This is the source code for the article:
PIPI: PTM-Invariant Peptide Identification Using Coding Method http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00485
The project was open sourced with the publication. Luckily, I did fork it at this timepoint from https://github.com/fcyu because now it is not available there anymore.
PTM-Invariant Peptide Identification.
Requirement:
- Java 1.8 or later.
- With Percolator installed.
Usage:
java -Xmx25g -jar PIPI.jar <parameter_file> <spectra_file>
<parameter_file>
: Parameter file. Can be downloaded along with PIPI.<spectra_file>
: Spectra file (mzXML or mgf).
example: java -Xmx25g -jar PIPI.jar parameter.def data.mzXML
Yu, Fengchao, Ning Li, and Weichuan Yu. "PIPI: PTM-Invariant Peptide Identification Using Coding Method" (under review).