Search for peptide synthesis side products of a certain mass
Synthesis of long peptides via solid phase peptide synthesis can often lead to a number of side products that include truncated peptides and peptides with deletions that decrease the yield of the synthesis and can be difficult to purify. This simple C++ utility is meant to help identify coupling steps that are problematic by determining which side products might be appearing in the LC-MS of the crude cleaved peptide mixture. The utility implements a simple recursive solution of the subset sum problem to find the candidate peptides.
The inputs to the program are a peptide string and the assumed molecular weight of the side product derived from LC-MS output. The program outputs all possible side products of peptide synthesis within a mass of +/- 1 of the input mass. When calculating peptide weights, we assume a C- terminal amide (mass difference -0.99) and a N-terminal acetyl group (mass difference +42.01). The tolerance or cap mass can be changed by modifying by changing the appropriate variables in peptidechecker.cpp and recompiling.
double CAP_MASS = 41.0265; double tolerance = 1.0;
Installation and Usage
- Download the repository and unzip it.
- Navigate to the peptide-checker folder in the command line using
- Compile in the command line using:
g++ -std=c++11 peptidechecker.cpp
- Execute in the command line using: