wolski / PIPI

PTM-Invariant Peptide Identification

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.

PIPI

PTM-Invariant Peptide Identification.

How to use it?

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

Cite

Yu, Fengchao, Ning Li, and Weichuan Yu. "PIPI: PTM-Invariant Peptide Identification Using Coding Method" (under review).