. This is essential for high sensitivity proteomics where low levels of peptide signals need to be accurately measured in a complex mixture, e.g. in plasma proteomics, peptidomics, immunopeptidomics or metaproteomics.

The publication summarizes a collaborative research effort led by Professor Matthias Mann, who holds dual appointments at the Max Planck Institute of Biochemistry in Martinsried, Germany and the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen in Denmark, together with the group of Professor Fabian Theis, who also holds dual appointments at the Helmholtz Center Munich in the German Research Center for Environmental Health, and in the Department of Mathematics at TU Munich, in Germany.