This is the collection of scripts used for the "Fecal metaproteomic profiling of leftover FIT samples" by Avershina et al, 2026
input/true_MaxLFQ_nohuman.xslx: MaxLFQ intensities of FIT and corresponding stool samples from anonimyzed individuals A,B and C and negative controls (only bacterial proteins are reported here)
input/meta.xslx: metadata for FIT and corresponding stool samples
input/simulated_FragPipe_output.xslx: Mock input file with simulated metaproteomic output from the FragPipe used as input for the preprocess.py script
preprocess.py: Filtering of the metaproteomics data and formatting input
protocol_reproducibility.py: Finding proteins consistently recovered between stool and FIT samples and calculating their intensities
samples_variation.py: PCA analysis of protein intensities; PCoA of Jaccard distances between the samples based on presence/absence of proteins
check_hydrophobicity.py: calculate GRAVY scores for the protein sequences
- Python ≥ 3.9
- pandas
- numpy
- scikit-bio
- biopython
- stats
- scanpy
- scipy
- statsmodels
- statannotations
- anndata
- matplotlib
- seaborn
Ekaterina Avershina
University of Oslo
Email: ekateria@uio.no
Trine B Rounge
University of Oslo
Email: t.b.rounge@uio.no