Table II. Example: filtering results in pseudospectrum 144 (Supplemental Table S1, pcgroup = 144).

DGTS 36:4 is rejected by the isotope filter. O₁ PC 36:4, O₁ PS 40:3, and O₃ PC 38:4 are cross-identified in negative mode, thus disqualifying the other annotations. The adduct filter maintains O₁ PC 36:4 as [M+H]⁺ adduct only; the [M+Na]⁺ adduct is flagged false to avoid redundancy. None of the annotations violated the retention filter rules. O₁ PC 34:3, PC 36:5, and O₁ PC 36:4 were validated by their MS/MS spectra because all of them contain the PC-specific head group (Supplemental Table S6). Both O₁ PC 36:4 adducts ([M+H]⁺ and [M+Na]⁺) were confirmed by their MS/MS spectra. Only O₁ PC 36:4 [M+H]⁺ passes all filters. Rt, Retention time (in seconds). “NA” in the “MS/MS Filter” column indicates either no available MS/MS spectrum or no applicable fragmentation rules for the lipid class.

Formula_ID	m/z	Rt	Sum Formula	Name	Adduct	Monoisotopic Mass	Error/ppm	Base Peak	Isotope Filter	Bothmode Filter	Adduct Filter	Retention Filter	MS/MS Filter	All Filters
1403	772.5484	298.57	C42H78N1O9P1	O1 PC 34:3	[M+H]+	771.5414	0.14	False	True	False	False	True	True	False
5012	772.5484	298.57	C44H79N1O7	DGTS 34:3	[M+K]+	733.5857	0.29	False	True	False	False	True	NA	False
637	780.5546	298.56	C44H78N1O8P1	PC 36:5	[M+H]+	779.5465	-1.28	False	True	False	False	True	True	False
1414	798.5641	298.56	C44H80N1O9P1	O1 PC 36:4	[M+H]+	797.5571	0.11	True	True	True	True	True	True	True
5023	798.5641	298.56	C46H81N1O7	DGTS 36:4	[M+K]+	759.6013	0.26	True	False	False	False	True	NA	False
3828	820.5461	298.56	C44H80N1O9P1	O1 PC 36:4	[M+Na]+	797.5571	0.01	False	True	True	False	True	True	False
11190	902.5487	298.57	C46H84N1O11P1	O1 PS 40:3	[M+2Na-H]+	857.5782	0.27	False	NA	True	False	True	NA	False
11749	902.5487	298.57	C46H84N1O11P1	O3 PC 38:4	[M+2Na-H]+	857.5782	0.27	False	NA	True	False	True	NA	False