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The favored mass window is still open.
Even when the mass window is set to 2 mDa these peaks are present and only when a mass window of 1 mDa is used do these peaks disappear.
When the mass window is increased from 0.05 to 1 Da (sets 7, 9, 10), the number of detected markers is decreased, but more importantly, many more false positives are included in sets 9 and 10.
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The relative precursor mass window was set to 200 (full width half mass).
The precursor mass window was 300 ppm (full width at half-maximum) in relative mode.
For the used LTQ Orbitrap XL instrument, this mass window was set to ±10 ppm.
The collision gas was atmospheric and the precursor mass window was ±5 Da.
Settings for cluster formation were first pass S/N 5 in 20% of all spectra and second pass S/N 2. Cluster mass window was 0.3% of the mass.
We note, however, that the experimental product ions were generated by enabling the database search with a fragment ion tolerance of 1 amu, thus contaminant product ions within this mass window are possible.
The extraction, alignment, deconvolution, and further processing of raw GC/MS data were referred to the protocols of literature [ 47- 49], except the mass window was set to 70 600 m/z.
The selected mass extraction window was < 5 ppm, since mass deviation was < 1.5 ppm for β-carotene.
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