README.md

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What is it?

decryptM is a quantitative chemical-proteomics approach to characterize pathway engagement of biomolecules (e.g. drugs) in cells. These molecules are applied in a dose- or time-dependent manner. The modulation of ten-thousands posttranslational modifications (such as phosphorylation, acetylation, and ubiquitinylation) are then recorded by mass spectrometry in parallel. Read more about the technique in our recent publication.

Here, you can access the decryptM pipeline, which is written completely in Python. We hope that this pipeline will enable other researchers to implement the decryptM approach in their labs more quickly.

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We have developed a better way of analyzing dose-response curves using p-values for individual curves.

For more information, please visit:

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Installation:

1. Download the code of this repository and place it next to your data

2. Install the virtual environment manager anaconda to install package dependencies safely (https://www.anaconda.com/).

3. Move to the repository in your shell

(base)$ cd <path_to_repository>

4. Install the decryptM environment

(base)$ conda env create -f ./environment.yml

5. Activate the decryptM environment

(base)$ conda activate decryptM
(decryptM)$

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Run pipeline

1. Search your TMT-data with MaxQuant (v.1.6.x.x)

A copy of version 1.6.12.0 can be downloaded via pride.

2. In case of global proteome data, transform the proteinGroups.txt file

(decryptM)$ python ./decryptM/pg_transform.py <in_path>

3. Fill out the parameter toml-file for each dataset

Each dataset comes with a parameter file. This file contains all necessary information for each processing batch. Multiple experiments can be processed together if they share the same experimental parameter structure.

For more information about the toml parameters, see the comments in the toml file.

4. Run the pipeline script

(decryptM)$ python ./decryptM/pipeline.py -q -p <toml_path>

Depending on the number of curves, the execution may take several hours.

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