Gas-phase purification for accurate isobaric tag-based quantification

Patent metadata

Field	Value
Publication number	US-10852306-B2
Application number	US-201715611232-A
Country	US
Kind code	B2
Filing date	Jun 1, 2017
Priority date	Apr 4, 2011
Publication date	Dec 1, 2020
Grant date	Dec 1, 2020

Abstract

Described herein are mass spectrometry systems and methods which improve the accuracy of isobaric tag-based quantification by alleviating the pervasive problem of precursor interference and co-isolation of impurities through gas-phase purification. During the gas-phase purification, the mass-to-charge ratios of precursor ions within at least a selected range are selectively changed allowing ions having similar unmodified mass-to-charge ratios to be separated before further isolation, fragmentation or analysis.

First claim

What is claimed is:

1. A mass spectrometer system for analyzing an isobarically labeled analyte, the system comprising:
an ion source for generating ions from the isobarically labeled analyte in a mixture with one or more molecules able to generate contaminant ions during mass spectrometry;
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 mixture during MS 1 stage ionization;
(b) identify a target range of mass-to-charge ratios of the first distribution of precursor ions, wherein said target range includes mass-to-charge ratios of precursor ions generated from the isobarically labeled analyte as well as contaminant ions;
(c) via the first separation optics, isolate precursor ions from the first distribution of precursor ions, where the isolated precursor ions have mass-to-charge ratios within the identified target range, wherein precursor ions outside of the identified target range are removed from communication with the ion reaction optics;
(d) reacting the isolated precursor ions within the identified target range to selectively change the mass-to-charge ratios of the isolated precursor ions by a known amount, thereby generating a distribution of mass-to-charge-manipulated precursor ions, wherein precursor ions outside of the identified target range are not reacted;
(e) identify a desired range of mass-to-charge ratios of the distribution of mass-to-charge-manipulated precursor ions, wherein the desired range includes mass-to-charge ratios of precursor ions generated from the isobarically labeled analyte and manipulated by a known amount as described in step (d), and wherein the desired range does not include mass-to-charge ratios of contaminant ions manipulated as described in step (d);
(f) via the second separation optics, separate mass-to-charge-manipulated precursor ions having a mass-to-charge ratio within the desired range from mass-to-charge-manipulated contaminant ions having a mass-to-charge ratio outside of the desired range, thereby generating isolated mass-to-charge-manipulated precursor ions having a mass-to-charge ratio within the desired range, wherein the mass-to-charge-manipulated contaminant ions are removed from communication with the ion fragmentation optics;
(g) fragment ions corresponding to the isolated mass-to-charge-manipulated precursor ions during MS 2 fragmentation, thereby generating first product ions, wherein the mass-to-charge-manipulated contaminant ions are not fragmented; and
(h) measure the mass-to-charge ratios of the first product ions, thereby generating first product ion mass spectrometry data.

2. The system of claim 1 , wherein the controller further controls the ion optics and detector so as to:
(i) generate a second distribution of precursor ions from the isobarically labeled analyte;
(j) identify a range of mass-to-charge ratios of the second distribution of precursor ions;
(k) fragment ions corresponding to the range of mass-to-charge ratios of the second distribution of precursor ions, thereby generating second product ions;
(l) measure the mass-to-charge ratios of the second product ions, thereby generating second product ion mass spectrometry data; and
(m) analyze the second product ion mass spectrometry data.

3. The system of claim 1 , wherein, to selectively change the mass-to-charge ratios of the isolated precursor ions, the controller further controls the ion optics and detectors to:
subject the first distribution of precursor ions to reaction with a predetermined species to selectively change the mass-to-charge ratios of precursor ions in the identified target range of mass-to-charge ratios, thereby generating the distribution of mass-to-charge-manipulated precursor ions, wherein the reaction with a species to selectively change the mass-to-charge ratios of the range of mass-to-charge ratios comprises a proton-transfer reaction.

4. The system of claim 1 , further comprising a second ion detector in communication with the first ion separation optics for detecting ions separated according to their mass-to-charge ratios and generating first precursor ion mass spectrometry data corresponding to the first distribution of precursor ions.

5. The system of claim 1 , wherein the controller controls the ion optics and detector so as to:
(j) fragment ions corresponding to the isolated mass-to-charge-manipulated precursor ions, thereby generating first product ions;
wherein the isolated mass-to-charge-manipulated precursor ions are fragmented by beam-type collisionally activated dissociation, ultraviolet photo-dissociation, infrared photodissociation, electron transfer dissociation, electron capture dissociation, surface induced dissociation, or resonant excitation collisionally activated dissociation.

6. The system of claim 1 , wherein the isobarically labeled analyte comprises proteins or peptides and the controller controls the ion optics and detectors to analyze the isobarically labeled analyte to quantify the amount of proteins or peptides in the analyte.

7. The method of claim 1 , wherein the identified target range of mass-to-charge ratios of the second distribution of precursor ions does not include ions having a mass-to-charge ratio less than 200 m/z units.

Assignees

• Wisconsin Alumni Res Found

Inventors

• Coon Joshua J
• Westphall Michael S

Classifications

• G01N33/6848 Primary

  Methods of protein analysis involving mass spectrometry · CPC title

• H01J49/0072

  by ion/ion reaction, e.g. electron transfer dissociation, proton transfer dissociation · CPC title

• G01N2458/00

  Labels used in chemical analysis of biological material · CPC title

• G01N33/483

  Physical analysis of biological material · CPC title

• Y10T436/24

  Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry · CPC title