MaxLFQ does not quantify proteins only present in a single sample

[MatthewThe]

Proteins that only occur in a single sample get assigned an LFQ intensity of 0.0. This can be confusing for the end user, e.g. in cases where the protein is expected to only occur in a single sample. The more intuitive result would be to use the summed intensity, provided at least minPeptideRatiosLFQ peptides were identified.

The reason for the 0.0 intensity, is that no peptide ratios can be computed between two samples:

picked_group_fdr/picked_group_fdr/columns/lfq.py

Lines 150 to 151 in 94c778c

	if len(logMedianPeptideRatios) == 0:
	return [0.0] * numExperiments

More generally, this also applies to situations where multiple peptides are detected for a protein, but each peptide was only identified in a single sample. However, here, the summed intensity might give the wrong impression that there were peptides in common between the two samples.