# US 10,976,321 B2 · Mass spectrometric quantitation

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- Number: US 10,976,321 B2
- Document ID: US10976321B2
- Status: Granted
- Kind: B2
- Application number: 15/412,555
- Filed: 2017-01-23
- Published: 2017-05-25
- Granted: 2021-04-13
- Earliest claimed: 2007-03-12
- Assignees: Electrophoretics Limited
- Applicants: Electrophoretics Limited
- Inventors: Peter Schulz-Knappe; Ian Pike; Karsten Kuhn
- Web page: https://patentgrep.com/patent/US10976321B2

## CPC

- G01N 33/58: involving labelled substances (G01N33/53 takes precedence)
- G01N 1/28: Preparing specimens for investigation {including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q}(mounting specimens on microscopic slides G02B21/34; means for supporting the objects or the materials to be analysed in electron microscopes H01J37/20 {; laboratory gas handling apparatus B01L5/00})
- G01N 33/6848: {Methods of protein analysis involving mass spectrometry}
- G01N 33/6851: {Methods of protein analysis involving laser desorption ionisation mass spectrometry}
- G01N 33/96: involving blood or serum control standard
- H01J 49/0009: {Calibration of the apparatus}
- G01N 2001/2893: {Preparing calibration standards}
- G01N 2333/4703: Regulators; Modulating activity
- G01N 2333/765: Serum albumin, e.g. HSA
- G01N 2333/775: Apolipopeptides
- G01N 2458/15: Non-radioactive isotope labels, e.g. for detection by mass spectrometry
- G01N 2560/00: Chemical aspects of mass spectrometric analysis of biological material
- G01N 2570/00: Omics, e.g. proteomics, glycomics or lipidomics; Methods of analysis focusing on the entire complement of classes of biological molecules or subsets thereof, i.e. focusing on proteomes, glycomes or lipidomes
- Y10T 436/105831: Protein or peptide standard or control [e.g., hemoglobin, etc.]
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- H01J: ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS (spark-gaps H01T; electric arc lamps H05B31/00; particle accelerators H05H)
- Y10T: TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION

## Abstract

Provided is a method of assaying for an analyte, including combining a test sample having the analyte, with a calibration sample having at least two different aliquots of the analyte, each aliquot having a different known quantity of the analyte. The test sample and each aliquot are differentially labeled with one or more isobaric mass labels each with a mass spectrometrically distinct mass marker group, such that the test sample and each aliquot of the calibration sample can be distinguished by mass spectrometry. The method further includes determining by mass spectrometry the quantity of analyte in the test sample and in each aliquot, and calibrating the quantity of analyte in the test sample against known and determined quantities of analytes in the aliquots.

## Claims

### Claim 1

A method of assaying for an analyte, comprising:
a) covalently, labelling a test sample comprising the analyte with one or more isobaric mass labels to provide labeled test sample;
b) covalently labelling a calibration sample comprising at least two different aliquots of the analyte, each analyte aliquot having a different known quantity of the analyte, with two or more isobaric mass labels to provide labeled calibration sample; wherein the test sample and each analyte aliquot of the calibration sample are differentially labelled with one or more isobaric mass labels, each with a mass spectrometrically distinct mass marker group, such that the test sample and each analyte aliquot of the calibration sample can be distinguished by mass spectrometry;
c) combining the labeled test sample with the labeled calibration sample;
d) determining by mass spectrometry the quantity of the analyte in the test sample and the quantity of analyte in each analyte aliquot in the calibration sample, and calibrating the quantity of the analyte in the test sample against the known and determined quantities of the analytes in the aliquots in the calibration sample.

### Claim 2 (depends on 1)

The method according to claim 1, wherein the test sample comprises a plurality of different analytes and a calibration sample is provided for each different analyte, and wherein step (d) is repeated for each different analyte, wherein the plurality of analytes are peptide fragments of a protein or polypeptide which are produced by chemical or enzymatic processing of the protein or polypeptide prior to step (c), and/or wherein the at least two different aliquots of each calibration sample are selected such that each calibration sample provides a range of quantities of the analyte which are different to the range of quantities of analyte in a calibration sample for a different analyte; and
wherein the aliquots are taken from a sample which is a standardized form of the test sample.

### Claim 3 (depends on 1)

The method according to claim 1, wherein a plurality of test samples are assayed for an analyte, wherein each of the plurality of test samples is assayed for the same analyte, and/or wherein each of the test samples is differentially labelled with one or more of the isobaric mass labels and combined with the calibration sample in step (c), and the quantity of the analyte in each sample is determined simultaneously in step (d), or alternatively wherein each test sample is labelled with the same mass label, and steps (c) and (d) are repeated for each different sample, wherein the same calibration sample is used for each test sample to be assayed.

### Claim 4 (depends on 1)

The method according to claim 1, wherein the method comprises a further step of combining the differentially labelled aliquots to produce a calibration sample prior to step (c).

### Claim 5 (depends on 1)

The method according to claim 1, wherein step (d) comprises:
i) in a mass spectrometer selecting and fragmenting ions of a mass to charge ratio corresponding to the analyte labelled with the mass label, detecting and producing a mass spectrum of fragment ions, and/or identifying the fragment ions corresponding to the mass marker groups of the mass labels;
ii) determining the quantity of the analyte in each test sample on the basis of the quantity of their mass marker groups in a mass spectrum relative to the quantities of the mass marker groups from the aliquots of the calibration sample in the same mass spectrum.

### Claim 6 (depends on 1)

The method according to claim 1, wherein the quantity of an analyte in each aliquot in the calibration sample is a known absolute quantity, wherein the absolute quantity of an analyte in a test sample is determined in step (d).

