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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 bacteria at the species and genus levels using open access data from SpectraBank. Results revealed that conserved mass peaks existed for all bacterial species examined. Large number of conserved mass peaks such as that of Escherichia coli and Morganella morganii suggested more closely-related strains of a species though functional annotation of the mass peaks is required to provide a deeper understanding of the mechanisms underlying the conservation of specific proteins. On the other hand, strains of Staphylococcus aureus and Pseudomonas putida had the least number of conserved mass peaks. Presence of conserved mass peaks in many genus provided further evidence that MALDI-TOF MS microbial identification had a biological basis in identification of microbial species to the genus level. In addition, it also highlighted that a subset of proteins could define the taxonomical boundary between the species and genus level. Finally, existence of only one conserved mass peak in Bacillus genus corroborated the difficulty of discriminating Bacillus species based on MALDI-TOF mass spectra. Similarly, no conserved mass peak at the genus level could be found for the Staphylococcus genus. Overall, existence of conserved mass peaks of bacteria at the species and genus levels 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.
This version includes additional analysis of conservation of mass peaks at the genus and species levels.
List of conserved mass peaks of bacterial species
Tabulation of conserved mass peaks of individual bacterial species