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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

  1. Download the repository and unzip it.
  2. Navigate to the peptide-checker folder in the command line using cd YOUR_DIRECTORY_PATH.
  3. Compile in the command line using:
g++ -std=c++11 peptidechecker.cpp
  1. Execute in the command line using:
./a.out

Web application Alternative

For users without C++ or the desire to deal with the command line, the logic from this program has been implemented in a web application using R Shiny. Source code for the web application is here.

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C++ utility for finding candidates for side products of solid phase peptide synthesis

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