PytatoDIA 0.4.0

A Toolbox for Proteomic Analyses and Data Visualization

Pytato: A Toolbox for for DIA Proteomics

Pytato is a dual-enzyme proteomics search engine that leverages the information provided by complementary proteolysis to improve peptide and protein identification in data-independent proteomics experiments.

Experimental Example

Enyzme1=Trypsin Enzyme2=Thermolysin

Features

• Custom Python-based pipeline for streamlined analysis
• Support for multiple proteases to improve protein identification confidence
• Generation of theoretical spectra for improved peptide matching

Installation

git clone https://github.com/TTCooper-PhD/Pytato.git

Install the required python packages:

pip install -r requirements.txt

Usage

• Prepare your Enzyme1 and Enzyme2-digested samples and acquire LC-MS/MS data in DIA mode.

For a list of available enzymes and their cleavage rules, see the Available Enzymes document.

• Process raw data files and generate spectral libraries for both Enzyme1 and Enzyme2 samples.
• Run Pytato by providing the necessary input files and parameters.

python pytato.py --enzyme1_data trypsin_data.mzML --enzyme2_data thermolysin_data.mzML  --output output_directory

Output

Pytato generates multiple output files containing the results of the analysis. (Add specific details about the output files here).

Examples

(Provide a detailed example command with input and expected output)

Contribution

We welcome contributions to the Pytato project. Please see our contribution guidelines for more details.

License

(Provide details about the project's license)

Contact

For questions or feedback, please contact us at (Your contact info).