Darwin’s Tree of Life is Numbered. Resolving the Origins of Species by Mass

Structural Phylogenetics with Protein Mass Spectrometry: A Proof-of-Concept

It is demonstrated, for the first time, that a mass spectrometry approach (known as phylonumerics) can be successfully implemented for structural phylogenetics investigations to chart the evolution of a protein's structure and function. Illustrated for the compact globular protein myoglobin, peptide masses produced from the proteolytic digestion of the protein across animal species generate trees congruent to the sequence tree counterparts. Single point mutations calculated during the same mass tree building step can be followed along interconnected branches of the tree and represent a viable structural metric. A mass tree built for 15 diverse animal species, easily resolve the birds from mammal species, and the ruminant mammals from the remainder of the animals. Mutations within helix-spanning peptide segments alter both the mass and structure of the protein in these segments. Greater evolution is found in the B-helix over the A, E, F, G and H helices. A further mass tree study, of six more closely related primate species, resolves gorilla from the other primates based on a P22S mutation within the B-helix. The remaining five primates are resolved into two groups based on whether they contain a glycine or serine at position 23 in the same helix. The orangutan is resolved from the gibbon and siamang by its G-helix C110S mutation, while homo sapiens are resolved from chimpanzee based on the Q116H mutation. All are associated with structural perturbations in such helices. These structure altering mutations can be tracked along interconnecting branches of a mass tree, to follow the protein's structure and evolution, and ultimately the evolution of the species in which the proteins are expressed. Those that have the greatest impact on a protein's structure, its function, and ultimately the evolution of the species, can be selectively tracked or monitored.

25 Years Responding to Respiratory and Other Viruses with Mass Spectrometry

This review article presents the development and application of mass spectrometry (MS) approaches, developed in the author's laboratory over the past 25 years, to detect; characterise, type and subtype; and distinguish major variants and subvariants of respiratory viruses such as influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All features make use of matrix-assisted laser desorption ionisation (MALDI) mass maps, recorded for individual viral proteins or whole virus digests. A MALDI-based immunoassay in which antibody-peptide complexes were preserved on conventional MALDI targets without their immobilisation led to an approach that enabled their indirect detection. The site of binding, and thus the molecular antigenicity of viruses, could be determined. The same approach was employed to study antivirals bound to their target viral protein, the nature of the binding residues, and relative binding affinities. The benefits of high-resolution MS were exploited to detect sequence-conserved signature peptides of unique mass within whole virus and single protein digests. These enabled viruses to be typed, subtyped, their lineage determined, and variants and subvariants to be distinguished. Their detection using selected ion monitoring improved analytical sensitivity limits to aid the identification of viruses in clinical specimens. The same high-resolution mass map data, for a wide range of viral strains, were input into a purpose-built algorithm (MassTree) in order to both chart and interrogate viral evolution. Without the need for gene or protein sequences, or any sequence alignment, this phylonumerics approach also determines and displays single-point mutations associated with viral protein evolution in a single-tree building step.

SEQUENCE-FREE PHYLOGENETICS WITH MASS SPECTROMETRY

An alternative, more rapid, sequence-free approach to build phylogenetic trees has been conceived and implemented. Molecular phylogenetics has continued to mostly focus on improvement in tree construction based on gene sequence alignments. Here protein-based phylogenies are constructed using numerical data sets ("phylonumerics") representing the masses of peptide segments recorded in a mass mapping experiment. This truly sequence-free method requires no gene sequences, nor their alignment, to build the trees affording a considerable time and cost-saving to conventional phylogenetics methods. The approach also calculates single point amino acid mutations from a comparison of mass pairs from different maps in the data set and displays these at branch nodes across the tree together with their frequency. Studies of the consecutive, and near-consecutive, ancestral and descendant mutations across interconnected branches of a mass tree allow putative adaptive, epistatic, and compensatory mutations to be identified in order to investigate mechanisms associated with evolutionary processes and pathways. A side-by-side comparison of this sequence-free approach and conventional gene sequence phylogenetics is discussed.

Detection of SARS CoV-2 coronavirus omicron variant with mass spectrometry

Mass mapping using high resolution mass spectrometry can rapidly distinguish the omicron variant of the SARS-CoV2 coronavirus strains from other major variants of concern based on insertions, deletions and mutations within the surface spike protein.

Detection and evolution of SARS-CoV-2 coronavirus variants of concern with mass spectrometry

Mass mapping using high-resolution mass spectrometry has been applied to identify and rapidly distinguish SARS-CoV-2 coronavirus strains across five major variants of concern. Deletions or mutations within the surface spike protein across these variants, which originated in the UK, South Africa, Brazil and India (known as the alpha, beta, gamma and delta variants respectively), lead to associated mass differences in the mass maps. Peptides of unique mass have thus been determined that can be used to identify and distinguish the variants. The same mass map profiles are also utilized to construct phylogenetic trees, without the need for protein (or gene) sequences or their alignment, in order to chart and study viral evolution. The combined strategy offers advantages over conventional PCR-based gene-based approaches exploiting the ease with which protein mass maps can be generated and the speed and sensitivity of mass spectrometric analysis.

Protein phylogenetics with mass spectrometry. A comparison of methods

Advances in protein mass spectrometry have provided the ability to identify and sequence proteins with unprecedented speed, sensitivity and accuracy. These benefits now offer advantages for studies of protein evolution and phylogeny avoiding the need to generate and align DNA sequences which can prove time consuming, costly and difficult in the case of large genomes and for highly diverse organisms. The methods of phylogenetic analysis using protein mass spectrometry can be classified into three categories: (1) de novo protein sequencing followed by multiple sequence alignment for classical phylogenetic reconstruction, (2) direct phylogenetic reconstruction using expressed protein mass profiles exploited in microbial biotyping applications, and (3) the construction of trees using proteolytic peptide mass map or fingerprint data. This review describes the three approaches together with the relevant tools and algorithms required to implement them. It also compares each of these alternative protein based methods alongside conventional gene sequence based phylogenetics.