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US 2008/0167197 A1Published application
Mass labels
AssigneeElectrophoretics Limited
InventorsGunter Schmidt, Andrew Hugin Thompson, Robert Alexander Walker Johnstone
Life of this patent
Estimating the term…
Abstract
Provided herein are sets of mass labels. Each mass label in a set includes: 1) a mass marker moiety; 2) a mass normalisation moiety; and 3) a cleavable linker connecting the mass marker moiety to the mass normalisation moiety. Each mass marker moiety is characterized as having a mass different from that of all other mass marker moieties in the set as determined by mass spectrometry. Further, each mass normalisation moiety ensures that each mass label in the set has substantially the same mass as determined by mass spectrometry.
Claims80
1-33. (canceled)
A method of analysis, which method comprises detecting an analyte by identifying by mass spectrometry a mass label or a combination of mass labels relatable to the analyte, wherein the mass label is selected from:
- (a) a mass label from a set of two or more mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, the mass marker moiety being fragmentation resistant, wherein each mass normalisation moiety ensures that each mass label in the set has the same aggregate mass as determined by mass spectrometry, and wherein each mass marker moiety has a mass different from that of all other mass marker moieties as determined by mass spectrometry, and wherein all the mass labels in the set are distinguishable from each other by mass spectrometry;
- or
- (b) a mass label from an array comprising two or more sets of mass labels as defined in (a), wherein the aggregate mass of each of the mass labels of any one set in the array is different from the aggregate mass of each of the mass labels of every other set in the array.
A method of two-dimensional mass spectrometric analysis, which method comprises:
- (a) providing one or more analytes, each analyte being labelled with a mass label or a combination of mass labels, wherein the mass labels are
- selected from:
- (i) mass labels from a set of two or more mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, the mass marker moiety being fragmentation resistant, wherein each mass normalisation moiety ensures that each mass label in the set has the same aggregate mass as determined by mass spectrometry, and wherein each mass marker moiety has a mass different from that of all other mass marker moieties as determined by mass spectrometry, and wherein all the mass labels in the set are distinguishable from each other by mass spectrometry;
- or
- (ii) mass labels from an array comprising two or more sets of mass labels as defined in (i), wherein the aggregate mass of each of the mass labels of any one set in the array is different from the aggregate mass of each of the mass labels of every other set in the array;
- (b) cleaving the mass labels from the analytes;
- (c) detecting the mass labels;
- (d) dissociating the mass labels in the mass spectrometer, to release the mass marker moieties from the mass normalisation moieties;
- (e) detecting the mass marker moieties;
- and
- (f) identifying the analytes on the basis of the mass spectrum of the mass labels and the mass spectrum of the mass marker moieties.
8 more elements
A method of analysis, which method comprises:
- (a) subjecting a mixture of labelled analytes to a first separation treatment on the basis of a first property of the analytes;
- (b) subjecting the resulting separated analytes to a second separation treatment on the basis of a second property of the analytes;
- and
- (c) detecting an analyte by detecting its label;
- wherein the analytes are labelled with a mass label from a set or an array of mass labels selected from:
- (i) mass labels from a set of two or more mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, the mass marker moiety being fragmentation resistant, wherein each mass normalisation moiety ensures that each mass label in the set has the same aggregate mass as determined by mass spectrometry, and wherein each mass marker moiety has a mass different from that of all other mass marker moieties as determined by mass spectrometry, and wherein all the mass labels in the set are distinguishable from each other by mass spectrometry;
- or
- (ii) mass labels from an array comprising two or more sets of mass labels as defined in (i), wherein the aggregate mass of each of the mass labels of any one set in the array is different from the aggregate mass of each of the mass labels of every other set in the array.
5 more elements
A method for characterising a nucleic acid, which comprises:
- (a) providing a population of nucleic acid fragments, each fragment having cleavably attached thereto a mass label selected from:
- (i) a mass label from a set of two or more mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, the mass marker moiety being fragmentation resistant, wherein each mass normalisation moiety ensures that each mass label in the set has the same aggregate mass as determined by mass spectrometry, and wherein each mass marker moiety has a mass different from that of all other mass marker moieties as determined by mass spectrometry, and wherein all the mass labels in the set are distinguishable from each other by mass spectrometry;
- or
- (ii) a mass label from an array comprising two or more sets of mass labels as defined in (i), wherein the aggregate mass of each of the mass labels of any one set in the array is different from the aggregate mass of each of the mass labels of every other set in the array;
- (b) separating the fragments on the basis of their length;
- (c) cleaving each fragment to release its mass label;
- and
- (d) determining each mass label by mass spectroscopy to relate the feature of each fragment to the length of the fragment.
5 more elements
A method for characterising nucleic acid, which method comprises generating Sanger ladder nucleic acid fragments from one or more nucleic acid templates, in the presence of at least one labelled terminating base, and identifying the length of the fragment, and the terminating base of the fragment, wherein the label is relatable to the terminating base and is a mass label selected from
- (a) a mass label from a set of two or more mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, the mass marker moiety being fragmentation resistant, wherein each mass normalisation moiety ensures that each mass label in the set has the same aggregate mass as determined by mass spectrometry, and wherein each mass marker moiety has a mass different from that of all other mass marker moieties as determined by mass spectrometry, and wherein all the mass labels in the set are distinguishable from each other by mass spectrometry;
- or
- (b) a mass label from an array comprising two or more sets of mass labels as defined in (a), wherein the aggregate mass of each of the mass labels of any one set in the array is different from the aggregate mass of each of the mass labels of every other set in the array.
