Where are my interactions?
All interactions are in Final_Interactions_XX_precision.csv ("XX" is the chosen precision of the interaction list, set in experimental_design.rtf). This is in the folder Output/Data/Interactions/. This folder also has other interaction tables, such as Final_Interactions_list_condition1only_50_precision.csv, which is the interactions only predicted in condition1. Interaction figures are in the folder Output/Figures/Interactions - particularly interesting figures are precision-vs-number-of-interactions (Final_precision_XX.png) and elution curves for the 200 best interactions (in the BestInteractions folder).
Where are my complexes?
Complexes built from all predicted interactions are listed in Complexes_All_interactions.csv. This is in the Output/Data/Complexes/ folder. Figures of complexes are in the Output/Figures/Complexes/ folder.
Where are my fold changes (between conditions)?
Fold changes are listed in Fold_change_condition1vscondition2.csv in folder Output/Data/FoldChanges/. (If there are more than two conditions, "condition1andcondition2" might be, say, "condition1andcondition3".) Figures for every individual protein are in Output/Figures/FoldChanges/IndividualProteins. If there are no FoldChange tables or figures, you might only have one condition. If there are no figures in the IndividualProteins folder, you probably have "Plots of fold changes (FoldChanges)" set to "No" in experimental_design.rtf.
What are all these output files?
See TablesAndFigures.
What is the major protein groups input file?
PrInCE was built to use output from MaxQuant, which returns protein identifications as protein groups. A discussion of what protein groups are is here http://www.nature.com/nprot/journal/v11/n12/box/nprot.2016.136_BX2.html. In brief they're groups of proteins that MaxQuant can't tell apart. Major_protein_groups.csv has a header, has one protein group per row, and is comma-separated. See test data in the Input/ folder for an example. Note: This file is optional! PrInCE runs just fine without it.