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Related Concept Videos

Phosphorylation01:02

Phosphorylation

50.5K
The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...
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Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Related Experiment Video

Updated: Jul 19, 2025

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae
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Phospho-Analyst: An Interactive, Easy-to-Use Web Platform To Analyze Quantitative Phosphoproteomics Data.

Haijian Zhang1, Joel R Steele1, Hossein Valipour Kahrood1,2

  • 1Monash Proteomics & Metabolomics Platform, Monash Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.

Journal of Proteome Research
|August 16, 2023
PubMed
Summary

Phospho-Analyst is a new web tool simplifying the analysis of phosphoproteomic data. It provides easy, one-click differential expression analysis and visualization for researchers.

Keywords:
RShinyAppbioinformaticsdata analysismass spectrometryphosphoproteomicsstatistical analysisweb-based software tool

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Proteomics

Background:

  • Phosphoproteomics enables comprehensive identification and quantification of phosphorylated peptides and proteins.
  • MaxQuant is a popular software suite for analyzing phosphoproteomic datasets.
  • A lack of user-friendly tools hinders downstream statistical analysis and interpretation of complex phosphoproteomic outputs.

Purpose of the Study:

  • To develop an easy-to-use, interactive web application for reproducible analysis and visualization of phosphoproteomic data.
  • To provide a tool that supports researchers without prior expertise in proteomics, statistics, or bioinformatics.
  • To enable normalization of phosphoproteomic results to total protein abundance for accurate identification of phosphorylation changes.

Main Methods:

  • Development of Phospho-Analyst, an interactive web application.
  • Implementation of "one-click" differential expression analysis.
  • Integration of automatic normalization to total protein abundance when available.

Main Results:

  • Phospho-Analyst offers a user-friendly interface for complex phosphoproteomic data analysis.
  • The tool facilitates reproducible differential expression analysis and meaningful visualization.
  • Automatic normalization ensures that only genuine changes in phosphorylation are identified.

Conclusions:

  • Phospho-Analyst addresses the need for accessible tools in phosphoproteomic data analysis.
  • The application empowers researchers of all skill levels to interpret phosphoproteomic results effectively.
  • Phospho-Analyst is freely available with a detailed manual.