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EP0998749A1 - Matrices volatiles pour spectrometrie de masse a desorption/ionisation assistee par matrice - Google Patents

Matrices volatiles pour spectrometrie de masse a desorption/ionisation assistee par matrice

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Publication number
EP0998749A1
EP0998749A1 EP98926132A EP98926132A EP0998749A1 EP 0998749 A1 EP0998749 A1 EP 0998749A1 EP 98926132 A EP98926132 A EP 98926132A EP 98926132 A EP98926132 A EP 98926132A EP 0998749 A1 EP0998749 A1 EP 0998749A1
Authority
EP
European Patent Office
Prior art keywords
matrix
mass
large organic
organic molecule
molecule
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP98926132A
Other languages
German (de)
English (en)
Inventor
Joanna M. Hunter
Hua Lin
Christopher H. Becker
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Sequenom Inc
Original Assignee
Genetrace Systems Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Genetrace Systems Inc filed Critical Genetrace Systems Inc
Publication of EP0998749A1 publication Critical patent/EP0998749A1/fr
Withdrawn legal-status Critical Current

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Classifications

    • H—ELECTRICITY
    • H01—ELECTRIC ELEMENTS
    • H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
    • H01J49/00—Particle spectrometers or separator tubes
    • H01J49/02—Details
    • H01J49/10—Ion sources; Ion guns
    • H01J49/16—Ion sources; Ion guns using surface ionisation, e.g. field-, thermionic- or photo-emission
    • H01J49/161—Ion sources; Ion guns using surface ionisation, e.g. field-, thermionic- or photo-emission using photoionisation, e.g. by laser
    • H01J49/164—Laser desorption/ionisation, e.g. matrix-assisted laser desorption/ionisation [MALDI]
    • H—ELECTRICITY
    • H01—ELECTRIC ELEMENTS
    • H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
    • H01J49/00—Particle spectrometers or separator tubes
    • H01J49/02—Details
    • H01J49/04—Arrangements for introducing or extracting samples to be analysed, e.g. vacuum locks; Arrangements for external adjustment of electron- or ion-optical components
    • H01J49/0468—Arrangements for introducing or extracting samples to be analysed, e.g. vacuum locks; Arrangements for external adjustment of electron- or ion-optical components with means for heating or cooling the sample

Definitions

  • This invention relates to volatile photoabsorbing matrices having a low sublimation temperature for use in the mass spectrometric analysis of large, nonvolatile molecules.
  • This invention also relates to methods for preparing samples containing large, nonvolatile analyte molecules for laser desorption mass spectrometry employing such matrices.
  • Genetic polymorphisms and mutations can manifest themselves in several forms, such as point polymorphisms or point mutations where a single base is changed to one of the three other bases; deletions where one or more bases are removed from a nucleic acid sequence and the bases flanking the deleted sequence are directly linked to each other; insertions where new bases are inserted at a particular point in a nucleic acid sequence adding additional length to the overall sequence; and expansions and reductions of repeating sequence motifs. Large insertions and deletions, often the result of chromosomal recombination and rearrangement events, can lead to partial or complete loss of the activity of a gene. Of these forms of polymorphism, in general the most difficult type of change to screen for and detect is the point polymorphism because it represents the smallest degree of molecular change.
  • Gel electrophoresis of nucleic acids primarily provides relative size information based on mobility through the gel matrix. If calibration standards are employed, gel electrophoresis can be used to measure absolute and relative molecular weights of large biomolecules with some moderate degree of accuracy; even then, the accuracy is typically only 5% to 10%. Also the molecular weight resolution is limited. In cases where two DNA fragments with the identical number of base pairs can be separated, for example, by using high concentration polyacrylamide gels, it is still not possible to identify which band on a gel corresponds to which DNA fragment without performing secondary labeling experiments.
  • gel electrophoresis techniques can only determine size and cannot provide any information about changes in base composition or sequence without performing more complex sequencing reactions.
  • Gel-based techniques for the most part, are dependent on labeling or staining methods to visualize and discriminate between different nucleic acid fragments.
  • SSCP Single strand conformational polymorphism
  • DGGE denaturing gradient gel electrophoresis
  • CCM chemical cleavage at mismatch
  • EMC enzymatic mismatch cleavage
  • CFLP cleavage fragment length polymorphism
  • MALDI matrix-assisted laser desorption/ionization
  • TOF MS time-of-flight mass spectrometry
  • ES electrospray ionization
  • the MALDI mass spectrometric technique can also be used with methods other than time-of-flight, for example, magnetic sector, Fourier-transform ion cyclotron resonance, quadrupole, and quadrupole trap.
