Open AccessInfluence of Post-Translational Modifications on Protein Identification in Database Searches
Author(s) -
Fanni Bugyi,
Dániel Szabó,
Győző Szabó,
Ágnes Révész,
Veronika F.S. Pape,
Eszter SoltészKatona,
Eszter Tóth,
Orsolya Kovács,
Tamás Langó,
Károly Vékey,
László Drahos
Publication year - 2021
Publication title -
acs omega
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.779
H-Index - 40
ISSN - 2470-1343
DOI - 10.1021/acsomega.0c05997
Subject(s) - mascot , identification (biology) , posttranslational modification , protein function , proteomics , computational biology , computer science , database search engine , function (biology) , biology , search engine , biochemistry , genetics , information retrieval , botany , enzyme , political science , gene , law
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.