ProSIMSIt

Combining SIMSI-Transfer and Oktoberfest rescoring for improved multi-batch TMT results.

Hamood, F., Gabriel, W., Pfeiffer, P., Kuster, B., Wilhelm, M., The, M.; Publication pending.

Test dataset

For testing ProSIMSIt, we recommend downloading the phosphoproteome raw files from this publication: Zecha, J., Bayer, F. P. et al., Decrypting drug actions and protein modifications by dose- and time-resolved proteomics. Science (New York, N.Y.) 2023, 380, 93–101.

PRIDE link for .raw files and MaxQuant search results: https://www.ebi.ac.uk/pride/archive/projects/PXD057211/

ProSIMSIt Instructions

We recommend installing ProSIMSIt via Poetry. To install Poetry, please follow the instructions on the Poetry website.

Installation

To install ProSIMSIt, clone the repository and make a poetry environment:

git clone
cd ProSIMSIt
poetry install

Setting up the configuration file

To properly set all parameters for ProSIMSIt, a config.toml file is required. An example file is provided in the repository, which can be used as a template.

For a detailed description of all config parameters, please refer to the Wiki.

Running ProSIMSIt

ProSIMSIt can be executed via the command line in the generated environment:

poetry python -m prosimsit -c /path/to/config.toml