Hi, I was able to successfully run the quantms pipeline and got the qpx outputs. I was attempting to use these with mokume but ran across several issues. Every feature in the feature.parquet file has

unique = null

. Current mokume requires

unique = true

, leaving zero features and causing a later DirectLFQ division-by-zero error. There is also the issue of peptide counts needed for deqms processing, which I'm not sure if this processing step computes that.