Overview
Phospho-Analyst: An easy-to-use interactive web-platform to analyze and visualize phosphoproteomics data preprocessed with MaxQuant.
Phospho-Analyst is an easy-to-use, interactive web application developed to perform differential expression analysis with “one click” and to visualize label-free quantitative phosphoproteomics datasets preprocessed with MaxQuant. Phospho-Analyst provides a wealth of user-analytic features and offers numerous publication-quality result output graphics and tables to facilitate statistical and exploratory analysis of label-free quantitative datasets.
Sidebar tabs
- Analysis: perform your own analysis
- Demo: familiarise yourself with Phospho-Analyst by browsing through pre-analysed results
- Datasets: download example dataset files
- User Guide: download an in-depth manual
Related Tools
-
LFQ-Analyst for analysing label-free quantitative proteomics dataset https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst
-
Analyst Suites for additional analyst Apps: https://analyst-suites.org/
Getting Started
Quick Start
- Upload your Phospho (STY)Sites.txt generated by MaxQuant.
-
Phosphosite experimental design:
either upload a text file or modify the template.
Interactive phosphosite experimental design table
-
Upload your
Protein Group.txt (Optional)
generated by MaxQuant.
( Attention : this is not the proteinGroup.txt file that is found in the same folder as the “Phospho (STY) Sites.txt" file. The proteinGroup.txt file must be from a separate MaxQuant search that assessed the proteomic changes in these samples. If you are unsure about which proteinGroup.txt file to choose, please consider to ignore this option. )
-
Protein experimental design (Optional):
either upload a text file or modify the template.
Interactive protein experimental design table
- Optional: Adjust the p-value cut-off, the log2 fold change cut-off, the normalisation type, the imputation type, FDR correction method and/or peptides localization prob cut-off in the Advanced Options.
- Press "Start Analysis".
- Hint: Use the User Guide tab for a detailed explanation of inputs, advanced options and outputs.
- Note: The experimental design file is not the 'mqpar.xml' file from MaxQuant. Use the Datasets tab to download example files provided.
Results Table
- Volcano plot
- Heatmap
- Individual Plot
- Abundance Plot
- Result Plots
Select phosphosite from Results Table to highlight on the plot OR drag the mouse on plot to show expression of phosphosites in Table, ANOVA function only worked for more than two groups.
Select one or more rows from Results Table to plot individual phosphosite intesities across conditions and replicates
Select protein from Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
Select protein from Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
Results Table
- Volcano plot
- Heatmap
- Individual Plot
- Result Plots
Select protein from Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table, ANOVA function only worked for more than two groups.
Select one or more rows from Results Table to plot individual protein intesities across conditions and replicates
- Gene Ontology
- Pathway enrichment
- Enrichment
Scatter plot: log2 fold changes
QC Plots
Side-by-side comparison
Results Table
- Volcano plot
- Heatmap
- Individual Plot
- Result Plots
Select phosphosite from Results Table to highlight on the plot OR drag the mouse on plot to show expression of phosphosites in Table, ANOVA function only worked for more than two groups.
Select one or more rows from Results Table to plot individual protein intesities across conditions and replicates
Options
Pre-filter Results table, Venn plot and Upset plot by the Sliders of each condition/group below, and/or the Filter Condition
Number of replicates present
Subset Results Table
Results Table
Results Table
- Volcano plot
- Heatmap
- Individual Plot
- Abundance Plot
- Result Plots
Select phosphosite from Results Table to highlight on the plot OR drag the mouse on plot to show expression of phosphosites in Table, ANOVA function only worked for more than two groups.
Select one or more rows from Results Table to plot individual protein intesities across conditions and replicates
Select protein from Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
Select protein from Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
Results Table
- Volcano plot
- Heatmap
- Individual Plot
- Result Plots
Select protein from Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table, ANOVA function only worked for more than two groups.
Select one or more rows from Results Table to plot individual protein intesities across conditions and replicates
- Gene Ontology
- Pathway enrichment
- Enrichment
Scatter plot: log2 fold changes
QC Plots
Side-by-side comparison
Results Table
- Volcano plot
- Heatmap
- Individual Plot
- Result Plots
Select phosphosite from Results Table to highlight on the plot OR drag the mouse on plot to show expression of phosphosites in Table, ANOVA function only worked for more than two groups.
Select one or more rows from Results Table to plot individual protein intesities across conditions and replicates
Options
Pre-filter Results table, Venn plot and Upset plot by the Sliders of each condition/group below, and/or the Filter Condition
Number of replicates present
Subset Results Table
Results Table
Example Datasets
Dowanloadable Example datasets:
The datasets are the raw data files used in Demo Tab
User Guide
Phospho-Analyst: Manual
A detail online user manual can be accessed here.
Contact Us
For any feedback or question regarding Phospho-Analyst, please contact the Monash Proteomics and Metabolomics Facility:
- Haijian Zhang: hailey.zhang1(at)monash.edu
- Anup Shah: anup.shah(at)monash.edu
- Ralf Schittenhelm: ralf.schittenhelm(at)monash.edu
Or leave comments to our GitHub: here.
News and Updates
- 16-08-2023: Phospho-Analyst paper published online in Journal of Proteome Research (JPR)
- 18-07-2023: Phospho-Analyst GitHub repository made public