Comparing Peptide Spectra Matches Across Search Engines

  • Rune Matthiesen
  • Gorka Prieto
  • Hans Christian Beck
Part of the Methods in Molecular Biology book series (MIMB, volume 2051)


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.

Key words

Database dependent search Peptide assignments 



R.M. is supported by Fundação para a Ciência e a Tecnologia (FCT investigator program 2012), iNOVA4Health—UID/Multi/04462/2013, a program financially supported by Fundação para a Ciência e Tecnologia/Ministério da Educação e Ciência, through national funds and is cofunded by FEDER under the PT2020 Partnership Agreement. This work is also funded by FEDER funds through the COMPETE 2020 Programme and National Funds through FCT – Portuguese Foundation for Science and Technology under the projects number PTDC/BTM-TEC/30087/2017 and PTDC/BTM-TEC/30088/2017.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Rune Matthiesen
    • 1
  • Gorka Prieto
    • 2
  • Hans Christian Beck
    • 3
  1. 1.Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal
  2. 2.Department of Communications Engineering, Faculty of Engineering of BilbaoUniversity of the Basque Country (UPV/EHU)BilbaoSpain
  3. 3.Department of Clinical Biochemistry and PharmacologyOdense University HospitalOdense CDenmark

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