@MattWFoster I don't think you can say much about the labeling reaction at the peptide level after mixing. You can sum total intensities per sample (channel) and see if some are low. (Note that tags are around 92% at tag mass and 8% in adjacent channels, so you have limits for how small intensity totals can be.) A low intensity could mean poor labeling or inaccurate protein/peptide assay. You need to fix the low channels before the final run. A variable mod search does not make much sense.