timsTOF immunopeptide prediction

Here you can find code developed to assess the new TOF Prosit 2023 model for the identification of immunopeptides measured on timsTOF instruments. More information can be found in the preprint: Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF.

Where to find the data

The mass spectrometry datasets are available via the PRIDE partner repository with the identifier PXD043844 (non-tryptic timsTOF dataset), PXD019086 (tryptic timsTOF dataset; reanalysis available on MSV000092462), PXD038782 (comparison dataset; reanalysis available on MSV000092461), and PXD040740 (SCP dataset; reanalysis available on RMSV000000693.1).

Where to find the prediction model

The timsTOF fragment ion intensity prediction can be found on Koina (https://koina.proteomicsdb.org/docs/#post-/Prosit_2023_intensity_TOF/infer).