  • MALDI-TOF MS involves laser pulses focused on a small sample plate on which analyte molecules (i.e. nucleic acids) are embedded in either a solid or liquid matrix which is typically a small, highly absorbing material, such as a small aromatic organic molecule.
  • analyte molecules i.e. nucleic acids
  • the volatilization of intact fragile molecules benefits from the use of matrix-assisted laser desorption ionization because the radiative energy from the laser pulse is coupled indirectly into the analyte through the matrix molecules.
  • the analyte molecules are crystallized with a large molar excess of a photoabsorbing matrix (see U.S. Patent Nos. 4,920,264 and 5,1 18,937, incorporated herein by reference).
  • An advance in MALDI analysis of polynucleotides was the discovery of 3-hydroxypicolinic acid (3 -HP A) as a suitable matrix for mixed-base oligonucleotides (Wu, et al., 1993).
  • the laser pulses transfer energy to the matrix causing a microscopic ablation and concomitant ionization of the analyte molecules, producing a gaseous plume of intact, charged nucleic acids in single-stranded form. It is thought that upon laser excitation the matrix molecules are rapidly heated and ejected into the gas phase, carrying analyte molecules into the expansion plume of molecules and ions. It is thought that gas-phase ion-molecule collisions subsequently ionize the neutral analyte molecules in the near-surface region, often via proton transfer. The matrix thus functions as both an energy- and charge-transfer species. If double- stranded nucleic acids are analyzed, the MALDI-TOF MS typically results in detection of mostly charged denatured single-stranded nucleic acids.
  • the ions generated by the laser pulses are accelerated to a fixed kinetic energy by a strong electric field and then passed through an electric field-free region in vacuum, traveling with a velocity corresponding to their respective mass-to-charge ratios (m/z).
  • m/z mass-to-charge ratios
  • the smaller m/z ions will travel through the vacuum region faster than the larger m/z ions thereby causing a separation.
  • the ions collide with a detector that generates a signal as each set of ions of a particular mass-to-charge ratio strikes the detector.
  • 10 to 100 mass spectra resulting from individual laser pulses are summed together to make a single composite mass spectrum with an improved signal-to-noise ratio.
  • the mass of an ion (such as a charged nucleic acid) is measured by using its velocity to determine the mass-to-charge ratio by time-of-flight analysis.
  • the mass of the molecule directly correlates with the time it takes to travel from the sample plate to the detector. The entire process takes only microseconds. In an automated apparatus, tens to hundreds of samples can be analyzed per minute.
  • MALDI-TOF MS has one of the largest mass ranges for mass spectrometric devices.
  • the current mass range for MALDI-TOF MS is from 1 to 1,000,000 Da (measured recently for a protein) (Nelson et al, 1995).
  • Mass resolution is the measure of an instrument's ability to produce separate signals from ions of similar mass. Mass resolution is defined as the mass, m, of an ion signal divided by the full width of the signal, ⁇ m, usually measured between points of half-maximum intensity. Mass accuracy is the measure of error in designating a mass to an ion signal. The mass accuracy is defined as the ratio of the mass assignment error divided by the mass of the ion and can be represented as a percentage.
  • the mutant nucleic acid containing the base transversion will either decrease or increase by 9 Da in total mass as compared to the wild type nucleic acid.
  • mass spectrometry to directly detect these transversions. it must therefore be able to detect a minimum mass change, ⁇ m, of approximately 9 Da.
  • a distinguishing level of mass accuracy relative to another known peak in the spectrum is sufficient to resolve ambiguities. For example, if there is a known mass peak 1000 Da from the mass peak in question, the relative position of the unknown to the known peak may be known with greater accuracy than that provided by an absolute, previous calibration of the mass spectrometer.
  • DNA sequencing by MALDI-MS DNA sequencing by MALDI-MS.
  • MALDI-MS DNA sequencing by MALDI-MS.
  • For laser desorption mass spectroscopy techniques to successfully analyze macromolecules requires that one stably laser-desorb molecules into a vapor phase, and separate and detect (and thereby determine the mass of) the volatilized molecules by mass spectroscopy.
