PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications.
BACKGROUND
Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understanding of key signal transduction mechanisms. However, with increasing availability of deep, quantitative datasets in diverse species, there is a growing need for tools to facilitate cross-species comparison of PTM data. This is particularly important because functionally important modification sites are more likely to be evolutionarily conserved; yet cross-species comparison of PTMs is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites. Here, we addressed this by developing a web-based software tool, PhosphOrtholog ( www.phosphortholog.com ) that accurately maps protein modification sites between different species. This facilitates the comparison of datasets derived from multiple species, and should be a valuable tool for the proteomics community.


RESULTS
Here we describe PhosphOrtholog, a web-based application for mapping known and novel orthologous PTM sites from experimental data obtained from different species. PhosphOrtholog is the only generic and automated tool that enables cross-species comparison of large-scale PTM datasets without relying on existing PTM databases. This is achieved through pairwise sequence alignment of orthologous protein residues. To demonstrate its utility we apply it to two sets of human and rat muscle phosphoproteomes generated following insulin and exercise stimulation, respectively, and one publicly available mouse phosphoproteome following cellular stress revealing high mapping and coverage efficiency. Although coverage statistics are dataset dependent, PhosphOrtholog increased the number of cross-species mapped sites in all our example data sets by more than double when compared to those recovered using existing resources such as PhosphoSitePlus.


CONCLUSIONS
PhosphOrtholog is the first tool that enables mapping of thousands of novel and known protein phosphorylation sites across species, accessible through an easy-to-use web interface. Identification of conserved PTMs across species from large-scale experimental data increases our knowledgebase of functional PTM sites. Moreover, PhosphOrtholog is generic being applicable to other PTM datasets such as acetylation, ubiquitination and methylation.
Charles Perkins Centre, School of Molecular Biosciences, University of Sydney, Camperdown, NSW, 2006, Australia. rima.chaudhuri@sydney.edu.au.|Diabetes and Obesity Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia. rima.chaudhuri@sydney.edu.au.
Rima
R
Chaudhuri
Lowy Packer Building, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia. a.sadrieh@victorchang.edu.au.
Arash
A
Sadrieh
Charles Perkins Centre, School of Molecular Biosciences, University of Sydney, Camperdown, NSW, 2006, Australia. nolan.hoffman@sydney.edu.au.|Diabetes and Obesity Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia. nolan.hoffman@sydney.edu.au.
Nolan J
NJ
Hoffman
Charles Perkins Centre, School of Molecular Biosciences, University of Sydney, Camperdown, NSW, 2006, Australia. benjamin.parker@sydney.edu.au.|Diabetes and Obesity Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia. benjamin.parker@sydney.edu.au.
Benjamin L
BL
Parker
Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany. humphrey@biochem.mpg.de.
Sean J
SJ
Humphrey
Charles Perkins Centre, School of Molecular Biosciences, University of Sydney, Camperdown, NSW, 2006, Australia. jacqueline.stoeckli@sydney.edu.au.|Diabetes and Obesity Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia. jacqueline.stoeckli@sydney.edu.au.
Jacqueline
J
Stöckli
Lowy Packer Building, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia. a.hill@victorchang.edu.au.
Adam P
AP
Hill
Charles Perkins Centre, School of Molecular Biosciences, University of Sydney, Camperdown, NSW, 2006, Australia. david.james@sydney.edu.au.|Diabetes and Obesity Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW, 2010, Australia. david.james@sydney.edu.au.
David E
DE
James
School of Mathematics and Statistics, University of Sydney, Camperdown, NSW, 2006, Australia. jean.yang@sydney.edu.au.
Jean Yee Hwa
JY
Yang
D000818:Animals; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D051379:Mice; D010766:Phosphorylation; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism*; D051381:Rats; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D020543:Proteome