This year’s ABRF iPRG study focused on “the evaluation of proteomics laboratories in identifying modified peptides present in a complex mixture.” Researchers were invited to analyze a common LC-MS/MS dataset, and report both the unmodified and modified peptides found in the data. PEAKS achieved outstanding performance in terms of both the total number of correctly identified peptides, and the number of correctly identified modified peptides that were spiked in the sample. This is another public study demonstrating that PEAKS is an excellent tool for large-scale in-depth proteomics analysis.
Different from many other tools that solely rely on database searching, PEAKS integrates four different algorithms for the identification of database peptides, PTMs, mutations, and de novo sequences, respectively. This in-depth analysis with multiple algorithms enables the accurate and sensitive identification of both unmodified and modified peptides simultaneously, ensuring that no peptide in your data is left unidentified.
More details can be found here.