  • the ability to stably desorb the macromolecule depends on the availability of a suitable light absorbing matrix that will allow one to stably laser-desorb DNA molecules from a solid state to a gaseous state, and permit separation of DNA molecules having only a nucleotide or so difference in length. Putting that into perspective, the difference in mass between a polynucleotide having 30 versus 31 nucleotide represents about a 3% difference in mass (about 9610 v.
  • compositions and methods relating to the preparation of samples containing nonvolatile analyte molecules for mass analysis using a photoabsorbing, low-sublimation temperature matrix These matrix molecules provide a means for desorbing and ionizing nonvolatile, nonthermally-labile organic molecules such as biomolecules and synthetic polymers. Minimizing fragmentation of the parent analyte ion and/or reducing adduct formation leads to increased detection sensitivity and/or increased resolution and/or extension of the usable mass range.
  • the deleterious effects associated with widening kinetic energy spreads, fragmentation and the formation of matrix-analyte adducts are reduced by employing a matrix system, as disclosed herein, having lower intermolecular binding energies associated with increased volatility.
  • Lower binding energies can reduce fragmentation by minimizing the internal energy of the desorbed analyte, and can reduce adduct formation by lowering the binding energy of the analyte with its surrounding molecules.
  • the desorption of a volatile matrix at room temperature but cooled to maintain low vapor pressure in the mass spectrometer may also require less energy.
  • the present invention relates to a method for volatilization and mass spectrometric analysis of nonvolatile, or nonthermally labile, large organic molecules including biomolecules such as nucleic acids, for example, DNA and RNA; proteins and peptide nucleic acids (PNA); oligosaccharides, and other high molecular weight polymers.
  • biomolecules such as nucleic acids, for example, DNA and RNA; proteins and peptide nucleic acids (PNA); oligosaccharides, and other high molecular weight polymers.
  • the invention generally provides a method for determining the mass of a large organic molecule.
  • the method typically includes contacting a large organic molecule, the mass of which one desires to determine, with a photoabsorbing, or light absorbing, low-sublimation temperature matrix to produce a matrix:molecule mixture.
  • This contacting step may be carried out by dissolving the large organic molecule to be analyzed in a solution containing the matrix.
  • the matrix.molecule mixture is then irradiated by a light source, such as a laser, to desorb, ionize, and produce an ionized large organic molecule.
  • the ionized large organic molecule is then separated from other constituents, such as the matrix:molecule mixture or other matrix.molecule adducts, using mass spectrometry and the mass of the ionized large organic molecule determined. While any mass spectrometry is contemplated for use with the present invention, time-of-flight mass spectrometry is preferred.
  • the matrix:molecule mixture typically comprises a physical mixture of the matrix with the molecule to be analyzed. It may or may not contain adducts of the matrix with the molecule. Although if adducts are formed, they will typically be only weakly associated such that they may be readily dissociated upon irradiation, desorption, and ionization.
  • the sample stage is cooled to less than 273° K, typically to from about 150° K to 200° K or to about 180 K. While it is contemplated that the sample stage may be cooled by any suitable means, it may typically be cryongenically cooled by liquid nitrogen.
  • the solution containing the matrix may generally contain one or more solvents.
  • the solvents will be water and/or organic solvents, such as ethanol, methanol, toluene, acetone, and acetonitrile.
  • the solvents are substantially evaporated, typically to dryness. In preferred embodiments, the solvents are evaporated at room temperature. After evaporating the solvent, the resulting solid or crystalline molecule- matrix mixture is cooled to a vapor pressure between about 10 "10 Torr and about 10 "5 Torr.
  • the matrix for use in the present invention is generally a volatile, light-absorbing, hydroxy-bearing matrix.
  • volatile matrices are those that are volatile at room temperature at ambient or reduced pressures.
  • the matrix may be a phenol, a hydroxyquinoline, or a hydroxynaphthalene. Where the matrix is a phenol, it will preferably be 4-nitrophenol. Where the matrix is a hydroxyquinoline, it will preferably be 8- hydroxyquinoline. It is also generally preferred that the matrix have a molecular weight of between about 90 Da and about 400 Da. Different classes of analyte molecules may also require different matrix systems.
  • the matrix should typically not react or interact strongly with the analyte and the analyte should be soluble in the matrix crystals.
  • the matrix has a high sublimation rate between the temperatures of 20°C to 200°C (or a low sublimation temperature).
