Retrospective non-target analysis to support regulatory water monitoring: from masses of interest to recommendations via in silico workflows

Environmental Sciences Europe

Table 1 Quality control checks within the prescreening workflow applied to the MS1 and MS2 spectral data for each case

Quality control check	Description	Positive mode threshold	Negative mode threshold
1	Availability of MS1 precursor	Presence/absence
2	Minimum MS1 intensity	1 × 10⁵	1 × 10⁴
3	Maximum MS1 noise level	3x (average baseline intensity)
4	Availability of MS2 corresponding to MS1 precursor	Presence/absence
5	MS1–MS2 alignment window	0.3 min (i.e. ± 0.15 min)
6	Deduplication of cases	Highest MS1 intensity
7	Minimum peak width and overall shape (manual QC)	0.1 min

Thresholds apply to data measured using an Orbitrap instrument. Checks 1–5 are part of the automated prescreening workflow, while checks 6–7 were performed manually