FragPipe-Analyst is an easy-to-use, interactive web application developed to perform differential expression analysis with “one click” and to visualize quantitative proteomic datasets analyzed using FragPipe computational platform. It is compatible with the LFQ-MBR, TMT, and DIA quantification workflows in FragPipe. FragPipe-Analyst is based on the original LFQ-Analyst code.
- Differential expression analysis
- Enrichment analysis (GO/Pathways)
- Imputation (optional)
- Data visualization
- Sample correlation
- Missing values inspection
- Sample coverage
- Protein intensity plots for selected protein(s)
- Imputation effect evaluation
- Analysis: perform your own analysis
- Documentation: Learn more about how to use FragPipe-Analyst
- Questions/Suggestions/Bug reports: Ask us in our GitHub forum .
- Documentation/Tutorials: Learn more here .
- Servers: Our production (stable) server is at https://fragpipe-analyst.org/ but we also provide our latest dev server http://fragpipe-analyst.nesvilab.org/ with most recent updates and bug fixes.
- Choose the type of experiment you performed. Currently, DDA-based LFQ (MS1-based or spectral count), TMT, and DIA are supported.
- For DDA LFQ:
- Upload gene-level report [abundance/ratio]_gene_[normalization].tsv generated by TMT-Integrator (TMT-I) in FragPipe (we recommend abundance_gene_MD.tsv file). If peptide option is enabled in the server, TMT-I peptide report could also be used alternatively.
- Upload experiment_annotation.tsv file. Edit the template file generated by FragPipe; Check here for details.
- For DIA:
- Optional: Adjust the p-value cut-off, the log2 fold change cut-off, missing value imputation, FDR correction method in the Advanced Options . Note that the missing value imputation method is set by default to “Perseus-like” for DDA LFQ and DIA, and to “No imputation” for TMT.
- Press 'Run'
- Hint: Check the Documentation tab for a detailed explanation of inputs, advanced options and outputs
Pre-filtering Results table and Venn plot based on preference Filter Condition if has, and/or changing the Sliders of each condition/group below
Subset Results Table
Number of samples present
- Read our documentation and tutorial here .
- Report issues and ask questions here .
- FragPipe-Analyst is open-source! You are more than welcome to contribute .
- Learn more about our FragPipe here .
- The user manual of original LFQ-Analyst can be accessed here .
For any feedback or question regarding FragPipe-Analyst, please contact the Proteomics & Integrative Bioinformatics Lab (P.I. Alexey Nesvizhskii; University of Michigan):
- Professor Alexey Nesvizhskii: email@example.com
News and Updates
- 12-02-2022: FragPipe-Analyst is first released for beta testing.
- 07-13-2022: FragPipe-Analyst is first created.