1. Data input

A. Import peptide file:

File format: A comma separated file (.csv) where the first column is the peptide sequence, and following columns are intensity values. Headers should be used. It is helpful to have the conditions of your samples in the header.
File format: The peptide.txt output file from MaxQuant or MetaLab.

B. Add treatment information

Auto condition formatting will try and match your treatment conditions with your samples. If your sample names contain your treatment, this is a great option. Try typing your control and treatment names in the boxes above. If you have more than one treatment, please push the button to add another treatment option.

2. Check sample names and sample conditions


Note: you can update your sample names here. Condition names are either auto filled or can be typed in. Please use the drop down options for conditions.

3. Analysis options

A. Data Normalization

Note: If you opt for no normalization, we highly recommend you normalize your data using your own methods before uploading to pepFunk. If you'd like to know more about our normalization technique, please see our manuscript (https://doi.org/10.1093/bioinformatics/btaa289).

B. Choose log transformation

C. Choose peptide-to-KEGG database


Note: Your database must be comma separated (.csv) where the first column is the peptide sequence the second column is the KO term, and the third column is the number of times that peptide was annotated with the KO term.

About pepFunk, a metaproteomic peptide-centric functional enrichment workflow.

Welcome to pepFunk!
pepFunk allows you to complete a peptide-focused functional enrichment workflow for gut microbiome metaproteomic studies. This workflow uses KEGG annotation for pathway enrichment, alongside Gene Set Variation Analysis (GSVA) adapted for peptide data. By completing analysis on peptides, rather than proteins, we lose less information and retain more statistical power. We curated peptide database specific to human gut microbiome studies for computational speed.