How to cite
Please always cite the main publication
Please cite the Prosit model(s) you are using
When using Prosit
Gessulat S, Schmidt T, Zolg DP et al. (2019), PROSIT: Proteome-wide prediction of peptide tandem mass spectra by deep learning, Nature Methods.
Wilhelm M, Zolg DP, Graber M et al. (2021), Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics, Nature Communications.
When using Prosit-TMT
Gabriel W, The M, Zolg D et al. (2022), Prosit-TMT: Deep Learning Boosts Identification of TMT-Labeled Peptides, Analytical Chemistry.
When using Prosit-timsTOF
Adams C, Gabriel W, Laukens K et al. (2024), Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF, Nature Communications.
When using Prosit-XL
Kalhor M, Saylan C, Picciani M et al. (2025), Prosit-XL: enhanced cross-linked peptide identification by fragment intensity prediction to study protein interactions and structures, Nature Communications.
Please cite in case you use quantification
The M, Samaras P, Kuster B, Wilhelm, M. (2022), Reanalysis of ProteomicsDB using an accurate, sensitive, and scalable false discovery rate estimation approach for protein groups, Molecular & Cellular Proteomics.