  • the low-sublimation temperature matrix may typically have a sublimation rate at room temperature of at least 0.1 ⁇ m.min " at a pressure of about 10 " Torr or less and preferably the sublimation rate at these conditions is from about 0.01 ⁇ wnin " to about 0.1 mm.min " .
  • the matrix is a crystalline solid.
  • the terms "photo absorbing” or "light absorbing” refer to the ability of the matrix to absorb the desorption light sufficiently strong to aid in the desorption and ionization of the large organic molecule.
  • the matrices will absorb light between the wavelengths of approximately 200 ran and approximately 20,000 nm although it will be understood that this absorption is not continuous.
  • the photoabsorbing matrix have an abso ⁇ tion coefficient greater than about 10 L.c ⁇ '.mor 1 , up to and including an abso ⁇ tion coefficient of 10 L.cm “ .mol " , at the wavelength of the desorbing and ionizing radiation.
  • the method of the invention is useful for determining the mass of virtually any large organic molecule.
  • the mass of a polymer may be determined using the methods of the invention.
  • the polymer to be analyzed will be a biopolymer, such as a nucleic acid, a polypeptide, a peptide nucleic acid (PNA), an oligosaccharide, or a mass-modified derivative thereof.
  • the molecule to be analyzed is a nucleic acid, it will be understood that it may be, for example, a DNA or an RNA.
  • the analyte should typically be purified to minimize the presence of salt ions and other molecular contaminants. These impurities may reduce the intensity and quality of the mass spectrometric signal to a point where either (i) the signal is undetectable or unreliable, or (ii) the mass accuracy and/or resolution is below the value necessary for the particular application, such as to detect the type of polymo ⁇ hism expected or sequence the analyte.
  • a preferred method to purify the analyte is to immobolize it on a solid support and wash it remove impurities, such as sodium and potassium ions. The analyte may then be released from the solid support and contacted with the matrix.
  • the size of the analyte to be analyzed should also be within the range where there is sufficient mass resolution and accuracy. Mass accuracy and resolution significantly degrade as the mass of the analyte increases.
  • SNPs single nucleotide polymo ⁇ hisms
  • the method of the invention will allow for the mass determination of any large organic molecule having a mass of greater than about 1 ,000 Da. More specifically, one may determine the mass of a molecule having a mass of greater than about 27,000 Da, greater than about 30,000 Da, greater than about 50,000 Da, greater than about 75,000 Da, greater than about 100,000 Da, greater than about 150,000 Da, greater than about 175,000 Da, greater than about 200,000 Da, greater than about 250,000 Da, or even greater than about 315,000 Da.
  • the organic molecule will typically have a mass of less than 5,00,000 Da, 3,000,000 Da or 1 ,000,000 DA. In some embodiments, the organic molecule may have a mass of less than 500,000 or 300,000 Daltons.
  • the desorbing step To perform the desorbing step, one will generally expose the matrix:molecule mixture to a source of energy to desorb the large organic molecule from the matrix.
  • the source of energy used for deso ⁇ tion of the large organic molecule will preferably be a laser beam.
  • the laser beam used to desorb and ionize the large organic molecule may be any laser but is preferably a pulsed laser.
  • the deso ⁇ tion step will include applying an energy of about 20 kN followed by a pulse of energy of about 2.7 kV.
  • the pulse of energy comprises light having a wavelength of about 355 nm.
  • the mass of the large organic molecule may then be determined by summing the mass spectra over a number of laser pulses, preferably about 200 laser pulses or about 1000 laser pulses, or any number of pulses therebetween, such as, for example, about 250 laser pulses, about 300 laser pulses, about 350 laser pulses, about 500 laser pulses, about 750 laser pulses, etc.
  • a number of laser pulses preferably about 200 laser pulses or about 1000 laser pulses, or any number of pulses therebetween, such as, for example, about 250 laser pulses, about 300 laser pulses, about 350 laser pulses, about 500 laser pulses, about 750 laser pulses, etc.
  • lower numbers of pulses, especially very low numbers of pulses such as 10 or 20 or 50 pulses, etc. may give less accurate results, and higher numbers of pulses becomes unnecessarily repetitive and lower the efficiency and cost-effectiveness of the method.
  • the invention also provides a method for preparing a sample of large organic molecules for mass spectral analysis.
