Figure 6. Manually constructed classification tree for the partitioning of analytes into compartments and intermediate units based on their estimated subcellular distribution as well as compartmental abundance and variability.

The classification tree was used to assign an analyte into a group defining its subcellular distribution type (type) and an associated mode (mode) which represents one of the resolved compartments or the overlap between them. Assignments are based on the mean and standard deviations of the subcellular distribution, estimated using the best fit algorithm (BFA), for each analyte based on the three independent gradient data. Analytes with insufficiently explained subcellular distributions according to the selected compartment-specific markers are accounted as unexplained and are not further considered in this tree. Analytes revealing sufficiently explained fits are accounted as ‘shared’ if the minimum of the percentage value (min  =  mean - SD) in the most abundant compartment is overlapping with the maximum percentage value (max  =  mean + SD) of any other considered compartment. The corresponding mode is defined by the overlapping compartments regarding the most abundant compartment. Analytes are considered ‘specific’ with the mode according to the estimated most abundant compartment, if the minimum of the most abundant compartment is ≥75% and the values of all other (low abundant) compartments are negligible, i.e. ≤10%. If the minimum in the most abundant compartment is larger than the sum of the maxima among the other compartment and ≥66.67% (2/3 compartments), analytes are accounted as ‘dominantly’ distributed in the respective compartment. Analytes are accounted as ‘enriched’ in a compartment, if the value of the most abundant fraction is ≥50% than the sum of the other compartment. If none of this decisions result in an assignment the analyte is considered as being shared but with enrichment in a particular compartment (‘shared*’).