WO1996036986B1 - Methods and apparatus for sequencing polymers with a statistical certainty using mass spectrometry - Google Patents

Methods and apparatus for sequencing polymers with a statistical certainty using mass spectrometry

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Publication number
WO1996036986B1
WO1996036986B1 PCT/US1996/007146 US9607146W WO9636986B1 WO 1996036986 B1 WO1996036986 B1 WO 1996036986B1 US 9607146 W US9607146 W US 9607146W WO 9636986 B1 WO9636986 B1 WO 9636986B1
Authority
WO
WIPO (PCT)
Prior art keywords
polymer
fragments
mass
charge ratio
exonuclease
Prior art date
Application number
PCT/US1996/007146
Other languages
French (fr)
Other versions
WO1996036986A1 (en
Filing date
Publication date
Priority claimed from US08/447,175 external-priority patent/US5869240A/en
Application filed filed Critical
Priority to JP08535084A priority Critical patent/JP2001500606A/en
Priority to EP96916490A priority patent/EP0827628A1/en
Publication of WO1996036986A1 publication Critical patent/WO1996036986A1/en
Publication of WO1996036986B1 publication Critical patent/WO1996036986B1/en

Links

Abstract

The method and apparatus disclosed herein are useful for sequencing polymers using mass spectrometry. The methods involve differing ratios of hydrolyzing agent to polymer disposed upon a reaction surface adapted for use with a mass spectrometer. The methods further involve integrating data obtained from mass spectrometry analysis of a plurality of series of hydrolyzed polymer fragments, and provide statistical interpretation paradigms and computer software therefor. The apparatus involves a mass spectrometer sample holder, having hydrolyzing agent disposed thereon, which is useful for adapting any mass spectrometer for polymer sequencing.