  • This method typically includes providing a solution comprising a large organic molecule to be analyzed, a matrix molecule comprising a volatile, light-absorbing hydroxy-bearing matrix molecule, and a solvent, and evaporating the solvent to provide a solid crystalline matrix containing the molecule to be analyzed.
  • the present invention applies to MALDI mass spectrometry of all classes of nonvolatile, large organic compounds, with synthetic polymers and biopolymers preferred.
  • the present invention is particularly preferred for mass analysis of biopolymers such as nucleic acids, proteins, PNAs and oligosaccharides due to the fragile nature of these molecules.
  • the method utilizes pulsed laser deso ⁇ tion/ionization mediated by a matrix followed by mass spectrometric separation and detection of the analyte molecules.
  • the matrix may be a crystalline solid or a liquid at room temperature, with crystalline solids being preferred.
  • the preferred matrix has a high sublimation rate in vacuum at room temperature and absorbs the deso ⁇ tion light strongly.
  • crystalline solid, light absorbing compounds having hydroxy functionalities, but not carboxylic functionalities for use as a matrix in mass analysis.
  • the matrix compounds may be phenols, hydroxyquinolines or hydroxynaphthalenes.
  • the crystalline solids, 8- hydroxyquinoline and 4-nitrophenol, which are volatile at room temperature, are particularly preferred as matrices in accordance with the present invention.
  • analyte is a large organic molecule of greater than about 1,000 Da.
  • the large organic analyte is a polymer.
  • the polymer is a biopolymer.
  • the biopolymer is a polynucleic acid, and in still further embodiments the biopolymer is an oligonucleotide.
  • the biopolymer is a protein, polypeptide, or oligosaccharide.
  • the sample is placed on a cooled sample stage in order to maintain a low vapor pressure of the sample in the vacuum chamber of the mass spectrometer.
  • the sample stage is cooled below about 273 °K, more typically between about 170 to about 190°K, and most typically to about 180°K.
  • FIG. 1 is a laser deso ⁇ tion/ionization time-of-flight mass spectrum of a mixture of single-stranded DNA oligomers 89, 90, and 91 nucleotides in length obtained using 8- hydroxyquinoline as the matrix.
  • the laser wavelength was 355 nm.
  • FIG. 2 is a laser deso ⁇ tion ionization time-of-flight mass spectrum of a double- stranded PCR product at 315 kDa per strand (greater than approximately 1000 nucleotides in length) using a 4-nitrophenol matrix.
  • the laser wavelength was 355 nm.
  • hydroxy functionalities but not carboxylic functionalities
  • matrices in MALDI mass spectrometry.
  • Hydroxy functionalities offer advantage over carboxylic functionalities due to their increased acidity in the excited state (Huppert et al., 1981) and also typically provide lower intermolecular binding energies to increase volatility.
  • matrix compounds include, but are not limited to, hydroxyquinolines, phenols, and hydroxynaphthalenes.
  • Samples are prepared by dissolving the analyte in a solution containing the matrix molecule, with the bulk of the solution being one or more solvents which are subsequently allowed to evaporate before mass analysis begins.
  • the analyte will be present in the solution at a concentration of about 0.05 M to about 1.0 M.
  • the solvent evaporation may be conducted at a temperature range of about 20°C to about 30°C, with room temperature, about 25°C being most preferred.
  • the evaporation results in the formation of a crystalline matrix, composed in part (between about 30% by weight to about 100% by weight) of the subject matrix molecule.
  • the matrix molecular weight is greater than about 90 Da, preferably between about 90 Da and about 400 Da.
  • volatile, light-absorbing, hydroxy-bearing matrix molecules are termed herein as volatile, light-absorbing, hydroxy-bearing matrix molecules.
  • volatile refers to a molecule having a sublimation rate at room temperature of greater than or equal to 0.1 ⁇ m «min " ' at a pressure of about 10 " Torr or less
  • light absorbing refers to a molecule having an abso ⁇ tion coefficient greater than about 10 l.cm “1 «mol "1 .
  • Two low-sublimation-temperature molecules in particular function effectively as matrices for MALDI of nonvolatile organic molecules for detection by mass spectrometry.
  • the former is especially effective for high-resolution analysis of DNA less than approximately 100 nucleotides (30 kDa), and the latter is especially effective for sensitive detection of higher mass molecules.