(canceled)
A method for sequencing nucleic acid, which method comprises:
- (a) obtaining a target nucleic acid population comprising one or more single-stranded DNAs to be sequenced, each of which is present in a unique amount and bears a primer to provide a double-stranded portion of the nucleic acid for ligation thereto;
- (b) contacting the nucleic acid population with an array of hybridisation probes, each probe comprising a label cleavably attached to a known base sequence of predetermined length, the array containing all possible base sequences of that predetermined length and the base sequences being incapable of ligation to each other, wherein the contacting is carried out in the presence of ligase under conditions to ligate to the double-stranded portion of each nucleic acid the probe bearing the base sequence complementary to the single-stranded nucleic acid adjacent the double-stranded portion thereby to form an extended double-stranded portion which is incapable of ligation to further probes;
- and
- (c) removing all unligated probes;
- followed by the steps of:
- (d) cleaving the ligated probes to release each label;
- (e) recording the quantity of each label by mass spectrometry;
- and
- (f) activating the extended double-stranded portion to enable ligation thereto;
- wherein
- (g) steps (b) to (f) are repeated in a cycle for a sufficient number of times to determine the sequence of the or each single-stranded nucleic acid by determining the sequence of release of each mass label, wherein the mass label is selected from:
- (i) a mass label from a set of two or more mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, the mass marker moiety being fragmentation resistant, wherein each mass normalisation moiety ensures that each mass label in the set has the same aggregate mass as determined by mass spectrometry, and wherein each mass marker moiety has a mass different from that of all other mass marker moieties as determined by mass spectrometry, and wherein all the mass labels in the set are distinguishable from each other by mass spectrometry;
- or
- (ii) a mass label from an array comprising two or more sets of mass labels as defined in (i), wherein the aggregate mass of each of the mass labels of any one set in the array is different from the aggregate mass of each of the mass labels of every other set in the array.
11 more elements
A method for characterising a sample comprising peptides, polypeptides and/or proteins, which method comprises:
- (a) providing a sample comprising peptides, polypeptides and/or proteins, each peptide, polypeptide and/or protein having cleavably attached thereto a mass label, or a combination of mass labels selected from:
- (i) mass labels from a set of two or more mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, the mass marker moiety being fragmentation resistant, wherein each mass normalisation moiety ensures that each mass label in the set has the same aggregate mass as determined by mass spectrometry, and wherein each mass marker moiety has a mass different from that of all other mass marker moieties as determined by mass spectrometry, and wherein all the mass labels in the set are distinguishable from each other by mass spectrometry;
- or
- (ii) mass labels from an array comprising two or more sets of mass labels as defined in (i), wherein the aggregate mass of each of the mass labels of any one set in the array is different from the aggregate mass of each of the mass labels of every other set in the array,
- wherein each peptide, polypeptide and/or protein is relatable to its label or combination of labels;
- (b) analysing the labelled peptides, polypeptides and/or proteins, by mass spectrometry to detect the labels.
3 more elements
Use of a mass label selected from:
- (a) a mass label from a set of two or more mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, the mass marker moiety being fragmentation resistant, wherein each mass normalisation moiety ensures that each mass label in the set has the same aggregate mass as determined by mass spectrometry, and wherein each mass marker moiety has a mass different from that of all other mass marker moieties as determined by mass spectrometry, and wherein all the mass labels in the set are distinguishable from each other by mass spectrometry;
- or
- (b) a mass label from an array comprising two or more sets of mass labels as defined in (a), wherein the aggregate mass of each of the mass labels of any one set in the array is different from the aggregate mass of each of the mass labels of every other set in the array,
- in a method of analysis by mass spectrometry.
1 more element
A set of two or more probes, each probe in the set being different and being attached to a unique mass label or a unique combination of mass labels selected from:
- (a) mass labels from a set of two or more mass labels, each mass label in the set comprising a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, the mass marker moiety being fragmentation resistant, wherein each mass normalisation moiety ensures that each mass label in the set has the same aggregate mass as determined by mass spectrometry, and wherein each mass marker moiety has a mass different from that of all other mass marker moieties as determined by mass spectrometry, and wherein all the mass labels in the set are distinguishable from each other by mass spectrometry;
- or
- (b) mass labels from an array comprising two or more sets of mass labels as defined in (a), wherein the aggregate mass of each of the mass labels of any one set in the array is different from the aggregate mass of each of the mass labels of every other set in the array.
An array of probes comprising two or more sets of probes, wherein each probe in any one set is attached to a unique mass label, or a unique combination of mass labels, from a set of mass labels wherein each mass label in the set comprises:
- a mass marker moiety attached via a cleavable linker to a mass normalisation moiety, the mass marker moiety being fragmentation resistant, wherein each mass normalisation moiety ensures that each mass label in the set has the same aggregate mass as determined by mass spectrometry, and wherein each mass marker moiety has a mass different from that of all other mass marker moieties as determined by mass spectrometry, and wherein all the mass labels in the set are distinguishable from each other by mass spectrometry,
- and wherein the probes in any one set are attached to mass labels from the same set of mass labels, and each set of probes is attached to mass labels from unique sets of mass labels from an array of mass labels comprising two or more sets of mass labels, wherein the aggregate mass of each of the mass labels of any one set in the array is different from the aggregate mass of each of the mass labels of every other set in the array.
Dependencies are inferred from the claim text.