title: Phylogenetic Analysis Using Protein Mass Spectrometry.
abstract: Through advances in molecular biology, comparative analysis of DNA sequences is currently the cornerstone in the study of molecular evolution and phylogenetics. Nevertheless, protein mass spectrometry offers some unique opportunities to enable phylogenetic analyses in organisms where DNA may be difficult or costly to obtain. To date, the methods of phylogenetic analysis using protein mass spectrometry can be classified into three categories: (1) de novo protein sequencing followed by classical phylogenetic reconstruction, (2) direct phylogenetic reconstruction using proteolytic peptide mass maps, and (3) mapping of mass spectral data onto classical phylogenetic trees. In this chapter, we provide a brief description of the three methods and the protocol for each method along with relevant tools and algorithms.
authors.affiliation: Prince of Wales Clinical School, UNSW Australia, Sydney, NSW, 2052, Australia.|Lowy Cancer Research Centre, UNSW, Corner of High and Botany St, Kensington, NSW, 2033, Australia.
authors.forename: Shiyong
authors.initials: S
authors.lastname: Ma
authors.affiliation: Prince of Wales Clinical School, UNSW Australia, Sydney, NSW, 2052, Australia.|Lowy Cancer Research Centre, UNSW, Corner of High and Botany St, Kensington, NSW, 2033, Australia.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Downard
authors.affiliation: Prince of Wales Clinical School, UNSW Australia, Sydney, NSW, 2052, Australia. jason.wong@unsw.edu.au.|Lowy Cancer Research Centre, UNSW, Corner of High and Botany St, Kensington, NSW, 2033, Australia. jason.wong@unsw.edu.au.
authors.forename: Jason W H
authors.initials: JW
authors.lastname: Wong
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D019143:Evolution, Molecular; D013058:Mass Spectrometry / Q000379:methods; D010455:Peptides; D010802:Phylogeny; D011506:Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D059748:Proteolysis; D012984:Software; D064878:Web Browser; D057188:Workflow
chemical_list: D010455:Peptides; D011506:Proteins
keywords: De novo sequencing; Mass mapping; Mass tree; Molecular evolution; Phylogenetic tree; Phylogenetics