Claims

6 7
AMENDED CLAIMS
[received by the International Bureau on 3 December 1996 (03.12.96); original claims 1, 3-7, 18, 19, 43, 45, 46 and 61 amended; new claims 108 and 109 added; remaining claims unchanged (14 pages)]
1. A method of obtaining sequence information about a polymer comprising a plurality of monomers of known mass, said method comprising the steps of:
a) providing a set of polymer fragments, each differing by one or more monomers;
b) measuring a difference x between the mass-to-charge ratio of at least one pair of fragments;
c) asserting a mean difference μ between the mass-to-charge ratio of the pair of fragments measured in step b, wherein μ corresponds to a known mass-to-charge ratio of one or more differing monomers;
d) selecting a desired confidence level for μ;
e) analyzing x to determine if it is statistically different from μ at the selected confidence level; and
f) determining if the asserted mean μ is assignable to the mass difference x with the selected confidence level based upon the analysis in step e).
2. The method of claim 1 wherein a statistical difference determined in the analysis of step e) indicates that the asserted mean μ is not assignable to the mass difference x with the selected confidence level.
3. The method of claim 1 comprising repeating steps c) through f) for a plurality of desired values of μs. 6 8
4. The method of claim 1 wherein the analysis of step e) comprises a two-tailed t-test for an experimental mean.
5. The method of claim 1 wherein the analyzing in step e) comprises:
g) repeating step b) a number of times, n, to determine a measured mean mass-to-charge ratio difference x between at least one pair of fragments;
h) determining a standard deviation s ofthe mean mass-to-charge ratio difference x determined in step g);
i) comparing x to the asserted mean difference μ;
j) repeating steps c) through i) for a plurality of desired values of μs.
6 9
6. The method of claim 5 comprising repeating steps b) through j) for additional pairs of fragments.
7. The method of claim 5 wherein the comparing in step i) comprises taking the absolute value ofthe asserted mean difference.
8. The method of claim 5 further comprising the step of determining the number of measurements, n, based upon the analysis in step e).
9. The method of claim 1 wherein the polymer is a biopolymer.
10. The method of claim 9 wherein the biopolymer is selected from the group consisting of DNAs, RNAs, PNAs, proteins, peptides, carbohydrates and modified forms thereof.
11. The method of 1 further comprising the step of hydrolyzing the polymer to obtain the polymer fragments in step a).
12. The method of claim 1 further comprising hydrolyzing, on a reaction surface, the polymer with a hydrolyzing agent.
13. The method of claim 12 wherein the polymer is hydrolyzed on a reaction surface, said surface providing differing amounts of a hydrolyzing agent which hydrolyzes said polymer thereby to break inter-monomer bonds.
14. The method of claim 11, 12 or 13 wherein the hydrolyzing agent is an exohydrolase or an endohydrolase.
15. The method of claim 14 wherein hydrolyzing with said exohydrolase produces a series of fragments comprising a sequence-defining ladder of said polymer.
16. The method of claim 15 wherein the exohydrolase is selected from the group consisting of: exonucleases, exoglycosidases, and exopeptidases. 7 0
17. The method of claim 16 wherein the exopeptidase is selected from the group consisting of carboxypeptidase Y, carboxypeptidase A, carboxypeptidase B, carboxypeptidase P, aminopeptidase 1, leucine aminopeptidase, proline aminodipeptidase and cathepsin C.
7 ]
18. The method of claim 16 wherein the exoglycosidase is selected from the group consisting of
a) α - ■ Mannosidase I b) α - - Mannosidase c) β - ■ Hexosaminodase d) β - ■ Galactosidase e) α - - Fucosidase I and II f) α - - Galactosidase g) α - - Neuraminidase and h) a - - Glucosidase I and II
19. The method of claim 16 wherein the exonuclease is selected from the group consisting of
a) λ- exonuclease b) t7 Gene 1 exonuclease c) exonuclease III d) Exonuclease I e) Exonuclease V f) Exonuclease II and g) DNA Polymerase II.
20. The method of claim 14 wherein hydrolyzing with said endohydrolase produces a series of fragments defining a map of said polymer.
21. The method of claim 20 wherein said endohydrolase is an endopeptidase selected from the group consisting of: trypsin, chymotrypsin, endo-proteinase Lys-C, endoproteinase Arg-C and thermolysin. 7
22. The method of claim 12 wherein the agent is a hydrolyzing agent other than an enzyme.
23. The method of claim 12 wherein said agent capable of hydrolyzing said polymer comprises a combination of at least one enzyme and at least one agent other than an enzyme.
24. The method of claim 13 wherein the reaction surface comprises an array of discrete separable zones, each zone comprising a differing amount of said hydrolyzing agent.
38. The method of claim 12 wherein hydrolysis is accomplished by immobilizing said agent on said reaction surface.
39. The method of claim 12 wherein hydrolysis is accomplished using a hydrolyzing agent in liquid or gel form, said liquid or gel form being resistant to physical dislocation.
40. The method of claim 1 comprising the additional step of combining a light- absorbent matrix with said fragments prior to step b).
41. The method of claim 1 comprising the additional step of combining said polymer fragments with moieties for selectively shifting the mass of hydrolyzed sequences prior to step b).
42. The method of claim 1 comprising the additional step of combining said polymer fragments with moieties for improving ionization prior to step b).
43. A method for obtaining sequence information about a polymer comprising a series of different monomers of known mass, said method comprising the steps of:
a) providing a set of polymer fragments, each differing by one or more monomers;
b) measuring the mass-to-charge ratio difference x between a pair of fragments;
c) asserting a mean difference μ, which is related to a known mass-to-charge ratio of one or more monomers;
d) selecting a desired confidence level for μ; 7 4
e) repeating step b) to obtain a number of measurements n, thereby to determine the measured mean mass-to-charge ratio difference JC between the pair of fragments;
f) determining the standard deviation s ofthe measured mean mass-to-charge ratio difference x determined in st~p e;
g) calculating a test statistic tcaicuiated with the following algorithm:
x — μ n calculated — '
h) comparing the test statistic tcaicuiated calculated in step g to a t-distribution corresponding to the number of measurements and the desired confidence level; and
