US20020123055A1 - Mass spectrometric analysis of biopolymers - Google Patents

Mass spectrometric analysis of biopolymers Download PDF

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US20020123055A1
US20020123055A1 US09/932,369 US93236901A US2002123055A1 US 20020123055 A1 US20020123055 A1 US 20020123055A1 US 93236901 A US93236901 A US 93236901A US 2002123055 A1 US2002123055 A1 US 2002123055A1
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biopolymer
target
analog
fragment
putative
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David Estell
Grant Ganshaw
Christian Paech
Sigrid Paech
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Danisco US Inc
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Genencor International Inc
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Priority to US11/011,666 priority patent/US7396688B2/en
Assigned to GENENCOR INTERNATIONAL, INC. reassignment GENENCOR INTERNATIONAL, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: ESTELL, DAVID A., GANSHAW, GRANT, PAECH, CHRISTIAN, PAECH, SIGRID
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    • H—ELECTRICITY
    • H01—ELECTRIC ELEMENTS
    • H01J—ELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
    • H01J49/00—Particle spectrometers or separator tubes
    • H01J49/0027—Methods for using particle spectrometers
    • H01J49/0036—Step by step routines describing the handling of the data generated during a measurement
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/24—Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00—Chemistry: analytical and immunological testing
    • Y10T436/25—Chemistry: analytical and immunological testing including sample preparation
    • Y10T436/25125—Digestion or removing interfering materials

Definitions

  • the present invention relates to the analysis of biopolymers in crude solutions.
  • the invention relates to the determination, quantitation, and identification of biopolymers, such as polypeptides and oligonucleotides, using mass spectroscopic data obtained from fractioned mixtures.
  • Bairoch A Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28:45-48.
  • Protein concentration determination is at the heart of any study concerned with the catalytic efficiency of an enzyme. Even for highly purified enzymes the choice of first-principle methods for accurately measuring molar concentrations is restricted to a few techniques (amino acid, total nitrogen, and absorbance measurement (Pace et al., 1995), titration of oxidized sulfur (Guermant et al., 2000).
  • the present invention makes use of the subunit sequence as a unique tag of a biopolymer (e.g., the amino acid sequence of a specific protein), that can be exploited for determining the concentration in crude solutions.
  • a biopolymer e.g., the amino acid sequence of a specific protein
  • the present invention addresses the need for a straightforward and rapid technique for determining the specific concentration of one or more biopolymers (e.g., proteins, oligonucleotides, etc.) in a mixture, e.g., a cell-free culture fluid, a cell extract, or the entire complement of proteins in a cell or tissue.
  • biopolymers e.g., proteins, oligonucleotides, etc.
  • the present invention additionally provides a method for identifying a biopolymer fragment (e.g., peptide, oligonucleotide, etc.) derived from a larger biopolymer added to a solution that otherwise lacks such a biopolymer or fragment.
  • a biopolymer fragment e.g., peptide, oligonucleotide, etc.
  • the present invention provides a method for determining the absolute quantity of a target polypeptide, such as a selected protein, in a crude solution or mixture, comprising the steps of:
  • the solution or mixture can be, for example, a crude fermenter solution, a cell-free culture fluid, a cell extract, or a mixture comprising the entire complement of proteins in a cell or tissue.
  • Another aspect of the present invention provides a method for determining the absolute quantity of a target polynucleotide in a crude solution, comprising the steps of:
  • the target polynucleotide is an oligonucleotide.
  • Yet a further aspect of the present invention provides a method for verifying the presence and, optionally, determining the absolute quantity of a selected putative polypeptide, such as a protein, in a mixture containing a plurality of isotope-labeled cellular proteins from a selected cell type.
  • One embodiment of the method includes the steps of:
  • the putative polypeptide can be derived, for example, from a database of sequence information.
  • the fragmentation of the cellular polypeptide is determined to be substantially complete with respect to the cellular polypeptide fragment corresponding to the internal standard.
  • One embodiment provides the additional steps of:
  • the present invention provides a cell-culture extract, derived from a selected microorganism grown on media enriched in a specific isotope, said extract containing a known amount of a metabolically labeled polypeptide determined by a peptide-separation technique in combination with mass spectroscopy.
