Mass spectrometry for determining if a mutated variant of a target protein is present in a sample

Patent metadata

Field	Value
Publication number	US-11402385-B2
Application number	US-201515516083-A
Country	US
Kind code	B2
Filing date	Oct 1, 2015
Priority date	Oct 1, 2014
Publication date	Aug 2, 2022
Grant date	Aug 2, 2022

Abstract

A method of mass spectrometry determines if a mutated variant of a target protein is present in a sample. The method includes subjecting the sample to fragmentation so as to cause the target protein to fragment to form second generation fragment ions, and then mass analysing these fragment ions to obtain spectral data. The method determines if a mutated variant is present in the sample by determining that an ion in the spectral data has a mass to charge ratio that differs from the mass to charge ratio of an ion that would be observed if the target protein was a normal unmutated version of the target protein, and by an amount that corresponds to a mass difference that would be caused by the target protein being a mutated variant of the target protein.

First claim

The invention claimed is:

1. A method of mass spectrometry comprising:
introducing a blood sample into a mass spectrometer system without subjecting said blood sample to liquid chromatography or digestion;
using Atmospheric Pressure Electron Capture Dissociation (“Ap-ECD”) or Atmospheric Pressure Electron Transfer Dissociation (“Ap-ETD”) to subject said blood sample to fragmentation so as to cause haemoglobin proteins to dissociate to form first protein fragment ions; and
fragmenting at least some of said first protein fragment ions to form second fragment ions, wherein the step of fragmenting at least some of said first protein fragment ions comprises isolating a c8 fragment ion derived from a haemoglobin beta chain and then fragmenting the isolated c8 fragment ion so as to form the second fragment ions, wherein the isolated c8 fragment ion is fragmented using Collision Induced Dissociation (“CID”).

2. The method of claim 1 , wherein the step of using Ap-ECD or Ap-ETD to subject said blood sample to fragmentation comprises using said Ap-ECD or Ap-ETD to subject said blood sample to in-source fragmentation so as to cause the haemoglobin proteins to fragment to form the first protein fragment ions.

3. The method of claim 2 , further comprising using said first protein fragment ions and/or said second fragment ions to identify the location of haemoglobin sequence mutations.

4. The method of claim 1 , comprising
mass analysing said first protein fragment ions to obtain first spectral data; and
determining whether or not ions in the first spectral data are at mass-to-charge ratios corresponding to the mass-to-charge ratios at which ions would be detected if the haemoglobin proteins are normal, unmutated haemoglobin; and
optionally, further comprising providing an indication that the haemoglobin proteins are normal unmutated haemoglobin if the ions in the first spectral data are at mass-to-charge ratios corresponding to the mass-to-charge ratios at which ions would be detected if the haemoglobin proteins are normal unmutated haemoglobin.

5. The method of claim 1 , comprising
mass analysing said first protein fragment ions to obtain first spectral data; and
determining from the first spectral data if an ion is present at a mass-to-charge ratio corresponding to the mass-to-charge ratio at which an ion would be detected if the haemoglobin proteins are a mutated non-normal variant; and
optionally, further comprising providing an indication that the haemoglobin proteins are a mutated variant of haemoglobin.

6. The method of claim 1 , further comprising using said first protein fragment ions and/or said second fragment ions to identify the location of haemoglobin sequence mutations.

7. The method of claim 6 , comprising
mass analysing the second fragment ions to obtain second spectral data; and
determining from the second spectral data if an ion is present at a mass-to-charge ratio corresponding to the mass-to-charge ratio at which an ion would be detected if the haemoglobin proteins are a non-normal mutated variant.

8. The method of claim 7 , comprising determining that an ion in the second spectral data has a mass-to-charge ratio that differs from the mass-to-charge ratio of an ion that would be observed if normal unmutated haemoglobin had been analysed, and that differs by an amount that corresponds to a mass difference caused by the haemoglobin proteins being a non-normal variant or caused by a mutation/substitution of an amino acid of normal haemoglobin for another amino acid.

