Prosit

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.

This task estimates the optimal collision energy (CE) based on a given search result. You need to upload a RAW file as well as the MaxQuant's msms.txt for calibration.
Prosit will:

Select a random subset of high-scoring PSMs
Predict those in for each CE from 18 to 39.
Calculate which CE achieves highest correlations with the experimental spectra

Please note: Sequences with amino acid U or O are not supported. Modifications except "M(ox)" are not supported. Each C is treated as Cysteine with carbamidomethylation (fixed modification in MaxQuant).
Also note: Antivirus software may cancel large uploads - turn it off if you experience upload resets.

Upload Files msms.txt and RAW file.

MaxQuant's msms.txt from a finished search. Note, amino acid U or O are not supported

RAW file that was searched (restricted to Thermo Fisher HCD Orbitrap). File size is limited to 2GB.

Model Select intensity and iRT model for prediction

Isobaric Label If TMT model is selected

Task ID Check if everything is correct and submit the task

This task generates a spectral library either by digesting a given FASTA file, or by predicting a list of peptides given in a CSV file. You need to provide a collision energy (CE) for prediction. To estimate an optimal CE for prediction, please use "CE Calibration".
When a FASTA file is provided, Prosit will:

Digest the FASTA, for the given parameters (i.e. protease).
Predict all spectra at the given collision energy.

When a CSV with peptides is provided, Prosit will directly predict all spectra.
Please note: Antivirus software may cancel large uploads - turn it off if you experience upload resets.

Settings Indicate collision energy, the maximum number of missed cleavages, and number of oxidized methionines per peptide.

How would you like to provide the list of peptides?

CSV Format

Please provide all three columns below and use , as a separator.

modified_sequence Use upper case letters in the column and indicate oxidized Methionine with "M(ox)". Sequence length is restricted to the range of 7 to 30. Each C is treated as Cysteine with carbamidomethylation. Prosit does not support U or O as amino acids.
collision_energy Use integer values from 10 and 50.
precursor_charge Use integer values from 1 to 6.
fragmentation Either HCD or CID, Use upper case letters.*

*Only for TMT model

Upload Files Fasta or CSV with list of peptides

CSV Format

Please provide all three columns below and use , as a separator.

modified_sequence Use upper case letters in the column and indicate oxidized Methionine with "M(ox)". Sequence length is restricted to the range of 7 to 30. Each C is treated as Cysteine with carbamidomethylation. Prosit does not support U or O as amino acids.
collision_energy Use integer values from 10 and 50.
precursor_charge Use integer values from 1 to 6.
fragmentation Either HCD or CID, Use upper case letters.*

*Only for TMT model

containing peptide sequence, collision energy and precursor charge.

Model Select intensity and iRT model for prediction

Isobaric Label If TMT model is selected

Task ID Check if everything is correct and submit the task

Output format

This task rescores an existing MaxQuant search (FDR 100%) using features generated from fragmentation prediction. You need to upload a RAW file as well as the MaxQuant's msms.txt file from a search.
Prosit will:

Calibrate itself against the RAW.
Predict all sequences in the msms.txt.
Use the predicted spectra to generate features for percolator.
Run percolator to rescore the search.

Please note: You need a MaxQuant search at 100% FDR, otherwise targets may be filtered by MaxQuant's FDR calculation before rescoring. Sequences with amino acid U or O are not supported. Modifications except "M(ox)" are not supported. Each C is treated as Cysteine with carbamidomethylation (fixed modification in MaxQuant).
Also note: Antivirus software may cancel large uploads - turn it off if you experience upload resets.

Upload Files msms.txt and RAW file.

MaxQuant's msms.txt from a finished search. Note, amino acid U or O are not supported.

RAW file that was searched (restricted to Thermo Fisher HCD Orbitrap). File size is limited to 2GB.

Model Select intensity and iRT model for prediction

Isobaric Label If TMT model is selected

Task ID Check if everything is correct and submit the task