Annotation of ribosomal protein mass peaks in MALDI-TOF mass spectra of bacterial species and their phylogenetic significance
Authors: Ng Wenfa 
Published: July 2020

Although MALDI-TOF mass spectrometry based microbial identification has achieved a level of accuracy that facilitate its use in classifying microbes to the species and strain level, questions remain on the identities of the mass peaks profiled from individual microbial species. Specifically, in the popular approach of comparing the mass spectrum of known and unknown microbes for identification purposes, the identities of the mass peaks were not taken into consideration. This study sought to determine if ribosomal proteins could account for some of the mass peaks profiled in MALDI-TOF mass spectra of different bacterial species. Using calculated molecular mass of ribosomal proteins for annotating mass peaks in bacterial species’ MALDI-TOF mass spectra downloaded from the SpectraBank database, this study revealed that ribosomal proteins could account for the low molecular weight mass peaks of <10000 Da. However, contrary to published reports, ribosomal proteins could not account for most of the mass peaks profiled. In particular, the data revealed that between 1 and 6 ribosomal protein mass peaks could be annotated in each mass spectrum. Annotated ribosomal proteins were S16, S17, S18, S20 and S21 from the small ribosome subunit, and L27, L28, L29, L30, L31, L31 Type B, L32, L33, L34, L35 and L36 from the large ribosome subunit. The ribosomal proteins with the most number of mass peak annotations were L36 and L29, with L34, L33, and L31 completing the list of ribosomal proteins with large number of annotations. Given the highly conserved nature of most ribosomal proteins, possible phylogenetic significance of the annotated ribosomal proteins were investigated through reconstruction of maximum likelihood phylogenetic trees. Results revealed that except for ribosomal protein L34, L31, L36 and S18, all annotated ribosomal proteins hold phylogenetic significance under the criteria of recapitulation of phylogenetic cluster groups present in the phylogeny of 16S rRNA. Phylogenetic significance of the annotated ribosomal proteins was further verified by the phylogenetic tree constructed based on the concatenated amino acid sequence of L29, S16, S20, S17, L27 and L35. Finally, analysis of the structure of the annotated ribosomal proteins did not reveal a high conservation of structure of the ribosomal proteins. Collectively, small low molecular weight (<10000 Da) ribosomal proteins could annotate some of the mass peaks in MALDI-TOF mass spectra of various bacterial species, and most of the ribosomal proteins hold phylogenetic significance. However, structural analysis did not identify a conserved structure for the annotated ribosomal proteins. Annotation of ribosomal protein mass peaks in MALDI-TOF mass spectra highlighted the deep biological basis inherent in the mass spectrometry-based microbial identification method. Subject areas biochemistry, biotechnology, microbiology, evolution, ecology

Significance of the work

While MALDI-TOF MS has been successfully used in identification of different microbes to the species and strain level through the comparison of mass spectra of known and unknown microbes, the approach (known as mass spectrum fingerprinting) remains lacking in the biological basis that underpins the technique. This study sought to uncover some of the biological basis that underpins MALDI-TOF MS microbial identification through the annotation of profiled mass peaks with ribosomal proteins. Previous studies have linked different ribosomal proteins to mass peaks in MALDI-TOF mass spectra of bacteria; however, broad spectrum verification of the finding across multiple species across different genera remain lacking. Using a collection of MALDI-TOF mass spectra of 110 bacterial species and strains catalogued in SpectraBank, this study sought to annotate ribosomal protein mass peaks in the mass spectra. Results revealed that small, low molecular weight ribosomal proteins of molecular mass < 10000 Da could annotate between 1 and 6 mass peaks in the catalogued mass spectra. This was smaller than the number of ribosomal proteins mass peaks postulated by previous studies. Overall, 16 ribosomal proteins (S16, S17, S18, S20, S21, L27, L28, L29, L30, L31, L31 Type B, L32, L33, L34, L35, and L36) were annotated with the most number of mass peaks annotations coming from L36 and L29. Reconstruction of phylogenetic trees of the annotated ribosomal proteins revealed that most of the ribosomal proteins hold phylogenetic significance with respect to the phylogeny of 16S rRNA. This provided further evidence that a deep biological basis is present in the approach of using mass spectrometry profiling of biomolecules for identifying bacterial species.

Highlights

Ribosomal protein mass peaks were annotated in MALDI-TOF mass spectra of bacterial species across multiple genera.

Annotated ribosomal proteins were S16, S17, S18, S20, S21 for the small ribosome subunit, and L27, L28, L29, L30, L31, L31 Type B, L32, L33, L34, L35, L36 for the large ribosome subunit.

Between 1 and 6 ribosomal protein mass peaks were annotated per mass spectrum, a number significantly lower than that implied by other studies.

Annotated ribosomal proteins were small, low molecular weight ribosomal proteins of molecular mass < 10000 Da.

Phylogenetic tree reconstruction revealed the phylogenetic significance of most annotated ribosomal proteins except ribosomal protein L34, L31, L36 and S18.

Multi-locus sequence typing of L29, S16, S20, S17, L27 and L35 further showed the phylogenetic significance of ribosomal proteins in recapitulating the phylogeny of 16S rRNA.

Structural analysis of annotated ribosomal proteins did not find conserved structure. Thus, the reasons for the annotation of particular ribosomal proteins over others remain unknown.