i) determining if the asserted mean μ is assignable to the mass difference x with the selected confidence level based upon the comparison in step h.
7 5
44. The method of claim 43 further comprising a comparison ofthe calculated test statistic tcaicuiated in step g) to a t-distribution corresponding to the number of measurements and the desired confidence level.
45. The method of claim 43 further comprising repeating steps b) - i) for additional pairs of fragments thereby to obtain sequence information.
46. The method of claim 43 further comprising the step of determining the number of measurements, n, based upon the comparison in step h).
47. The method of claim 43 wherein the polymer is a biopolymer.
48. The method of claim 47 wherein the biopolymer is selected from the group consisting of DNAs, RNAs, PNAs, proteins, peptides, carbohydrates and modified forms thereof.
49. The method of claim 43 further comprising the step of hydrolyzing the polymer with a hydrolyzing agent to create the fragments in step a).
50. The method of claim 49 wherein the hydrolyzing agent is an exohydrolase which produces a series of fragments comprising a sequence-defining ladder of said polymer.
51. The method of claim 50 wherein the exohydrolase is selected from the group consisting of: exonucleases, exoglycosidases, exopeptidases.
52. The method of claim 51 wherein the exopeptidase is selected from the group consisting of carboxypeptidase Y, carboxypeptidase A, carboxypeptidase B, carboxypeptidase P, aminopeptidase 1, leucine aminopeptidase, proline aminodipeptidase and cathepsin C. 7 6
53. The method of claim 51 wherein the exoglycosidase is selected from the group consisting of
a) α - Mannosidase I b) α - Mannosidase c) β - Hexosaminidase d) β - Galactosidase e) α - Fucosidase I and II f) α - Galactosidase
7 7
g) α - Neuraminidase and h) α - Glucosidase I and II.
54. The method of claim 51 wherein the exonuclease is selected from the group consisting of
a) Exonuclease b) λ- exonuclease c) t7 Gene 1 exonuclease d) exonuclease III e) Exonuclease I f) Exonuclease V g) Exonuclease II h) DNA Polymerase II.
55. The method of claim 49 wherein the hydrolyzing agent is other than an enzyme.
56. The method of claim 49 wherein the agent comprises a combination of at least one enzyme and at least one agent other than an enzyme.
57. The method of claim 49 wherein hydrolysis is performed on a reaction surface, said surface providing differing amounts of a hydrolyzing agent.
58. The method of claim 57 wherein the reaction surface comprises an array of discrete separable zones, each zone comprising a differing amount of said hydrolyzing agent.
59. The method of claim 49 wherein the reaction surface comprises a continuous concentration gradient ofa hydrolyzing agent.
60. The method of claim 43 further comprising adding a matrix to the polymer fragments before measuring the mass-to-charge ratio in step b). 7 8
61. A method for obtaining sequence information about a polymer having a plurality of monomers of known mass, said method comprising: a) providing a set of polymer fragments, each differing by one or more monomers; b) measuring a difference x between the mass-to-charge ratio ofa pair of fragments; c) asserting a mean difference μ between the mass-to-charge ratio ofthe pair of fragments measured in step b, wherein μ corresponds to a known mass- to-charge ratio of one or more monomers; d) selecting the desired confidence level for μ; e) analyzing x to determine if it is statistically different from μ at the selected confidence level; f) repeating steps b)-e) a number of times n, until a plurality of desired values of μs have been asserted; g) determining if the asserted mean μ is assignable to the mass difference x with the selected confidence level based upon the analysis in step e; and h) repeating steps b) -g) for additional pairs of fragments.
62. The method of claim 61 wherein the polymer is a biopolymer.
63. The method of claim 62 wherein the biopolymer is selected from the group consisting of DNAs, RNAs, PNAs, proteins, peptides, carbohydrates and modified forms thereof.
64. The method of claim 61 wherein the polymer fragments in step a) are created by concentration dependent hydrolysis ofthe polymer.
65. The method of claim 61 further comprising the step of hydrolyzing said polymer with a hydrolyzing agent to produce the polymer fragments in step a). 7 9
66. The method of claim 65 wherein the hydrolyzing agent is an exohydrolase.
67. The method of claim 66 wherein the hydrolysis caused by said exohydrolase produces a series of fragments defining a ladder of said polymer.
68. The method of claim 66 wherein the exohydrolase is selected from the group consisting of: exonucleases, exoglycosidases, and exopeptidases.
69. The method of claim 68 wherein the exoglycosidase is selected from the group consisting of
a) α - Mannosidase I b) α - Mannosidase c) β - Hexosaminidase d) β - Galactosidase e) α - Fucosidase I and II f) α - Galactosidase g) α - Neuraminidase and h) α - Glucosidase I and II.
8 0
107. The sample plate of any one of claims 78, 85, 99, 100 or 101 wherein said plate is disposable.
108. A method of obtaining information about the identity of a polymer comprising a plurality of monomers of known mass, said method comprising the steps of: a) providing a set of polymer fragments created by the endohydrolysis of said polymer; b) measuring the mass-to-charge ratio of a fragment; c) asserting a hypothetical identity for the fragment, wherein the hypothetical identity corresponds to a known identity of a fragment ofa reference polymer, said fragment having a known mass-to-charge ratio; d) selecting a desired confidence level for the hypothetical identity; and e) determining whether the measured mass-to-charge ratio is statistically different from the mass-to-charge ratio ofthe asserted hypothetical fragment; f) determimng if the asserted hypothetical identity is assignable to the measured mass-to-charge ratio ofthe fragment with the selected confidence level based upon the determination in step e; and g) repeating steps b)- e).
109. The method of claim 108 wherein the hypothetical identity in step c) corresponds to a known identity derived from a computer database of known sequences.
PCT/US1996/007146 1995-05-19 1996-05-17 Methods and apparatus for sequencing polymers with a statistical certainty using mass spectrometry WO1996036986A1 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
JP08535084A JP2001500606A (en) 1995-05-19 1996-05-17 Method and apparatus for statistically certain polymer sequencing using mass spectrometry
EP96916490A EP0827628A1 (en) 1995-05-19 1996-05-17 Methods and apparatus for sequencing polymers with a statistical certainty using mass spectrometry