  • a further aspect of the present invention provides a method for determining the identity of a target polypeptide fragment in a solution, comprising the steps of:
  • the target polypeptide is a protein.
  • the crude solution contains a plurality of different proteins.
  • the solution can be a crude fermenter solution, a cell-free culture fluid, a cell extract, a mixture comprising the entire complement of proteins in a cell or tissue, etc.
  • FIG. 1 UV traces of a tryptic co-digest of 15 N-subtilisin-DAI, indexed ( 15 N), and subtilisin, indexed (s). Peptide numbering refers to Table I.
  • FIG. 2 Total ion current chromatogram of selected peptides in FIG. 1.
  • A Peptide 3 of subtilisin (3 (s), upper panel) and peptide 3 of 15 N-subtilisin-DAI (3( 15 N), lower panel).
  • B TIC of peptides 5, 6, and 9 of the co-digest of 15 N-subtilisin-DAI, indexed ( 15 N), and subtilisin, indexed (s). Sequence differences between subtilisin-DAI and subtilisin reside on peptide 5 (N71D) and 6 (S101A, V102I). Amino acid sequence numbering is linear.
  • FIG. 3 Rapid tryptic digest of subtillin-DAI and 15 N-subtilisin-DAI and separation of peptides by RP-HPLC on a 2.0 ⁇ 50 mm C18 column (Jupiter, by Phenomenex). The quantitation by TIC peak area integration of corresponding peaks gave the result expected from enzyme activity assays and active site titrations (see FIGS. 1 and 2).
  • FIG. 4 SDS-PAGE of a fermentation broth concentrate of unknown origin.
  • B This material spiked with a known amount of 15 N-labeled purified subtilisin BPN′-Y217L and was digested with trypsin. The peptide mixture was separated by RP-HPLC on a C18 column (2.1 ⁇ 150 mm) and the eluate was recorded at 215 nm.
  • FIG. 5 Totoal ion current chromatogram of peptides 1, 2, and 3 from FIG. 3.
  • FIG. 6 Table I.: Sequence comparison, m/z values, and ratios of integrated TIC peak areas and UV absorbance peak areas for chromatogram in FIG. 1.
  • concentration measured by the co-digest technique for subtilisin and subtilisin-DAI was 8.15 and 7.13 mg/ml, respectively, while the given concentration (established by independent methods) was 7.99 and 7.03 mg/ml, respectively.
  • FIG. 7. Table II. Determination of concentration, activity and conversion factor for subtilisin-DAI variants determined by peptide mapping ( 15 N-isotope method) and by active site titration with a calibrated mung bean inhibitor solution using as internal standard a previously calibrated solution of subtilisin-DAI (Hsia et al., 1996). The range of target protein concentrations was 2 to 5 ⁇ g ml ⁇ 1 .
  • the present invention provides methods for the quantitation of biopolymers in crude, i.e., unpurified, solutions.
  • nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
  • the headings provided herein are not limitations of the various aspects or embodiments of the invention which can be had by reference to the specification as a whole. Accordingly, the terms defined immediately below are more fully defined by reference to the specification as a whole.
  • biopolymer as used herein means any large polymeric molecule produced by a living organism. Thus, it refers to nucleic acids, polynucleotides, polypeptides, proteins, polysaccharides, carbohydrates, lipids and analogues thereof.
  • biopolymer and “biomolecule” are used interchangeably herein.
  • an “isolated” biomolecule such as a nucleic acid or protein
  • nucleic acids and proteins which have been “isolated” thus include nucleic acids and proteins purified by standard purification methods.
  • the term also embraces nucleic acids and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.
  • a macromolecule composed of one to several polypeptides.
  • Each polypeptide consists of a chain of amino acids linked together by covalent (peptide) bonds. They are naturally-occurring complex organic substances composed essentially of carbon, hydrogen, oxygen and nitrogen, plus sulphur or phosphorus, which are so associated as to form sub-microscopic chains, spirals or plates and to which are attached other atoms and groups of atoms in a variety of ways.
  • a protein may comprise one or multiple polypeptides linked together by disulfied bonds. Examples of the protein include, but are not limited to, antibodies, antigens, ligands, receptors, etc.
