PST: parallel simulation tool to study open search methods for the identification of peptides with post-translational modifications

About PST

Tools utilizing the open search strategy like PIPI and MSFragger become popular because they provide promising results in identifying peptides with post-translational modifications (PTMs). However, their performance vary a lot as the number of PTMs changes in peptides and/or the quality of mass spectrum data varies. Currently, the understanding about the limit of open search methods is lacking.

Here we implement a parallel simulation tool for the investigation of the necessary conditions of open search methods. We generate simulated spectra from database sequences and then search these simulated spectra to verify the correctness of inferred labels. Details about our simulation results are in the paper below.


Related Publication
J. Dai*, F. Yu*, N. Li, and W. Yu. *Contributed equally to this work.
"Understanding the limit of open search in the identification of peptides with post-translational modifications — A simulation-based study",
Under review.
Part of the preliminary result has appeared as a poster in The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB 2017).

Where to download PST

Source code (updated 22 Mar 2018): PST_src.zip
(Downloads = )


Environment configuration

Please install Python 3 and NumPy to use this tool.


How to use it?

Please change the directory to the root of the package before starting simulations.
To start the simulations using tag-based open search, please use the following commands.

python3 scripts/run.py config/sample.json
python3 scripts/local_control.py output/Sample.Output.dat

To start the simulations using spectrum-based open search, please use the following commands.

python3 scripts/run_spec.py config/sample.spec.json
python3 scripts/local_control.py output/Sample.Spectrum.Output.dat

To view the content of the result file (.dat), please use

python3 scripts/echo.py output/Sample.Output.dat