Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing

peer-reviewed · Nature Communications · 2024

peer-reviewed · Nature Communications · 2024. Daniela Klaproth-Andrade et al. Unlike for DNA and RNA, accurate and high-throughput sequencing methods for proteins are lacking, hindering…
Date 2024-01-02
Type peer-reviewed
Venue Nature Communications
Publisher Springer Science and Business Media LLC
Contribution post-processor
DOI 10.1038/s41467-023-44323-7
Citations (OpenAlex) 42
Venue 2-year citedness 17.60

Preprint version: Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2023-01-05, bioRxiv)

Abstract

Unlike for DNA and RNA, accurate and high-throughput sequencing methods for proteins are lacking, hindering the utility of proteomics in applications where the sequences are unknown including variant calling, neoepitope identification, and metaproteomics. We introduce Spectralis, a de novo peptide sequencing method for tandem mass spectrometry. Spectralis leverages several innovations including a convolutional neural network layer connecting peaks in spectra spaced by amino acid masses, proposing fragment ion series classification as a pivotal task for de novo peptide sequencing, and a peptide-spectrum confidence score. On spectra for which database search provided a ground truth, Spectralis surpassed 40% sensitivity at 90% precision, nearly doubling state-of-the-art sensitivity. Application to unidentified spectra confirmed its superiority and showcased its applicability to variant calling. Altogether, these algorithmic innovations and the substantial sensitivity increase in the high-precision range constitute an important step toward broadly applicable peptide sequencing.

Authors

  1. Daniela Klaproth-Andrade · Technical University of Munich
  2. Johannes Hingerl · Technical University of Munich
  3. Yanik Bruns · Technical University of Munich
  4. Nicholas H. Smith · Technical University of Munich
  5. Jakob Träuble · Technical University of Munich
  6. Mathias Wilhelm · Technical University of Munich
  7. Julien Gagneur · Helmholtz Center Munich, Technical University of Munich

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