The different methods utilizing QC materials described above are vital when embarking on mass spectrometry-based proteomic analysis of hundreds or thousands of samples. Different QC level samples should be distributed throughout the run to provide near real-time evaluation of experimental issues and instrument performance, including changes in chromatographic separation, mass measurement accuracy and measurement sensitivity, and actionable go/no-go metric for the next sample injection. Here, QC2 materials run in parallel with the samples can be used to evaluate upstream preparation steps, e.g. homogenization, enzymatic digestion, and clean-up errors, which are the primary source of technical variability in a proteomics workflow , while QC3 samples serve as in-run SSTs, as they provide information on linearity and limit of quantitation. Any changes beyond acceptable margins can indicate the sequence of analyses should be interrupted and problems addressed before continuing. The troubleshooting can itself be aided by the full range of QC materials. Even when measurements are running smoothly, the QC materials aid in quantifying experimental and technical variability, and provide essential assurance to end-users seeking biological insights.