PytatoDIA 0.3

A Toolbox for Proteomic Analyses and Data Visualization

Pytato: A Dual-Enzyme Search Engine 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

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Contact

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