Table 2.

Selection criteria of data acquisition and post-processing techniques in TCM qualitative analysis.

Technique		Advantage	Limitation	Scope of application
DIA	DIA	Full coverage of MS1 and MS2 information	Loss link between precursor and product ions	Acquisition of MS/MS information of minor or trace compounds
DDA	PIL	Screening of only (or preferred) target ions in the list	Miss of novel compounds with new sub-structures or substituted groups	Target compounds with predictable molecular weights and/or m/z values
	DE	Detection of less abundant co-eluting ions	Quality loss of MS2 information of abundant ions	MS/MS information of both abundant and less abundant compounds in complex samples
	Mass tag	Selective screening of compounds that undergo in-source fragmentations	Not applicable to relatively stable compounds that cannot generate certain in-source fragmentation patterns	Compounds that can undergo certain in-source fragmentations with ISCID energy
	PIS	Requirements of little prior-knowledge about the exact structure of target compounds	Miss of compounds without selected product ions	Compounds with known specific product ions
	NLS	Targeted screening of modified or conjugated compounds that undergo neutral eliminations	Only compounds with certain neutral eliminations	Compounds with certain neutral eliminations
	MRM	High selectivity and sensitivity in screening target compounds	Low resolution and unable to screen unknown compounds without information of parent and product ions	Target compounds with known parent and product ions
Data post-processing	MDF	Selective screening of certain compounds or compound classes and remove of interferences	Requirements of a carefully-designed appropriate MDF region	Compounds with predictable mass range and mass defect range
	BS	Elimination of background signals, and exposure of target compounds	Poor selectivity of target compounds	Severe background interferences
	IPF	Specific screening of compounds with certain elements	Relatively narrow application scope	Compounds with distinct isotope pattern
	DIF	Rapid screening of target compounds that produce identical product ions	Miss of compounds without selected product ions	Compounds with known product ion
	NLF	Compounds that undergo neutral eliminations	Only compounds with certain neutral eliminations	Compounds with specific neutral loss
	MTSF	Rapid classification and characterization of unknown compounds	Need of MSn information for both template compounds and target compounds	Target compounds sharing the same sub-structures and similar MSn mass spectra as template compounds
	MN	Rapid classification and characterization of compounds without prior knowledge of the chemical structures	Manual interpretation of detailed structure information of unknown compounds based on the related known compounds	Compounds with MS/MS spectra
	SA	Rapid exploration of intrinsic relationships between compound structures and MS data	Further characterization and identification of compounds	Recognition of potential characteristic ions, discrimination of different structures and isomers
	DM	Alleviation of labor for mining structural information from large-scale datasets	Limited records in databases and requirements of further manual confirmation	Automatic search and annotation of compounds through on-line or in-house databases