Genome Biology (Dec 2023)

A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry

  • Yuji Sekiguchi,
  • Kanae Teramoto,
  • Dieter M. Tourlousse,
  • Akiko Ohashi,
  • Mayu Hamajima,
  • Daisuke Miura,
  • Yoshihiro Yamada,
  • Shinichi Iwamoto,
  • Koichi Tanaka

DOI
https://doi.org/10.1186/s13059-023-03096-4
Journal volume & issue
Vol. 24, no. 1
pp. 1 – 20

Abstract

Read online

Abstract MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including uncultured lineages. We present a new strategy for broad-spectrum identification of bacterial and archaeal isolates by MALDI-TOF MS using a large-scale database of protein masses predicted from nearly 200,000 publicly available genomes. We verify the ability of the database to identify microorganisms at the species level and below, achieving correct identification for > 90% of measured spectra. We further demonstrate its utility by identifying uncultured strains from mouse feces with metagenomics, allowing the identification of new strains by customizing the database with metagenome-assembled genomes.

Keywords