We now offer two new Prosit TMT models that will soon be published. One is for fragment intensities prediction (Prosit_TMT_intensity_2021) and the other is for iRT prediction (Prosit_TMT_irt_2021). The intensity model works with both CID and HCD fragmentation methods but you need to add fragmentation column to the input. We assume all the sequences are fully labeled and you don't need to add the tmt modification explicitly in your input files.
Prosit offers high quality MS2 predicted spectra for any organism and protease as well as iRT prediction. Prosit is part of the ProteomeTools (www.proteometools.org/) project and was trained on the project's high quality synthetic dataset. When using Prosit is helpful for your research, please cite "Gessulat, Schmidt et al. 2019" DOI 10.1038/s41592-019-0426-7.
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