  • Nonvolatile refers to a molecule which, when present in its pure, neat form and heated, does not sublimate intact to any significant extent. Also included in the definition of nonvolatile compounds are compounds which, when present in their pure neat form, cannot be practically analyzed by mass spectrometry when conventional gas chromatography methods are employed in the sampling process. Representative of such organic compounds are polynucleic acids, polypeptides, oligosaccharides, PNAs and synthetic polymers.
  • Biopolymers which are subject to fragmentation during mass analysis.
  • Representative biopolymers include polymers of amino acids, nucleic acids, saccharides, carbohydrates and polypeptides.
  • the mass spectrometry may be accomplished by one of several techniques such as time- of-flight, magnetic sector or ion trap.
  • the mass spectrometry technique for use with the present invention will be time-of-flight.
  • the volatility of the matrix crystals necessitates that the sample stage of the mass spectrometer be cooled to substantially below room temperature where the sublimation rate is between about 0.1 ⁇ m.min " and about 0.1 mm.min " .
  • a preferred approach is to use a liquid- nitrogen cooled sample stage, accomplished by flowing liquid nitrogen through a copper sample holder.
  • the sample is cooled to less than 273°K, preferably between about 170 and 190 °K or to about 180 °K.
  • Wavelengths from the ultraviolet to infrared may be employed, depending on the cooled matrix being analyzed. Generally, one of skill in the art will understand that the appropriate wavelength will be one where light abso ⁇ tion is significant for the molecule being analyzed.
  • the disclosed low-sublimation temperature matrices and methods for using them to determine the mass of a large organic molecule or prepare a large organic molecule for mass spectral analysis may be used in a variety of MS applications, such as MS sequencing of nucleic acids; MS analysis of single nucleotide polymo ⁇ hisms (SNPs); and MS analysis of simple sequence repeats (SSRs), short tandem repeats (STRs), and microsatellite repeats (MRs).
  • MS sequencing of nucleic acids MS analysis of single nucleotide polymo ⁇ hisms (SNPs); and MS analysis of simple sequence repeats (SSRs), short tandem repeats (STRs), and microsatellite repeats (MRs).
  • the methods disclosed herein may be used in nucleic acid sequencing methods involving obtaining nucleic acid fragments using a four base Sanger sequencing reaction, performing MS on the products and determining the nucleic acid sequence from the mass differences between the peaks.
  • the nucleic acid fragments may be obtained by hybridizing a DNA primer to a DNA template and extending the primer by a DNA polymerase in the presence of deoxy- and dideoxy- nucleotides.
  • the DNA template may generally contain the DNA fragment to be sequenced and a region complementary to the primer.
  • the DNA primers may also contain a biotin which allows for capture to a solid phase and a single, chemically cleavable internal linkage (such as a 5'-or 3'-(S)-phosphorothioate linkage which is cleavable by a silver ion catalyzed reaction).
  • a biotin which allows for capture to a solid phase
  • a single, chemically cleavable internal linkage such as a 5'-or 3'-(S)-phosphorothioate linkage which is cleavable by a silver ion catalyzed reaction.
  • the cleavage chemistry of the internal linkage combined with the biotin capture are described in U.S. Patent No. 5,700,642, inco ⁇ orated herein by reference.
  • the nucleic acid fragments may be further processed prior to MS analysis.
  • these processing steps involve binding the nucleic acid fragments to a streptavidin solid support, washing the bound fragments, and cleaving at the internal cleavage site to release the nucleic acid fragment from the solid support.
  • the bound fragments are first washed with a denaturant, such as aqueous NaOH, to remove unbound DNA and enzyme and then with a series of ammonium acetate washes.
  • the cleaved extension products may be prepared for MS analysis by drying; mixing the solid residue with the matrix material and ammonium citrate solution; spotting the mixture by pipette onto a plate; and allowing the mixture to dry.
  • the methods for MS SNP analysis are very similar to the DNA sequencing methods except that only dideoxynucleotides are employed.
  • low-sublimation temperature matrices may also be used for analyzing SSRs, STRs, and MRs involving the determination of the number of repetitive units contained in amplification products by MS.
  • the amplification products are typically obtained by hybridizing a DNA primer to a DNA target molecule and extending the primer by a DNA polymerase. Similar to the sequencing methods, the DNA primer contains a region complementary to the DNA target molecule adjacent to the SSR-, STR-, or MR-containing region. The primer may also contain biotin and internal cleavable linkages.
  • the sample stage was floated at 20 kV, and after some delay time (approximately several hundred nanoseconds, dependent on mass), ions were extracted by a 2.7 kV pulse and focused into a 1- meter flight tube.
