 Extracted-ion chromatogram baseline

An extracted-ion chromatogram baseline is a model of the signal underlying a selected chromatographic peak in an extracted ion chromatogram. Subtracting it helps assign an extracted-ion chromatogram peak area to the feature of interest. The baseline need not be zero or constant, and it is not automatically the signal from a separate reagent blank.

Let $E_W(t)$ be the signal from an extracted ion mass window $W$ and let $b(t)$ be the baseline over $[t_1,t_2]$. The assigned extracted-ion chromatogram peak area isThe time-ordered mass selection follows the IUPAC extracted ion profile definition; the baseline is an additional integration-model choice.^[ref]

An original example takes $0\le t\le 4\min$ and a baseline rising linearly from 1 to 3 signal units. Its integrated area is $4(1+3)/2=8$ signal-unit minutes. If the recorded trace has total area 20, the corrected area is 12. Using a constant baseline 1 would subtract only 4 and assign area 16: a 33% overestimate relative to 12. No recorded ion signal changed; only its allocation between baseline and peak changed.

If a fitted baseline is $b(t)=a+kt$ over a duration $L$ starting at $t=0$, then the subtracted area is $B=aL+k{L}^2/2$. Chromatographic baseline-area uncertainty therefore includes the joint uncertainty of the fitted intercept and slope:This is a direct application of correlated-input uncertainty propagation.^[ref]

Candidate baseline regions should be inspected for neighboring peaks, broad tails and drifting background. Two overlapping compounds can generate one smooth trace; subtracting a convenient baseline cannot establish chemical specificity. Record the integration boundaries, baseline model and treatment of negative corrected values. Those choices are necessary to interpret or reproduce a reported extracted-ion chromatogram peak area.