Prosit Transformer: A transformer for Prediction of MS2 Spectrum Intensities

Markus Ekvall, Patrick Truong, Wassim Gabriel, Mathias Wilhelm, Lukas Käll

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Machine learning has been an integral part of interpreting data from mass spectrometry (MS)-based proteomics for a long time. Relatively recently, a machine-learning structure appeared successful in other areas of bioinformatics, Transformers. Furthermore, the implementation of Transformers within bioinformatics has become relatively convenient due to transfer learning, i.e., adapting a network trained for other tasks to new functionality. Transfer learning makes these relatively large networks more accessible as it generally requires less data, and the training time improves substantially. We implemented a Transformer based on the pretrained model TAPE to predict MS2 intensities. TAPE is a general model trained to predict missing residues from protein sequences. Despite being trained for a different task, we could modify its behavior by adding a prediction head at the end of the TAPE model and fine-tune it using the spectrum intensity from the training set to the well-known predictor Prosit. We demonstrate that the predictor, which we call Prosit Transformer, outperforms the recurrent neural-network-based predictor Prosit, increasing the median angular similarity on its hold-out set from 0.908 to 0.929. We believe that Transformers will significantly increase prediction accuracy for other types of predictions within MS-based proteomics.

Original languageEnglish
Pages (from-to)1359-1364
Number of pages6
JournalJournal of Proteome Research
Issue number5
StatePublished - 6 May 2022


  • MS2 Spectra
  • Machine Learning
  • Proteomics
  • Transformers


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