Solution to Dark Matter Identified by Mass-Tolerant Database Search

  • Rune Matthiesen
Part of the Methods in Molecular Biology book series (MIMB, volume 2051)


Recently a mass-tolerant search approach was proposed which suggested novel types of abundant modification with delta masses that left many scratching their heads. These surprising new findings which were hard to explain were later referred to as dark matter of mass spectrometry-based proteomics. Rewards were promised for those who could solve these intriguing new findings. We propose here simple solutions to the novel delta masses identified by mass-tolerant database search.

Key words

Open search Validation 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 cofunded by FEDER under the PT2020 Partnership Agreement is acknowledged. 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
  1. 1.Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências MédicasUniversidade NOVA de LisboaLisboaPortugal

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