ms_workflow: add additional quality metrics to the differential abundance analysis output

• take the intensities of the standard as a minimal threshold to mark low-abundant proteins
• summarize MS/MS information as numeric value per gene and condition (e.g. percentage of MS/MS identifications per gene across all replicates); additionally include some summary of identification types per sample in the ms_data_prep.R script)
• report for which entries the proteinGroups order has been changed by sorting
• add information per gene whether the value for any replicate per condition has been imputed