Conserved mass peaks in MALDI-TOF mass spectra of bacterial species
- Published
- Accepted
- Subject Areas
- Biochemistry, Bioinformatics, Biotechnology, Computational Biology, Microbiology
- Keywords
- MALDI-TOF MS, microbial identification, strain, bacteria, species, mass spectrum fingerprinting, biomarkers, pattern recognition, conserved mass peaks, genus
- Copyright
- © 2018 Ng
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Conserved mass peaks in MALDI-TOF mass spectra of bacterial species. PeerJ Preprints 6:e3524v1 https://doi.org/10.7287/peerj.preprints.3524v1
Abstract
Microbes are identified based on their distinguishing characteristics such as gene sequence or metabolic profile. Nucleic acid approaches such as 16S rRNA gene sequencing provide the gold standard method for microbial identification in the contemporary era. However, mass spectrometry-based microbial identification is gaining credence through ease of use, speed, and reliability. Specifically, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in identifying bacteria, fungus, molds and archaea to the species level with high accuracy. The approach relies on the existence of unique mass spectrum fingerprint for individual microbial species. By comparing the mass spectrum of an unknown microbe with that catalogued in a reference database of known microorganisms, microbes could be identified through mass spectrum fingerprinting. However, the approach lacks fundamental biological basis given the relative difficulty in assigning specific protein to particular mass peak in the profiled mass spectrum, which hampers a deeper understanding of the mass spectrum obtained. This study seeks to examine the existence of conserved mass peaks in MALDI-TOF mass spectra of bacterial strains belonging to the same species in open access data from SpectraBank. Results revealed that conserved mass peaks existed for all bacterial species examined (Bacillus subtilis, Bacillus thuringiensis, Carnobacterium maltaaromaticum, Escherichia coli, Proteus vulgaris, Pseudomonas fluorescens, Pseudomonas fragi, Pseudomonas putida, Pseudomonas syringae, Serratia marcescens, Serratia proteamaculans, Staphylococcus aureus, and Stenotrophomonas maltophilia). Large number of conserved mass peaks such as that of E. coli might suggest more closely-related strains of a species though functional annotation of the mass peaks is required to provide deeper understanding of the mechanisms underlying the conservation of specific proteins. On the other hand, strains of S. aureus and P. putida had the least number of conserved mass peaks. Presence of conserved mass peaks in the genus Pseudomonas and Serratia provided further evidence that MALDI-TOF MS microbial identification had a biological basis in identification of microbial species to the genus level. On the other hand, it also highlighted that a subset of proteins could define the taxonomical boundary between the species and genus level. Overall, existence of conserved mass peaks in strains of the same bacterial species provided evidence of a firm biological basis in the mass spectrum fingerprinting approach of MALDI-TOF MS microbial identification. This could help identify specific species in mass spectrum of single or multiple microbial species. Further functional annotation of the conserved mass peaks could illuminate in greater detail the biological mysteries of why certain proteins are conserved in specific genus and species.
Author Comment
This is a preprint manuscript.
Supplemental Information
List of conserved mass peaks of bacterial species
Tabulation of conserved mass peaks of individual bacterial species