title: Use of MALDI-TOF mass spectrometry and a custom database to characterize bacteria indigenous to a unique cave environment (Kartchner Caverns, AZ, USA).
abstract: 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.
authors.affiliation: School of Mathematical and Natural Sciences, Arizona State University.
authors.forename: Lin
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Applied Maths NV.
authors.forename: Katleen
authors.initials: K
authors.lastname: Vranckx
authors.affiliation: Applied Maths NV.
authors.forename: Koen
authors.initials: K
authors.lastname: Janssens
authors.affiliation: School of Mathematical and Natural Sciences, Arizona State University; Todd.Sandrin@asu.edu.
authors.forename: Todd R
authors.initials: TR
authors.lastname: Sandrin
mesh_terms: D001130:Arizona; D001419:Bacteria / Q000145:classification*; D059552:Caves / Q000382:microbiology*; D016208:Databases, Factual; D004783:Environmental Microbiology; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*