Table 8 Useful information for filtering of candidates in NTS

Accurate mass

Set window as small as possible (< 5 ppm or < 2 mDa) based on added standards;

Check for adducts, ion-source fragments to avoid incorrect assignment of molecular ions

Very high

Higher resolution of Orbitrap helps differentiation of compounds with small mass differences

Isotope pattern

¹²C/¹³C, ³⁵Cl/³⁷Cl, ⁷⁹Br/⁸¹Br most relevant; isotopic fine structure (¹⁴N/¹⁵N, ³²S/³⁴S differentiation) only for very high-resolution measurements

Less reliable at trace levels or if the intensities of isotopes fall below limit of detection (LOD)

High

QTOF is generally more accurate than Orbitrap for ion ratios but Orbitrap resolves fine structure. In DIA or DDA with isolation window > 1 Da, isotope patterns are in MS2

Characteristic fragments

e.g., C₂F₅⁻, C₃F₇⁻ for PFAS; SO₃⁻ for sulfonated surfactants

Larger fragments provide more information

Very high

DDA is more specific, DIA offers more coverage. Intense peaks often exhibit more fragments with consistent ratios between them

Retention time

Accepted deviation depending on the prediction system, to be checked with standards

High

Not yet accurate enough to select candidates in isolation

Collision cross section (CCS)

< 2% deviation from predicted CCS values

High

Cleaner spectra with ion mobility but often intensity loss

Homologous series

Detection of specific mass increase (e.g., CH₂) and RT increase

Medium

Very useful for specific substance classes, such as PFAS and surfactants

Mass defect

O, F, P, S, Cl, Br have a negative mass defect and substances with these elements have a lower mass defect than CH substances

Medium

Very useful for specific substance classes, such as halogenated compounds (e.g., PFAS)

Library match

See Sect. “Spectral library search” for details. The use of merged spectra (different collision energies) can increase inter-instrument comparability

Very high

RT/RI/RTI needed to separate highly similar spectra of isomers