Coarse measures of system performance, such as "number of peptide spectral matches" of a known sample on a known gradient, are considered insufficient since such metrics can mask underlying issues with the system leading to false confidence, or simply not provide any actionable troubleshooting if the metric is too low. Therefore, there is a desire to provide more granular metrics, that include ID-free and ID-based metrics, covering protein extraction, digestion efficiency, chromatographic separation, ion mobility, mass spectrometry, tandem mass spectrometry and peptide and protein quantification. The ID-free metrics are those metrics that can be computed independently of identifying any peptides and cover aspects such as column pressure, electrospray stability, chromatographic peak width, overall signal (total ion chromatograms), mass measurement precision and charge state distribution . Through direct comparisons of tandem mass spectra, similarity between LC-MS/MS datasets can also be evaluated and used for experimental QC . ID-based metrics are those reliant on peptide identification, and include chromatographic reproducibility, mass measurement accuracy, collision energy, peptide identification rate and most quantitative QC metrics. This general dichotomy is useful to separate QC metrics into those that can be calculated immediately from the data, making few or no assumptions from those that first require running a data analysis pipeline, making many assumptions, in order to calculate the QC metrics. The former are more primitive, though their calculation is highly reliable and independent of search space (i.e., fasta)