As described above, the QC-level of a material dictates how and when it may be used, which in turn determines which information it can provide. Similarly, when the QC material is used establishes metrics points in time, which is essential before and during an experiment. Specific approaches to using QC materials within the experiment itself are important to discuss. In addition to SST before the run has started, QC materials can be used within runs to monitor changes in instrument performance. As a general heuristic, one out of every 20 samples should include some sort of QC check (i.e., 5 % samples are QC samples). This simple guideline does not replace the importance of proper experimental design and sample randomization. The QC samples may reveal batch effects, but they will not automatically correct them. Since replicates will be mentioned, for this paper we define them as follows: experimental replicate is a sample that was processed and analyzed independently more than once; technical replicate is a sample that was processed once but repeat measurements were taken on the instrument. More detailed descriptions and discussions of experimental design and QCs such as block designs, can be found here . The different QC materials that have been described above may be referred to as external QC (EQC), to differentiate this QC from a study pool QC (SPQC). An SPQC would be a QC2, but is laboratory (and experiment) specific, and not commercially available. In general, the use of both external QC (EQC) and study pool QC (SPQC) samples is important. In a multi-well plate format, the EQC and SPQC can be spaced between samples , related to upstream process batching if needed (though these same concepts can be applied within a normal sample queue as well as a plate format). Within plates it is also important to consider the location of samples to capture effects within the plate, such as the unequal effect of heating during protein digestion . Finally, when analyzing multiple plates, the same concepts of block design and normalization apply, and the use of QC materials can be essential to implementing, especially when the desire is to compare to historical data sets or those collected in other labs.