In either case, such issues are often not identified until the data set has been completely acquired, at which time the analyst becomes responsible for manually inspecting >2000 XICs at one time.
In the preliminary phase, the expert looks at all of the integrated XICs and creates an unbiased prealgorithm annotation that documents any potential problems, such as poor chromatography, inaccurate peak integration, and so forth.
For example, an experiment consisting of an assay of 10 peptide targets (3 transitions for a light and heavy peptide) and 40 sample injections would produce >2000 XICs to inspect.
In the data sets containing 3 MRM transitions for 10 analyte and SIS peptides and a 9-point calibration curve with a total of 2160 XICs, having to inspect only 240 XICs (or 120 analyte and 120 transition pairs) is a 10-fold reduction in the time required for analyzing the data.
These improvements were due in part to reducing the number of XICs requiring manual inspection to a smaller subset, thereby allowing the expert to evaluate the data more critically.
In this example, several XICs were flagged for manual inspection (18% of the total).