  • the terms “polypeptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues.
  • mixtures are produced which may contain individual components containing 100 or more amino acid residues or as few as one or two such residues.
  • amino acids dipeptides, tripeptides, etc.
  • polypeptides since the mixtures which are prepared for mass spectrometric analysis contain such components together with products of sufficiently high molecular weight to be conventionally identified as polypeptides.
  • Polypeptides may contain amino acids other than the 20 gene encoded amino acids.
  • Polypeptide(s) include those modified either by natural processes, such as processing and other post-translational modifications, but also by chemical modification techniques. Such modifications are well described in basic texts and in more detailed monographs, as well as in a voluminous research literature, and they are well known to those of skill in the art.
  • Polypeptides may be branched or cyclic, with or without branching. Cyclic, branched and branched circular polypeptides may result from post-translational natural processes and may be made by entirely synthetic methods, as well.
  • a linear molecule composed of two or more amino acids linked by covalent (peptide) bonds. They are called dipeptides, tripeptides and so forth, according to the number of amino acids present. These terms may be used interchangeably with polypeptide. See above.
  • a chain of nucleotides in which each nucleotide is linked by a single phospho-diester bond to the next nucleotide in the chain can be double- or single-stranded.
  • the term is used to describe DNA or RNA.
  • Polynucleotide(s) generally refers to any polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA.
  • Polynucleotide(s)” include, without limitation, single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions or single-, and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded, or a mixture of single- and double-stranded regions.
  • the RNA may be a mRNA.
  • polynucleotide(s) also includes DNAs or RNAs as described above that contain one or more modified bases.
  • DNAs or RNAs with backbones modified for stability or for other reasons are “polynucleotide(s)” as that term is intended herein.
  • DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as 4-acetylcytosine, to name just two examples are polynucleotides as the term is used herein. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art.
  • polynucleotide(s) as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including, for example, simple and complex cells.
  • the length of the polynucleotides may be 10 kb. In accordance with one embodiment of the present invention, the length of a polynucleotide is in the range of about 50 bp to 10 Kb, preferably, 100 bp to 1.5 kb.
  • a short molecule (usually 6 to 100 nucleotides) of single-stranded DNA.
  • “Oligonucleotide(s)” refer to short polynucleotides, i.e., less than about 50 nucleotides in length.
  • the oligonucleotides can be of any suitable size, and are preferably 24-48 nucleotides in length.
  • the length of a synthesized oligonucleotide is in the range of about 3 to 100 nucleotides.
  • the length of the oligonucleotide is in the range of about 15 to 20 nucleotides.
  • Restriction enzyme and restriction endonuclease are used interchangeably herein and refer to a protein that recognizes specific, short nucleotide sequences and cuts the DNA at those sites. There are three types of restriction endonuclease enzymes:
  • Type I Cuts non-specifically a distance greater than 1000 bp from its recognition sequence and contains both restriction and methylation activities.
  • Type II Cuts at or near a short, and often palindromic recognition sequence. A separate enzyme methylates the same recognition sequence. They may make the cuts in the two DNA strands exactly opposite one another and generate blunt ends, or they may make staggered cuts to generate sticky ends.
  • the type II restriction enzymes are the ones commonly exploited in recombinant DNA technology.
  • Type III Cuts 24-26 bp downstream from a short, asymmetrical recognition sequence. Requires ATP and contains both restriction and methylation activities.
  • the present invention contemplates the fragmentation of polynucleotides with restriction enzymes.
  • the restriction enzyme is a Type II.
  • the fragment polynucleotides are then resolved into individual components based on size.
  • the present invention makes use of the biomolecule (e.g., amino acid or nucleotide) sequence as a unique tag of a specific biopolymer (e.g., polypeptide or polynucleotide) that can be exploited for determining biopolymer concentration or identity in crude solutions, e.g., a crude fermenter solution, a cell-free culture fluid, a cell or tissue extract, etc.
  • a target biomolecule is selected for analysis and an analog thereof is generated. The analog is purified and calibrated, and a known amount is added as an internal standard to the solution to be assayed.
  • biopolymers of the mixture are then fragmented, e.g., by proteolytic digestion for proteins, and the resulting biomolecule-fragments are resolved, e.g., by way of chromatography.
