Analysis of 3274 bacterial isolates by rapid evaporative ionisation mass spectrometry (REIMS)

Analysis of bacterial composition using rapid evaporative ionisation mass spectrometry (REIMS) allows for the detection of metabolites that may be considered specific to particular taxons. This database of 3274 isolates covering gram positive and negative bacteria across 5 phyla, 12 classes, 24 orders, 49 families, 85 genera and 239 different species was used to determine m/z features with a high degree of specificity and sensitivity to particular taxonomic levels. To do so, a subset of 597 isolates was identified, from which ~5000 m/z variables were derived, of which 359 were identified as taxon specific markers (TSMs) using this code [1]. Validation was performed using the remaining observations from this dataset. Human colorectal cancer samples analysed by mass spectrometry imaging were also analysed as part of the study to determine if the TSMs could be detected from clinical samples. These files can be found in MTBLS289 [2].

[1] https://github.com/jsmckenzie/bacterialTSM
[2] https://www.ebi.ac.uk/metabolights/MTBLS289