Chemstation 101 – Dealing with Mass Defect in Low Resolution Scan Mode

While working on optimizing a rapid semivolatiles screening application meant for very low levels (0.1 – 6 ng on column), we noticed that the heavily chlorinated compounds had poorly defined peaks in the Qedit window, but appeared to have good responses when viewing the total ion chromatogram (TIC). Using pentachlorophenol (PCP) as an example, when the target ions are viewed, the quant ion (m/z = 266, bold black trace) drops to baseline before the qualifier ions (m/z = 264, 268). Our first thought was that the mass assignment had drifted and the instrument was out of tune.

pentachlorophenol quant ions.pptx

Pentachlorophenol quantification (black) and qualifier ion chromatogram

However, we were able to verify the instrument’s mass calibration by generating a detailed profile scan in tune and vacuum control. Next, we looked at the assigned mass value of the PCP molecular ions relative to the expected values and found that the assigned masses for the PCP isotopes were falling outside of the defined mass peak window in the quantitation method, causing a large portion of the response to be missed during data analysis.


Pentachlorophenol theoretical molecular ion mass vs. actual spectral data

ChemStation E.02.02 has a default mass peak window of -0.30 amu to +0.70 amu while PCP has a negative mass defect (0.15 amu less than the nominal mass value for each of the three primary molecular ions); when combined with the 5975’s seeming propensity to exaggerate negative mass defects, our target ions are falling on the edge (or outside of) the default peak width, which is biased towards a positive mass defect.

The easy solution is to center the mass peak window (±0.5 amu), but this isn’t really representative of the calibrated mass peak window, which is normally between 0.5 and 0.6 amu. A better solution, though it involves a bit more work, is to use an appropriately representative mass peak window (±0.3 amu in this case) and update your heavily halogenated target ions with their actual mass. Following this data processing correction, PCP showed excellent calibration linearity down to 0.1 ng on column, as shown below (though 2 of 3 injections failed to meet minimum relative response factor criteria (0.050 relative to phenanthrene-d10) at 0.1 ng on column).

corrected pentachlorophenol target ions and mass window

Pentachlorophenol quantification and qualifier ion chromatogram with corrected integration and mass peak width parameters

pentachlorophenol calibration

Pentachlorophenol calibration curve (0.1 to 6.0 ng on column)

I went ahead and calculated some of the theoretical masses for the other heavily halogenated compounds in 8270D. Each of the compounds listed below should link to a slide similar to the pentachlorophenol slide above.

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