CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction

J Proteome Res. 2018 Aug 3;17(8):2581-2589. doi: 10.1021/acs.jproteome.7b00836. Epub 2018 Jun 28.


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.

Keywords: MS/MS; chimeric spectra; database search; mixed spectra; retention time prediction; tandem mass spectrometry; validation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromatography, High Pressure Liquid / methods
  • HeLa Cells / chemistry
  • Humans
  • Peptides / analysis*
  • Search Engine
  • Tandem Mass Spectrometry / instrumentation
  • Tandem Mass Spectrometry / methods*
  • Tandem Mass Spectrometry / standards
  • Time Factors
  • Workflow*


  • Peptides