CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction
V. Dorfer, S. Maltsev, S. M. Winkler, K. Mechtler - CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction - Journal of Proteome Research, 2018, pp. 2581-2589
Coeluting peptides are still a major challenge for the identification and validation of MS/MS spectra, but carry great potential. To tackle these problems, we have developed the here presented CharmeRT workflow, combining a chimeric spectra identification strategy implemented as part of the MS Amanda algorithm with the validation system Elutator, which incorporates a highly accurate retention time prediction algorithm. For high-resolution data sets this workflow identifies 38−64% chimeric spectra, which results in up to 63% more unique peptides compared to a conventional single search strategy.