Use of MALDI-TOF mass spectrometry and a custom database to characterize bacteria indigenous to a unique cave environment (Kartchner Caverns, AZ, USA)

Lin Zhang, Katleen Vranckx, Koen Janssens, Todd Sandrin

Research output: Contribution to journalArticle

7 Scopus citations


MALDI-TOF mass spectrometry has been shown to be a rapid and reliable tool for identification of bacteria at the genus and species, and in some cases, strain levels. Commercially available and open source software tools have been developed to facilitate identification; however, no universal/standardized data analysis pipeline has been described in the literature. Here, we provide a comprehensive and detailed demonstration of bacterial identification procedures using a MALDI-TOF mass spectrometer. Mass spectra were collected from 15 diverse bacteria isolated from Kartchner Caverns, AZ, USA, and identified by 16S rDNA sequencing. Databases were constructed in BioNumerics 7.1. Follow-up analyses of mass spectra were performed, including cluster analyses, peak matching, and statistical analyses. Identification was performed using blind-coded samples randomly selected from these 15 bacteria. Two identification methods are presented: similarity coefficient-based and biomarker-based methods. Results show that both identification methods can identify the bacteria to the species level.

Original languageEnglish (US)
Article numbere52064
JournalJournal of Visualized Experiments
Issue number95
StatePublished - Jan 2 2015



  • BioNumerics
  • Biomarker
  • Database
  • Environmental Sciences
  • Environmental bacteria
  • Fingerprint
  • Identification
  • Issue 95
  • MALDI-TOF mass spectrometry
  • Similarity coefficient

ASJC Scopus subject areas

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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