Ion Mobility Mass Spectrometry
of Peptide Ions: Effects of Drift Gas and Calibration Strategies
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Abstract
One difficulty in using ion mobility (IM) mass spectrometry
(MS) to improve the specificity of peptide ion assignments is that
IM separations are performed using a range of pressures, gas compositions,
temperatures, and modes of separation, which makes it challenging
to rapidly extract accurate shape parameters. We report collision
cross section values (Ω) in both He and N<sub>2</sub> gases
for 113 peptide ions determined directly from drift times measured
in a low-pressure, ambient temperature drift cell with radio-frequency
(rf) ion confinement. These peptide ions have masses ranging from
231 to 2969 Da, Ω<sub>He</sub> of 89–616 Å<sup>2</sup>, and Ω<sub>N<sub>2</sub></sub> of 151–801 Å<sup>2</sup>; thus, they are ideal for calibrating results from proteomics
experiments. These results were used to quantify the errors associated
with traveling-wave Ω measurements of peptide ions and the errors
concomitant with using drift times measured in N<sub>2</sub> gas to
estimate Ω<sub>He</sub>. More broadly, these results enable
the rapid and accurate determination of calibrated Ω for peptide
ions, which could be used as an additional parameter to increase the
specificity of assignments in proteomics experiments
