Koina/Prosit_2023_intensity_TOF

The Prosit_2023_intensity_TOF model in Koina compatible format developed by Charlotte Adams, et al.

The HCD Prosit 2020 model was fine-tuned using 277,781 MS/MS spectra of both tryptic and non-tryptic synthesized peptides measured on a timsTOF Pro. The model architecture remained unchanged. The data was split into three distinct sets with each peptide and subsequence of a peptide only included in one of the three: training (80%, 153,809 tryptic PSMs and 77,577 non-tryptic PSMs), validation (10%, 16,483 tryptic PSMs and 7,778 non-tryptic PSMs), and test (10%, 14,262 tryptic PSMs and 7,872 non-tryptic PSMs).
For this project, over 300,000 non-tryptic peptides from the ProteomeTools project were measured. Our measurements encompassed a range of collision energies from 20.81 EV to 69.77 eV. The data was analyzed using MaxQuant version 2.1.2.0 with carbamidomethylated cysteine specified as a fixed modification and methionine oxidation as a variable modification.
The HCD Prosit 2020 model was originally trained on approximately 30 million MS/MS spectra, consisting of 9 million MS/MS spectra of non-tryptic peptides and 21 million previously published tryptic MS/MS spectra. The comparison between the HCD Prosit 2020 model and the newly developed TOF Prosit 2023 model reveals a substantial improvement in normalized spectral contrast angle (SA) between predicted and experimental timsTOF MS/MS spectra for both non-tryptic and tryptic peptides. The TOF Prosit 2023 model achieved a SA ≥ 0.9 for 26.3% of non-tryptic spectra (compared to 2.4% with HCD Prosit 2020) and 42.1% of tryptic spectra (compared to 0.2% with HCD Prosit 2020).
The TOF Prosit 2023 model demonstrates consistent performance across different precursor charges, peptide lengths, and collision energies, with minimal bias towards C- and N-terminal amino acids. Both the tryptic and non-tryptic timsTOF data are available via PRIDE, with the identifiers PXD019086 and PXD043844, respectively.