Influence of Post-Translational Modifications on Protein Identification in Database Searches

Comprehensive analysis
of post-translation modifications (PTMs)
is an important mission of proteomics. However, the consideration
of PTMs increases the search space and may therefore impair the efficiency
of protein identification. Using thousands of proteomic searches,
we investigated the practical aspects of considering multiple PTMs
in Byonic searches for the maximization of protein and peptide hits.
The inclusion of all PTMs, which occur with at least 2% frequency
in the sample, has an advantageous effect on protein and peptide identification.
A linear relationship was established between the number of considered
PTMs and the number of reliably identified peptides and proteins.
Even though they handle multiple modifications less efficiently, the
results of MASCOT (using the Percolator function) and Andromeda (the
search engine included in MaxQuant) became comparable to those of
Byonic, in the case of a few PTMs.