Currently, most methods identify peptides with PTMs based on dynamic programming or enumeration. From a combinatorial perspective, identifying peptides with multiple PTMs is equivalent to finding the optimal PTM pattern that produces theoretical spectra most closely resembling the experimental spectra. However, existing methods resort to approximate solutions only, due to the challenge of the exponentially increasing number of PTM combinations as the number of PTMs in one peptide increases, resulting in unsatisfactory performance when identifying peptides with multiple PTMs.

Source code:       PIPI-C_code_on_GitHub

Usage:

with Java 8 (recommended):

java -Xmx8g -jar PIPI.jar parameter.def

with Java of higher versions:

java -Xmx8g -jar --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.base/java.lang=ALL-UNNAMED PIPI.jar parameter.def spectra_file output_directory

parameter.def can be download along with PIPI-C.