  • the signal output from the dual microchannel plate detector was amplified and digitized with 5 ns time resolution.
  • the preparative solution for the 8HQ matrix began by using 0.2 M 8HQ in 1 :1 (volume) acetone:butanone. To reduce alkali-metal adduct ion formation, to that initial 8HQ solution was added an equal volume of 50 mM aqueous diammonium citrate, resulting in a 25 mM final diammonium citrate concentration and 0.1 M 8HQ concentration.
  • 8HQ is known to chelate trace amounts of metal ions, especially copper, but the addition of CDTA (trans-1,2- diaminocyclohexane-N,N,N',N' tetraacetic acid monohydrate) effectively suppressed copper adducts in the mass spectrum; a small aliquot of concentrated CDTA was added to a much larger volume of the 8HQ solution to yield a lOmM CDTA concentration.
  • CDTA trans-1,2- diaminocyclohexane-N,N,N',N' tetraacetic acid monohydrate
  • the oligonucleotide sample was obtained from polymerase chain reaction (PCR) amplification of a short tandem repeat sequence at the human THOl (tyrosine hydroxylase gene) locus. One of the strands was captured, denatured, washed, then released to produce single-stranded products. An aliquot of aqueous solution of this THOl oligonucleotide (estimated 10 pmol quantity) was first evaporated in a vacuum evaporator to remove the water, and then one microliter of the matrix solution was added to the dried DNA. This resulting solution was pipetted onto a silicon substrate mounted on a copper sample holder. After air- drying of the solvent and resultant crystallization of the matrix, the sample was placed on the cryogenically-cooled sample stage in the mass spectrometer.
  • PCR polymerase chain reaction
  • FIG. 1 illustrates the mass resolution attainable for single-stranded oligonucleotides of about 27 kDa using 355 nm pulsed laser light for deso ⁇ tion and summing mass spectra over 200 laser pulses.
  • DNA oligomers containing 89, 90, and 91 nucleotides have a mass resolution (m/ ⁇ m) of 650, 625, and 700, respectively at full width at half height.
  • Spectra of oligonucleotides in 8HQ matrix typically have a low background ion signal and high signal-to-noise levels.
  • the preparative solution for the 4NP matrix was 0.5 M 4NP in 1 :1 (volume) methanol: water containing diammonium citrate at 50 mM final concentration.
  • One microliter of the matrix solution was added to dried DNA which was a double-stranded PCR product estimated at 10 pmol quantity derived from an unknown cDNA insert in a vector.
  • This resulting solution was pipetted onto a silicon substrate mounted on a copper sample holder. After air-drying of the solvent and resultant crystallization of the matrix, the sample was placed on the cryogenically-cooled sample stage in the mass spectrometer.
  • compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.
  • Tanaka et al "Protein and Polymer Analyses up to m/z 100 000 by Laser Ionization Time-of- flight Mass Spectrometry," Rapid Commun. in Mass Spectrometry, 2:151-153 (1988).

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Abstract

L'invention concerne un procédé de préparation d'échantillons en vue de la réalisation d'analyses de volatilisation et de spectrométrie de masse sur des molécules non volatiles à poids moléculaire élevé. Elle concerne également des molécules photo-absorbantes caractérisées par des vitesses de sublimation importantes à température de la pièce sous vide, lesquelles molécules, qui comportent, de préférence, des valences fonctionnelles hydroxy, sont destinées à être utilisées comme matrices pour la spectrométrie de masse à désorption/ionisation assistée par matrice. Les échantillons sont généralement refroidis dans le spectromètre de masse jusqu'à ce qu'ils atteignent des températures bien inférieures à la température de la pièce.
EP98926132A 1997-05-30 1998-05-29 Matrices volatiles pour spectrometrie de masse a desorption/ionisation assistee par matrice Withdrawn EP0998749A1 (fr)

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US5093297P 1997-05-30 1997-05-30
US50932P 1997-05-30
PCT/US1998/011003 WO1998054751A1 (fr) 1997-05-30 1998-05-29 Matrices volatiles pour spectrometrie de masse a desorption/ionisation assistee par matrice

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EP0998749A1 true EP0998749A1 (fr) 2000-05-10

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CA2302036C (fr) 2003-09-02
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WO1998054751A1 (fr) 1998-12-03

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