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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.


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  • Differential expression analysis
  • Enrichment analysis (GO/Pathways)
  • Imputation (optional)
  • Data visualization
    • PCA
    • Sample correlation
    • Heatmaps
    • Missing values inspection
    • Sample coverage
    • Protein intensity plots for selected protein(s)
    • Imputation effect evaluation

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  • Analysis: perform your own analysis
  • Documentation: Learn more about how to use FragPipe-Analyst

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  • Choose the type of experiment you performed. Currently, DDA-based LFQ (MS1-based or spectral count), TMT, and DIA are supported. Users could also choose to perform analysis at the protein or peptide levels.
  • For DDA LFQ:
    • For protein: Upload combined_protein.tsv generated by IonQuant in FragPipe
    • For peptide: Upload combined_peptide.tsv generated by IonQuant in FragPipe
    • Upload experiment_annotation.tsv file. Edit the template file generated by FragPipe; Check here for details.
    • Select quantification method (MS1-based Intensity or MaxLFQ Intensity, or spectral counts).
  • For TMT:
    • For protein or gene: Upload gene-level report [abundance/ratio]_gene_[normalization].tsv or protein-level report [abundance/ratio]_protein_[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.
    • For peptide: Upload peptide-level report [abundance/ratio]_peptide_[normalization].tsv generated by TMT-Integrator (TMT-I) in FragPipe (we recommend abundance_peptide_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:
    • For protein: Upload protein group (PG) matrix ( diann-output.pg_matrix.tsv ) generated by DIA-NN in FragPipe
    • For peptide: Upload precursor group matrix ( diann-output.pr_matrix.tsv ) generated by DIA-NN in FragPipe
    • Upload experiment_annotation.tsv file. Check here for details.
  • Optional: Adjust the missing value filter, normalization, missing value imputation, p-value cut-off, the log2 fold change cut-off, 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



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Select features from Results Table to highlight them on the plot

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Select one or more rows from Results Table to plot individual protein intesities across conditions and replicates

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Note: Currently, only human (default) and mouse data are supported.

Download Table

Note: Currently, only human data is supported

Download Table

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Filtering your identification result based on predeefined filter conditions, and/or changing the sliders of each condition below


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Select conditions/groups to generate the Venn plot. By default, more than three conditions/groups generates a 3D Venn plot, set Condition 3 as "NONE" to generate a 2D Venn plot

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  • Read our documentation and tutorial gateio .
  • 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 .

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For any feedback or question regarding FragPipe-Analyst, please contact the Proteomics & Integrative Bioinformatics Lab (P.I. Alexey Nesvizhskii; University of Michigan):

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  • 03-11-2024: Preprint of FragPipe-Analyst is available in bioRxiv.
  • 12-02-2022: FragPipe-Analyst is first released for beta testing.
  • 07-13-2022: FragPipe-Analyst is first created.

Proteomics & Integrative Bioinformatics Lab at the University of Michigan (P.I. Alexey Nesvizhskii) and the Monash Proteomics & Metabolomics Facility, Monash University (P.I. Ralf Schittenhelm).

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