SILAC Peptide Ratio Calculator: A Tool for SILAC Quantitation of Peptides and Post-Translational Modifications

This
paper describes an algorithm to assist in relative quantitation
of peptide post-translational modifications using stable isotope labeling
by amino acids in cell culture (SILAC). The described algorithm first
determines the normalization factor and then calculates SILAC ratios
for a list of target peptide masses using precursor ion abundances.
Four yeast histone mutants were used to demonstrate the effectiveness
of this approach for quantitation of peptide post-translational modifications
changes. The details of the algorithm’s approach for normalization
and peptide ratio calculation are described. The examples demonstrate
the robustness of the approach as well as its utility to rapidly determine
changes in peptide post-translational modifications within a protein.