### Claim 7 (depends on 1)

The method according to claim 1, wherein the quantity of analyte in each aliquot in the calibration sample is a known qualitative quantity, wherein the qualitative quantity is an expected range of quantities of analyte in a subject having a particular state, and/or wherein the calibrating step comprises calibrating the quantity of the analyte in the test sample against the known qualitative and determined quantities of the analytes in the aliquots of the calibration sample, wherein the percentage change in the amount of the analyte in the test sample is determined.

### Claim 8 (depends on 1)

The method according to claim 1, wherein the quantity of analyte in each different aliquot is selected to reflect the known or suspected variation in the quantity of the analyte in the test sample, preferably wherein aliquots are provided which comprise the analyte in quantities which correspond to the upper and lower limits, and optionally intermediate points within a range of the known or suspected quantities of the analyte found in test samples of healthy or diseased subjects.

### Claim 9 (depends on 1)

The method according to claim 1, wherein the different quantities of analyte present in the different aliquots correspond to the known or suspected quantity of analyte present in a test sample which has been incubated for different periods of time.

### Claim 10 (depends on 1)

The method according to claim 1, wherein the test sample and/or the aliquots of the calibration sample are from a plant or an animal, wherein the animal is a human.

### Claim 11 (depends on 1)

The method according to claim 1, wherein the calibration sample comprises an analyte in a quantity that indicates the efficacy and/or toxicity of a therapy, and/or wherein the test sample and/or the calibration sample comprises human or animal tissue, blood, plasma, serum, cerebrospinal fluid, synovial fluid, ocular fluid, urine, tears, tear duct exudates, lung aspirates, breast milk, nipple aspirate, semen, lavage fluid, cell extract, tissue culture extract, plant tissue, plant fluid, plant cell culture extract, a bacterial sample, a virus sample, fungus, fermentation broth, a foodstuff or a pharmaceutical composition, and/or wherein the analyte comprises a protein, a polypeptide, a peptide, an amino acid or a nucleic acid, a peptide-nucleic acid, a sugar, starch, a complex carbohydrate, a lipid, a polymer, or fragments thereof.

### Claim 12 (depends on 1)

The method according to claim 1, which further includes the step of separating the isobarically labelled analytes electrophoretically or chromatographically after step (c) but before step (d).

### Claim 13 (depends on 1)

The method according to claim 1, wherein the calibration sample comprises a further aliquot which comprises the analyte in a quantity which serves as a trigger during a mass spectrometric scan or during non-scanning tandem mass spectrometry to initiate a tandem mass spectrometry scan, wherein the analyte in the further aliquot is labelled with an isobaric mass label, or alternatively wherein the analyte in the further aliquot is labelled with a mass label which is chemically identical to but isotopically distinct and differing in mass from the isobaric mass labels of the other analytes in the calibration sample.

### Claim 14 (depends on 1)

The method according to claim 1, wherein the analyte in the sample is a protein, and the analyte in the calibration sample is a recombinant form of the protein in the sample.

### Claim 15 (depends on 1)

The method according to claim 1, wherein the mass label comprises the following structure:
X-L-M
wherein X is a mass marker moiety comprising the following group:
wherein the cyclic unit of the mass marker moiety is aromatic or aliphatic and comprises from 0-3 double bonds; each Z is independently N, N(R1), C(R1), CO, CO(R1), C(R1)2, O or S; X1 is N, C or C(R1); each R1 is independently H, a substituted or unsubstituted straight or branched C1-C6 alkyl group, a substituted or unsubstituted aliphatic cyclic group, a substituted or unsubstituted aromatic group or a substituted or unsubstituted heterocyclic group; and y is an integer from 0-10, L is a cleavable linker and M is a mass normalization moiety, wherein the cleavable linker attaching the mass marker moiety to the mass normalization moiety is a linker cleavable by Collision Induced Dissociation (CID), Electron Transfer Dissociation (ETD), Electron Capture Dissociation (ECD) or Surface Induced Dissociation (SID) using mass spectrometry.

### Claim 16 (depends on 4)

The method according to claim 4, wherein the labelling step comprises a step of reacting the analyte with a reactive mass label, wherein the reactive mass label comprises a mass label and a reactive functionality, wherein the reactive functionality is capable of reacting with any amino group on a polypeptide and comprises a nucleophile or an electrophile, and wherein the reactive functionality comprises the following group:
wherein each R2 is independently H, a substituted or unsubstituted straight or branched C1-C6 alkyl group, a substituted or unsubstituted aliphatic cyclic group, a substituted or unsubstituted aromatic group or a substituted or unsubstituted heterocyclic group.

### Claim 17 (depends on 15)

The method according to claim 15, wherein the mass label is a mass label from a set of two or more mass labels, wherein each mass normalization moiety ensures that a mass label has a desired aggregate mass, and wherein the set comprises:
mass labels having a mass marker moiety, each mass marker moiety having a mass different from that of all other mass marker moieties in the set, and each label in the set having a common aggregate mass,
and wherein all the mass labels in the set are distinguishable from each other by mass spectroscopy,
and wherein each mass label in the set has a mass adjuster moiety, selected from:
(a) an isotopic substituent situated within the mass marker moiety and/or within the mass normalization moiety, and
(b) substituent atoms or groups attached to the mass marker moiety and/or attached to the mass normalization moiety,
and/or wherein the mass adjuster moiety is selected from a halogen atom substituent, a methyl group substituent, and 2H, 15N, 13C, or 18O isotopic substituents.

### Claim 18 (depends on 17)

The method according to claim 17, wherein the mass adjuster moiety is 15N or 13C and the set comprises two mass labels having the following structures:
or five mass labels having the following structures:

### Claim 19 (depends on 17)

The method according to claim 17, wherein the mass adjuster moiety is 15N and 13C and the set comprises six mass labels having the following structures or stereoisomers of the following structures: