or search algorithm. The latter are likely more relevant for data interpretation, but dependent on assumptions being correct, e.g., a calculation of the efficiency of enzymatic digestion will not yield meaningful results if no missed cleavages were allowed in the database search. This is a trivial example, but data analysis methods also influence ID-based QC metrics in less conspicuous ways, for example the mass measurement error tolerance in the database search determines which set of peptides are identified, and in turn the peptides used to calculate mass measurement accuracy.