1.. It might need a better name
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It is a protein inferencer based on the IDpicker's algorithm from this journal article
Zhang, B., Chambers, M. C., & Tabb, D. L. (2007). Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. Journal of proteome research, 6(9), 3549–3557. https://doi.org/10.1021/pr070230d
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visualization package used seems to be not powerful enough to plot a bipartite graph with 43079 proteins and 86941 peptide (pre-collapse) or 9321 proteins with at least the same amount of peptides
update Monday, September 26, 2022
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EPIFANY refers to the tool reference in this paper.
Pfeuffer, J., Sachsenberg, T., Dijkstra, T., Serang, O., Reinert, K., & Kohlbacher, O. (2020). EPIFANY: A Method for Efficient High-Confidence Protein Inference. Journal of proteome research, 19(3), 1060–1072. https://doi.org/10.1021/acs.jproteome.9b00566
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The code for an implementation of IDPicker used for this project, while not removed from here yet, is being package and made available PyPI and it is associated with another remote repository