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US44605595A 1995-05-19 1995-05-19
US08/447,175 1995-05-19
US08/447,175 US5869240A (en) 1995-05-19 1995-05-19 Methods and apparatus for sequencing polymers with a statistical certainty using mass spectrometry
US08/446,055 1995-05-19

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WO1996036986A1 WO1996036986A1 (en) 1996-11-21
WO1996036986B1 true WO1996036986B1 (en) 1997-01-09

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US5605798A (en) 1993-01-07 1997-02-25 Sequenom, Inc. DNA diagnostic based on mass spectrometry
US6146854A (en) * 1995-08-31 2000-11-14 Sequenom, Inc. Filtration processes, kits and devices for isolating plasmids
US5777324A (en) 1996-09-19 1998-07-07 Sequenom, Inc. Method and apparatus for maldi analysis
DE19714558A1 (en) * 1997-04-09 1998-10-15 Joachim W Prof Dr Engels A new method for sequencing biopolymers using mass spectrometry
WO1998054571A1 (en) * 1997-05-28 1998-12-03 The Walter And Eliza Hall Institute Of Medical Research Nucleic acid diagnostics based on mass spectrometry or mass separation and base specific cleavage
NZ516848A (en) 1997-06-20 2004-03-26 Ciphergen Biosystems Inc Retentate chromatography apparatus with applications in biology and medicine
US6207370B1 (en) 1997-09-02 2001-03-27 Sequenom, Inc. Diagnostics based on mass spectrometric detection of translated target polypeptides
GB9821393D0 (en) 1998-10-01 1998-11-25 Brax Genomics Ltd Protein profiling 2
US6994969B1 (en) 1999-04-30 2006-02-07 Methexis Genomics, N.V. Diagnostic sequencing by a combination of specific cleavage and mass spectrometry
US20040198950A1 (en) 2001-04-30 2004-10-07 George Jackowski Biopolymer marker indicative of disease state having a molecular weight of 1518 daltons
DE10123711A1 (en) * 2001-05-15 2003-02-27 Wolfgang Altmeyer Procedure for determining the origin of biological materials
AU2004235331B2 (en) * 2003-04-25 2008-12-18 Sequenom, Inc. Fragmentation-based methods and systems for De Novo sequencing
WO2005024068A2 (en) 2003-09-05 2005-03-17 Sequenom, Inc. Allele-specific sequence variation analysis
EP2395098B1 (en) 2004-03-26 2015-07-15 Agena Bioscience, Inc. Base specific cleavage of methylation-specific amplification products in combination with mass analysis
WO2009138207A2 (en) * 2008-04-28 2009-11-19 Kuehn Andreas Method and arrangement for the control of measuring systems, corresponding computer programme and corresponding computer-readable storage medium
EP4032538A3 (en) 2009-03-02 2022-10-26 Massachusetts Institute of Technology Methods and products for in vivo enzyme profiling
WO2012116131A1 (en) * 2011-02-23 2012-08-30 Leco Corporation Correcting time-of-flight drifts in time-of-flight mass spectrometers
US10006916B2 (en) * 2011-03-15 2018-06-26 Massachusetts Institute Of Technology Multiplexed detection with isotope-coded reporters
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