Updates
LFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize proteomics data preprocessed
New Features
- Interactive experimental design template for users to modify
- Compatible with Fragpipe Tools
- New result plots- Abundance rank and comparison plots
- Absence/Presence of proteins Page
- Venn & UpSet plots on Absence/Presence Page
- Reupload Analysis outputs
- Significance levels on individual plots
- Able to add multifactors to differential analysis
Compatible Inputs
- MaxQuant outputs: proteinGroups.txt
- Fragpipe outputs: combined_protein.tsv
Upcomings
- Compatible with Proteome Discoverer outputs
Overview
LFQ-Analyst is an easy-to-use, interactive web application developed to perform differential expression analysis with “one click” and to visualize label-free quantitative proteomic datasets preprocessed with MaxQuant. LFQ-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 LFQ-Analyst by browsing through pre-analysed results
- User Guide: download an in-depth manual
Getting Started
Quick Start
- Upload your proteinGroups.txt generated by MaxQuant or combined_protein.tsv generated by Fragpipe
- Protein experimental design: either upload a text file or modify the template.
- Optional: Add multifactors, adjust the p-value cut-off, the log2 fold change cut-off, the imputation type, and/or FDR correction method 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 example file template provided.
(Add additional factor columns for a multifactor analysis)
LFQ Results Table
Select protein from LFQ Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
-
Significance levels
-
-
-
Select one or more rows from LFQ Results Table to plot individual protein intesities across conditions and replicates
Select protein from LFQ Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
Select protein from LFQ Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
- Gene Ontology
- Pathway enrichment
- Enrichment
Options
Pre-filter Results table and Venn plot by the Sliders of each condition/group below, and/or the Filter Condition
Number of replicates present
Subset Results Table
Results Table
User Guide
LFQ-Analyst: Manual
A detailed user manual can be accessed here.
Contact Us
For any feedback or question regarding LFQ-Analyst, please contact the Monash Proteomics and Metabolomics Platform:
- Ralf Schittenhelm: ralf.schittenhelm(at)monash.edu
- Haijian Zhang: hailey.zhang1(at)monash.edu
How to Cite LFQ-Analyst?
Please Cite: Shah AD, Goode RJA, Huang C, Powell DR, Schittenhelm RB. LFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize proteomics data preprocessed with MaxQuant. DOI: 10.1021/acs.jproteome.9b00496
News and Updates
- 27-12-2021: LFQ-Analyst being accessed by more than 5000 users worldwide
- 30-09-2021: LFQ-Analyst being accessed by more than 4000 users worldwide
- 03-05-2021: LFQ-Analyst being accessed by more than 3000 users worldwide
- 24-02-2021: Correlation plot now use all protein expression data
- 25-11-2020: LFQ-Analyst being accessed by more than 2000 users worldwide
- 07-04-2020: LFQ-Analyst being accessed by more than 1000 users worldwide
- 03-01-2020: LFQ-Analyst manuscript published in volume 19 of JPR
- 28-10-2019: LFQ-Analyst paper published online in Journal of Proteome Research (JPR)
- 02-10-2019: Svg figures download feature added
- 09-09-2019: Paired test support added
- 09-09-2019: Option to include single peptide observations in the analysis
- 19-02-2019: LFQ-Analyst made public
LFQ Results Table
Select protein from LFQ Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
-
Significance levels
-
-
-
Select one or more rows from LFQ Results Table to plot individual protein intesities across conditions and replicates
Select protein from LFQ Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
Select protein from LFQ Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
- Gene Ontology
- Pathway enrichment
- Enrichment
Options
Pre-filter Results table and Venn plot by the Sliders of each condition/group below, and/or the Filter Condition
Number of replicates present
Subset Results Table
Results Table
Reload Analysis
How to save RData file
-
Save
RData
file from your original analysis
- Upload output.RData file
- Press 'Reload Analysis'
LFQ Results Table
Select protein from LFQ Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
-
Significance levels
-
-
-
Select one or more rows from LFQ Results Table to plot individual protein intesities across conditions and replicates
Select protein from LFQ Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
Select protein from LFQ Results Table to highlight on the plot OR drag the mouse on plot to show expression of proteins in Table
- Gene Ontology
- Pathway enrichment
- Enrichment
Options
Pre-filter Results table and Venn plot by the Sliders of each condition/group below, and/or the Filter Condition