Hi there! In my output sample file, I have multiple intensities (-quantify was specified in my pipeline) for the same peptide. In proteomics analyses, it is standard to take the maximal value detected and I wanted to confirm if this was also the case for immunopeptidomics?

Hey @Emily Southworth . The TSV file in quantification mode (by using --quantify) additionally holds the columns rt_cf|0|1|.., mz_cf|0|1|.., intensity_cf|0|1|.., and charge_cf|0|1|.., where cf (consensus feature) represents the aggregated value of the individual MS runs (0|1|..) that are part of the Sample_Condition group in the input samplesheet. Use e.g. the individual intensities of MS runs to compare two groups and conduct a differential-presentation analysis. From https://nf-co.re/mhcquant/3.1.0/docs/output/ You normally take an aggregation method like mean, median etc. of those intensities, also in proteomics afaik. If you want to know more about the consensus feature, check out the feature finder publication (from the OpenMS docs)