Integrating Alternative Fragmentation Techniques into Standard LC-MS Workflows Using a Single Deep Learning Model Enhances Proteome Coverage

We built and characterised a mass spectrometer capable of performing CID (both beam type and resonant type), UVPD, EID and ECD in an automated fashion during an LCMS type experiment. We exploited this ability to generate large datasets through multienzyme deep proteomics experiments for characterisation of these activation techniques. As a further step, motivated by the complexity generated by these dissociation techniques, we developed a single Prosit deep learning model for fragment ion intensity prediction covering all of these techniques. The generated model has been made publicly available and has been utilised in FragPipe within its MSBooster module. Rescoring allowed both data-dependent acquisition (DDA) and data-independent acquisition (DIA) to achieve on average more than 10% increase in protein identifications across all dissociation techniques and enzymatic digestions. We demonstrate that these alternative fragmentation approaches can now be used within standard data analysis pipelines and can produce data competitive to CID in terms of eficiency, but in the cases of EID and UVPD with far richer and more comprehensive spectra.