Sequence‐free Phylogenetics With Mass Spectrometry

Abstract

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

“…Peptide signatures of unique mass can be used to identify the presence of mutations associated with the evolution of the virus without the need for gene or protein sequences. Further, the evolution of the virus can be correctly charted from the mass maps as has been shown previously for other viruses [18][19][20] and a wider range of organisms [25] by this laboratory. Such a mass spectrometry-based strategy offers an alternative to conventional PCR-based genetic detection and analysis of the virus [27] where, after RNA extraction from viral specimens, studies of its evolutionary dynamics require the relatively time-consuming generation, interpretation and processing of large genome sequence datasets.…”

“…This work stems from our previous work to detect, type and subtype and distinguish respiratory viruses [10,[12][13][14][15][16][17] including SARS-CoV-2 [12], employing highresolution mass spectrometry using signature peptides. This current study also demonstrates how such mass spectrometry data can also be used in the construction of phylogenetic trees [18,19], analogous to those derived using gene sequence data, to chart viral evolution [20].…”

“…3. Even without the use of any sequence data or their alignment [19], the mass tree correctly predicts the evolution of the beta, delta and gamma variants from the alpha UK lineage as well as the close association of the two delta variants. Even though the mass datasets do not represent complete S-protein coverage, and despite the very different nature of the data itself, the tree closely resembles the topology of a sequence tree built following the alignment of protein sequence data (across a common span of residues 16 to 1213) (Supplementary Fig.…”

“…This algorithm builds phylogenetic-like trees from mass map data generated experimentally or theoretically, or using some combination of both. Mass trees have been found to highly congruent with sequence-based trees in a series of studies [18][19][20]25].…”

Mass spectrometry analytical responses to the SARS-CoV2 coronavirus in review

“…Mutations in the SARS CoV-2 virus are now becoming more as the world’s population begins to be vaccinated, with those that help the virus to evade immune responses, vaccines and/or therapies are of most concern. It has been shown in a series of studies that have recently been reviewed [ 46 ], that mass map profiles can be used to generate phylogenetic trees that are highly congruent with sequence based trees. Importantly, the sequence-free mass approach can determine most common amino acid mutations from a pairwise comparision of mass differences alone that using a purpose built algorithm are also displayed at branch nodes across the tree.…”