Gas-Phase Purification for Accurate Isobaric Tag-Based Quantification

A mass spectrometer system for analyzing an isobarically labeled analyte, the system comprising:

• an ion source for generating ions from the isobarically labeled analyte;
• first ion separation optics in communication with the ion source for separating ions according to their mass-to-charge ratios;
• ion reaction optics in communication with the first ion separation optics for generating mass-to-charge-manipulated ions;
• ion fragmentation optics in communication with the first ion separation optics for generating product ions;
• second ion separation optics in communication with the ion fragmentation optics for separating ions according to their mass-to-charge ratios;
• a first ion detector in communication with the second ion separation optics for detecting ions separated according to their mass-to-charge ratios;
• a controller operably connected to the first and second ion separation optics, the ion reaction optics, the first ion detector, and the ion fragmentation optics;
• wherein the controller controls the ion optics and detector so as to:
• (a) generate a first distribution of precursor ions from the isobarically labeled analyte;
• (b) identify a range of mass-to-charge ratios of the first distribution of precursor ions;
• (c) selectively change the mass-to-charge ratios of precursor ions in the identified range of mass-to-charge ratios, thereby generating a distribution of mass-to-charge-manipulated precursor ions;
• (d) isolate a range of mass-to-charge ratios of the distribution of mass-to-charge-manipulated precursor ions, thereby generating isolated mass-to-charge-manipulated precursor ions;
• (e) fragment ions corresponding to the isolated mass-to-charge-manipulated precursor ions, thereby generating first product ions;
• (f) measure the mass-to-charge ratios of the first product ions, thereby generating first product ion mass spectrometry data;
• and
• (g) analyze the first product ion mass spectrometry data.