Comparing Peptide Spectra Matches Across Search Engines

Rune Matthiesen, Gorka Prieto, Hans Christian Beck

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


Mass spectrometry is extremely efficient for sequencing small peptides generated by, for example, a trypsin digestion of a complex mixture. Current instruments have the capacity to generate 50-100 K MSMS spectra from a single run. Of these ~30-50% is typically assigned to peptide matches on a 1% FDR threshold. The remaining spectra need more research to explain. We address here whether the 30-50% matched spectra provide consensus matches when using different database-dependent search pipelines. Although the majority of the spectra peptide assignments concur across search engines, our conclusion is that database-dependent search engines still require improvements.

Original languageEnglish
Pages (from-to)133-143
Number of pages11
JournalMethods In Molecular Biology (Clifton, N.J.)
Publication statusPublished - 1 Jan 2020


  • Database dependent search
  • Peptide assignments


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