RT Journal Article
SR Electronic
T1 Deep learning the collisional cross sections of the peptide universe from a million training samples
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.05.19.102285
DO 10.1101/2020.05.19.102285
A1 Meier, Florian
A1 Köhler, Niklas D.
A1 Brunner, Andreas-David
A1 Wanka, Jean-Marc H.
A1 Voytik, Eugenia
A1 Strauss, Maximilian T.
A1 Theis, Fabian J.
A1 Mann, Matthias
YR 2020
UL http://biorxiv.org/content/early/2020/05/21/2020.05.19.102285.abstract
AB The size and shape of peptide ions in the gas phase are an under-explored dimension for mass spectrometry-based proteomics. To explore the nature and utility of the entire peptide collisional cross section (CCS) space, we measure more than a million data points from whole-proteome digests of five organisms with trapped ion mobility spectrometry (TIMS) and parallel accumulation – serial fragmentation (PASEF). The scale and precision (CV <1%) of our data is sufficient to train a deep recurrent neural network that accurately predicts CCS values solely based on the peptide sequence. Cross section predictions for the synthetic ProteomeTools library validate the model within a 1.3% median relative error (R > 0.99). Hydrophobicity, position of prolines and histidines are main determinants of the cross sections in addition to sequence-specific interactions. CCS values can now be predicted for any peptide and organism, forming a basis for advanced proteomics workflows that make full use of the additional information.Competing Interest StatementThe authors have declared no competing interest.