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HIquant

Quantifying homologous proteins and proteoforms

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The Python code in this repository implements the HIquant algorythm for quantifying homologous proteins and proteoforms from bottom up mass-spec data. It is described and tested in:

Malioutov D., Chen T., Jaffe J., Airoldi E., Budnik B., Slavov N. Quantifying homologous proteins and proteoforms Molecular & Cellular Proteomics, Volume 18, Issue 1, 162 - 168 doi: 10.1074/mcp.TIR118.000947

Running this code:

This python code is tested on Max OS X 10.15.6 and using Python 3.8.5.

The script can be called from the command line and has 3 required arguments:

  1. The input file (see exampleInput.txt)
  2. Output file 1 - this has the inferred proteoform abundance
  3. Output file 2 - this has the confidence and error estimates for the inference

An example command line call is:

ed$ python3 ~/Documents/GitHub/HIquant/HIquant_run.py '/Users/ed/Documents/GitHub/HIquant/TestData_fromMCP.txt' '/Users/ed/Documents/GitHub/HIquant/Results/MCP_Output_1.csv' '/Users/ed/Documents/GitHub/HIquant/Results/MCP_Output_2.csv'

About the project

For more information, contact Slavov Laboratory or directly Prof. Nikolai Slavov

License

The HIquant code is distributed by an MIT license.

Contributing

Please feel free to contribute to this project by opening an issue or pull request.

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HIquant: An algorithm for quantifying homologous proteins and proteoforms from bottom-up mass-spec data

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