Problem	Solution
Pathology report has high stroma/necrosis in tissue sample	Discard the sample as most target proteins are from tumor cellularity.
Loss of Signal for SIS peptide	Discard this data or perform relative quantification by normalizing with an adjacent SIS peptide with similar signal intensity
Poor data for all proteins in a sample	Check histology of the patient sample and analyze another section
Batch-to-batch variability	Normalize data from the tissue samples by using the data from QC cell line samples