9. The method of claim 8 , wherein the mass difference is 30 Da; and/or wherein the mass difference corresponds to a mutation of glutamic acid to valine.

10. A method of mass spectrometry for determining if a mutated variant of a target protein is present in a sample, comprising:
introducing the sample comprising a target protein into a mass spectrometer, wherein the sample is not subjected to liquid chromatography or digestion prior to being introduced into the mass spectrometer;
subjecting the sample to fragmentation so as to cause said target protein to dissociate to form first protein fragment ions, wherein said fragmentation is Atmospheric Pressure Electron Capture Dissociation (“Ap-ECD”) or Atmospheric Pressure Electron Transfer Dissociation (“Ap-ETD”), and wherein said first protein fragment ions comprise c-type fragment ions formed by said Ap-ECD or Ap-ETD;
fragmenting at least some of said first protein fragment ions to form second fragment ions, wherein the step of fragmenting at least some of said first protein fragment ions comprises:
isolating one of said c-type fragment ions from other fragment ions and then fragmenting the isolated c-type fragment ion so as to form the second fragment ions, wherein the isolated c-type fragment ion is fragmented using Collision Induced Dissociation (“CID”), and wherein the isolated c-type fragment ion is a c8 fragment ion derived from a haemoglobin beta chain;

the method further comprising: mass analysing said second fragment ions to obtain first spectral data; and determining if an ion in the first spectral data has a first mass-to-charge ratio that differs from a second mass-to-charge ratio by an amount that corresponds to a mass difference that would be caused by the target protein being a mutated variant of said target protein, wherein the second mass-to-charge ratio is the mass-to-charge ratio of an ion that would be observed if said target protein is a normal unmutated version of said target protein.

11. The method of claim 10 , wherein:
said sample is, or comprises: blood; whole-blood; diluted blood; or diluted whole blood; and/or
wherein the target protein is subjected to ionisation prior to said step of subjecting the sample to fragmentation such that target protein ions are fragmented to form the first protein fragment ions and optionally wherein the target protein is ionised in an ion source to form the target protein ions.

12. The method of claim 10 , further comprising, when it is determined that an ion in the first spectral data has said first mass-to-charge ratio:
using the first mass-to-charge ratio of said ion in the first spectral data to identify a location of a mutation within a protein sequence of the target protein and identifying a type of variant of the target protein in the sample from the identified location; or
using the value of said mass difference to identify a type of mutation in a sequence of the target protein and identifying a type of variant of the target protein in the sample from the identified type of mutation.

13. The method of claim 10 , wherein the target protein is mass analysed in a precursor ion mode without first being fragmented; wherein when it is determined that an ion in the first mass spectral data has said first mass-to-charge ratio:
a related precursor ion detected in said precursor ion mode is considered and/or indicated as being a mutated precursor ion from a mutated variant of the target protein; and the method further comprises:
determining whether or not precursor ions detected in said precursor ion mode contain a precursor ion corresponding to a non-mutated version of the related precursor ion; and
when it is determined that the precursor ions contain both said mutated precursor ion and said non-mutated version of the related precursor ion, determining that a mutated variant of the target protein is a heterozygous variant of the target protein; and
when it is determined that the precursor ions contain said mutated precursor ion and not said non-mutated version of the related precursor ion, determining that a mutated variant of the target protein is a homozygous va

Assignees

• Micromass Ltd

Inventors

• Brown Jeffery Mark
• Morris Michael Raymond
• Williams Jonathan
• Green Brian

Classifications

• H01J49/0054

  by an electron beam, e.g. electron impact dissociation, electron capture dissociation · CPC title

• G01N33/6848 Primary

  Methods of protein analysis involving mass spectrometry · CPC title

• G01N33/6818

  Sequencing of polypeptides · CPC title

• H01J49/0072

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

• G01N33/68

  involving proteins, peptides or amino acids {(involving lipoproteins G01N33/92)} · CPC title