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Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF

Author

Listed:
  • Charlotte Adams

    (University of Antwerp)

  • Wassim Gabriel

    (Technical University of Munich)

  • Kris Laukens

    (University of Antwerp)

  • Mario Picciani

    (Technical University of Munich)

  • Mathias Wilhelm

    (Technical University of Munich
    Technical University of Munich)

  • Wout Bittremieux

    (University of Antwerp)

  • Kurt Boonen

    (University of Antwerp
    Flemish Institute for Technological Research (VITO))

Abstract

Immunopeptidomics is crucial for immunotherapy and vaccine development. Because the generation of immunopeptides from their parent proteins does not adhere to clear-cut rules, rather than being able to use known digestion patterns, every possible protein subsequence within human leukocyte antigen (HLA) class-specific length restrictions needs to be considered during sequence database searching. This leads to an inflation of the search space and results in lower spectrum annotation rates. Peptide-spectrum match (PSM) rescoring is a powerful enhancement of standard searching that boosts the spectrum annotation performance. We analyze 302,105 unique synthesized non-tryptic peptides from the ProteomeTools project on a timsTOF-Pro to generate a ground-truth dataset containing 93,227 MS/MS spectra of 74,847 unique peptides, that is used to fine-tune the deep learning-based fragment ion intensity prediction model Prosit. We demonstrate up to 3-fold improvement in the identification of immunopeptides, as well as increased detection of immunopeptides from low input samples.

Suggested Citation

  • Charlotte Adams & Wassim Gabriel & Kris Laukens & Mario Picciani & Mathias Wilhelm & Wout Bittremieux & Kurt Boonen, 2024. "Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48322-0
    DOI: 10.1038/s41467-024-48322-0
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    References listed on IDEAS

    as
    1. Wen-Feng Zeng & Xie-Xuan Zhou & Sander Willems & Constantin Ammar & Maria Wahle & Isabell Bludau & Eugenia Voytik & Maximillian T. Strauss & Matthias Mann, 2022. "AlphaPeptDeep: a modular deep learning framework to predict peptide properties for proteomics," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Mathias Wilhelm & Daniel P. Zolg & Michael Graber & Siegfried Gessulat & Tobias Schmidt & Karsten Schnatbaum & Celina Schwencke-Westphal & Philipp Seifert & Niklas Andrade Krätzig & Johannes Zerweck &, 2021. "Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    3. Brian C. Searle & Kristian E. Swearingen & Christopher A. Barnes & Tobias Schmidt & Siegfried Gessulat & Bernhard Küster & Mathias Wilhelm, 2020. "Generating high quality libraries for DIA MS with empirically corrected peptide predictions," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    4. Mathias Wilhelm & Daniel P. Zolg & Michael Graber & Siegfried Gessulat & Tobias Schmidt & Karsten Schnatbaum & Celina Schwencke-Westphal & Philipp Seifert & Niklas Andrade Krätzig & Johannes Zerweck &, 2021. "Author Correction: Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics," Nature Communications, Nature, vol. 12(1), pages 1-1, December.
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    7. Kevin L. Yang & Fengchao Yu & Guo Ci Teo & Kai Li & Vadim Demichev & Markus Ralser & Alexey I. Nesvizhskii, 2023. "MSBooster: improving peptide identification rates using deep learning-based features," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    8. David Gomez-Zepeda & Danielle Arnold-Schild & Julian Beyrle & Arthur Declercq & Ralf Gabriels & Elena Kumm & Annica Preikschat & Mateusz Krzysztof Łącki & Aurélie Hirschler & Jeewan Babu Rijal & Chris, 2024. "Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    Full references (including those not matched with items on IDEAS)

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