Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data.

Zhang, H; Steele, JR; Kahrood, HV; Lucas, DD; Shah, AD; Schittenhelm, RB

Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data.

Zhang, H Steele, JR Kahrood, HV Lucas, DD Shah, AD Schittenhelm, RB

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Publisher:: AMER CHEMICAL SOC
Publication Type:: Journal Article
Citation:: J Proteome Res, 2023, 22, (9), pp. 2890-2899
Issue Date:: 2023-09-01

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Field	Value	Language
dc.contributor.author	Zhang, H
dc.contributor.author	Steele, JR
dc.contributor.author	Kahrood, HV
dc.contributor.author	Lucas, DD
dc.contributor.author	Shah, AD
dc.contributor.author	Schittenhelm, RB
dc.date.accessioned	2024-05-21T21:48:58Z
dc.date.available	2024-05-21T21:48:58Z
dc.date.issued	2023-09-01
dc.identifier.citation	J Proteome Res, 2023, 22, (9), pp. 2890-2899
dc.identifier.issn	1535-3893
dc.identifier.issn	1535-3907
dc.identifier.uri	http://hdl.handle.net/10453/179093
dc.description.abstract	Phosphoproteomics is nowadays the method of choice to comprehensively identify and quantify thousands of phosphorylated peptides and their associated proteins with the goal of interrogating changes in signal transduction pathways and other cellular processes. One of the most popular software suites to analyze phosphoproteomic data sets is MaxQuant, which converts mass spectrometric raw data into quantitative information on phosphopeptides and proteins. However, despite the increased utilization of phosphoproteomics in biomedical research, simple and user-friendly tools supporting downstream statistical analysis and interpretation of these highly complex outputs are still lacking. We have therefore developed Phospho-Analyst, which─similar to its sibling LFQ-Analyst─is an easy-to-use, interactive web application specifically designed to reproducibly perform differential expression analyses with "one click" and to visualize phosphoproteomic results in a meaningful and practical manner. Furthermore, if quantitative total proteomic information is available for the same samples, Phospho-Analyst automatically normalizes all phosphoproteomic results to underlying protein abundance levels, thereby ensuring that only genuine changes in phosphorylation events are considered. As such, Phospho-Analyst can not only be used by experienced proteomic veterans but also by researchers without any prior knowledge in (phospho)proteomics, statistics, or bioinformatics. Phospho-Analyst, including a detailed manual, is freely available at https://analyst-suites.org/apps/phospho-analyst/.
dc.format	Print-Electronic
dc.language	eng
dc.publisher	AMER CHEMICAL SOC
dc.relation.ispartof	J Proteome Res
dc.relation.isbasedon	10.1021/acs.jproteome.3c00186
dc.rights	info:eu-repo/semantics/closedAccess
dc.subject	03 Chemical Sciences, 06 Biological Sciences
dc.subject.classification	Biochemistry & Molecular Biology
dc.subject.classification	31 Biological sciences
dc.subject.classification	34 Chemical sciences
dc.subject.mesh	Proteomics
dc.subject.mesh	Proteins
dc.subject.mesh	Software
dc.subject.mesh	Mass Spectrometry
dc.subject.mesh	Phosphorylation
dc.subject.mesh	Proteins
dc.subject.mesh	Proteomics
dc.subject.mesh	Phosphorylation
dc.subject.mesh	Software
dc.subject.mesh	Mass Spectrometry
dc.subject.mesh	Proteomics
dc.subject.mesh	Proteins
dc.subject.mesh	Software
dc.subject.mesh	Mass Spectrometry
dc.subject.mesh	Phosphorylation
dc.title	Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data.
dc.type	Journal Article
utslib.citation.volume	22
utslib.location.activity	United States
utslib.for	03 Chemical Sciences
utslib.for	06 Biological Sciences
pubs.organisational-group	University of Technology Sydney
pubs.organisational-group	University of Technology Sydney/Provost
pubs.organisational-group	University of Technology Sydney/Provost/Jumbunna
utslib.copyright.status	closed_access	*
dc.date.updated	2024-05-21T21:48:55Z
pubs.issue	9
pubs.publication-status	Published
pubs.volume	22
utslib.citation.issue	9

Abstract:

Phosphoproteomics is nowadays the method of choice to comprehensively identify and quantify thousands of phosphorylated peptides and their associated proteins with the goal of interrogating changes in signal transduction pathways and other cellular processes. One of the most popular software suites to analyze phosphoproteomic data sets is MaxQuant, which converts mass spectrometric raw data into quantitative information on phosphopeptides and proteins. However, despite the increased utilization of phosphoproteomics in biomedical research, simple and user-friendly tools supporting downstream statistical analysis and interpretation of these highly complex outputs are still lacking. We have therefore developed Phospho-Analyst, which─similar to its sibling LFQ-Analyst─is an easy-to-use, interactive web application specifically designed to reproducibly perform differential expression analyses with "one click" and to visualize phosphoproteomic results in a meaningful and practical manner. Furthermore, if quantitative total proteomic information is available for the same samples, Phospho-Analyst automatically normalizes all phosphoproteomic results to underlying protein abundance levels, thereby ensuring that only genuine changes in phosphorylation events are considered. As such, Phospho-Analyst can not only be used by experienced proteomic veterans but also by researchers without any prior knowledge in (phospho)proteomics, statistics, or bioinformatics. Phospho-Analyst, including a detailed manual, is freely available at https://analyst-suites.org/apps/phospho-analyst/.

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http://hdl.handle.net/10453/179093