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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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Phylogenetic Analysis Using Protein Mass Spectrometry.

Shiyong Ma^1,2, Kevin M Downard^1,2, Jason W H Wong^3,4

¹Prince of Wales Clinical School, UNSW Australia, Sydney, NSW, 2052, Australia.

Methods in Molecular Biology (Clifton, N.J.)

|December 16, 2016

Summary

Protein mass spectrometry provides novel phylogenetic analysis methods when DNA is unavailable. This study details three distinct approaches for molecular evolution research using mass spectrometry data.

Keywords:

De novo sequencing Mass mapping Mass tree Molecular evolution Phylogenetic tree Phylogenetics

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Area of Science:

Molecular Biology
Evolutionary Biology
Biochemistry

Background:

DNA sequence analysis is standard for molecular evolution and phylogenetics.
Protein mass spectrometry offers an alternative for phylogenetic studies, especially when DNA is inaccessible or expensive.

Purpose of the Study:

To explore the utility of protein mass spectrometry in phylogenetic analysis.
To categorize and describe existing methods for phylogenetic reconstruction using mass spectrometry data.

Main Methods:

The study outlines three primary methods for phylogenetic analysis using protein mass spectrometry.
Method 1: De novo protein sequencing followed by classical phylogenetic reconstruction.
Method 2: Direct phylogenetic reconstruction using proteolytic peptide mass maps.
Method 3: Mapping of mass spectral data onto established phylogenetic trees.

Main Results:

The chapter provides a concise overview of these three distinct methodologies.
Protocols, relevant tools, and algorithms for each method are discussed.

Conclusions:

Protein mass spectrometry presents valuable opportunities for phylogenetic analyses.
These methods are particularly relevant for organisms where DNA acquisition is challenging.