Comparing peptide spectra matches across search engines

Abstract

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.