  • One or more corresponding biomolecule-fragments pairs are then identified and analyzed by selected ion monitoring of a mass spectrometer.
  • a target polypeptide is selected for analysis and an analog of the target polypeptide is generated.
  • the target protein can be, for example, a protein that is known to be in a mixture, a putative protein (e.g., derived from a genome database search) that is potentially present in a mixture, or a known or putative protein segment or fragment (peptide).
  • the analog of the target polypeptide can be the target polypeptide itself or a unique segment or fragment (peptide) of the target polypeptide.
  • One or the other of the target polypeptide and analog is labeled so that the two can be distinguished from one another in subsequent mass analysis.
  • the analog is purified and its absolute quantity is determined in a solid quantity or in a solution by standard techniques (the analog is now said to be ‘calibrated’), and a known amount is employed as an internal standard in the solution to be assayed.
  • the polypeptides of the mixture are treated with a fragmenting activity, and the peptide components of the mixture are then resolved.
  • Corresponding peptide pairs are then analyzed by selected ion monitoring of a mass spectrometer. Peak area integration of such peptide pairs provides a direct measure for the amount of target polypeptide in the crude solution.
  • a target polynucleotide is selected for analysis and an analog of the target polynucleotide is generated.
  • the target polynucleotide can be, for example, a gene sequence that is known to be in a mixture, a putative gene (e.g., derived from a genome database search) that is potentially present in a mixture, or a known or putative polynucleotide or fragment (oligonucleotide).
  • the analog of the target polynucleotide can be the target polynucleotide itself or a unique segment or fragment (oligonucleotide) of the target polynucleotide.
  • One or the other of the target polynucleotide and analog is labeled so that the two can be distinguished from one another in subsequent mass analysis.
  • the analog is purified and its absolute quantity is determined in a solid quantity or in a solution by standard techniques (the analog is now said to be ‘calibrated’), and a known amount is employed as an internal standard in the solution to be assayed.
  • the polynucleotides of the mixture are treated with a fragmenting activity, and the oligonucleotide components of the mixture are then resolved.
  • Corresponding nucleotide-fragment pairs are then analyzed by selected ion monitoring of a mass spectrometer. Peak area integration of such nucleotide-fragment pairs provides a direct measure for the amount of target polynucleotide in the crude solution.
  • the biomolecule analog is labeled with a suitable stable isotope and calibrated.
  • the sample containing (or suspected of containing) the biomolecule of interest is aliquoted out such that the final concentration (after addition of the analog) in each aliquot is the same.
  • decreasing amounts of the known labeled biomolecule analog is added to each aliquot.
  • Each aliquot is subjected to mass spectrometry and their spectra analyzed for peaks corresponding to the labeled and unlabeled biomolecule of interest.
  • Corresponding biomolecule peaks of the same magnitude i.e., where the peak area ratio of labeled:unlabeled biomolecule equals one, indicates that the concentrations of each are the same.
  • one is able to determine the concentration of the unlabeled biomolecule of interest from the sample with the known concentration of the labeled analog when the ratio equals one.
  • neither the biomolecule of interest nor the analog are labeled with a stable isotope.
  • a known quantity of the analog is added in decreasing amounts to aliquots of the sample to be analyzed to yield a contaminated sample.
  • the contaminated sample is treated with a fragmenting activity, and the biomolecule components of the mixture resolved.
  • the resolved biomolecule-fragments, fragments, i.e., the corresponding biomolecule-fragment pairs, are then analyzed by mass spectrometry.
  • the contribution of the unlabeled contaminant will decrease as its concentration in the sample of interest decreases.
  • the contribution of the unlabeled analog to the spectral analysis becomes negligible and the concentration of the biomolecule of interest can be determined.
  • the concentration of the biomolecule of interest is determined by the intensity of the signal when the contribution of the analog is negligible and known concentration of the analog.
  • Labeling of the target or analog can be effected by any means known in the art.
  • a labeled protein or peptide can be synthesized using isotope-labeled labeled amino acids or peptides as precursor molecules.
  • Preferred labeling techniques utilize stable isotopes, such as 18 O, 15 N, 13 C, or 2 H, although others may be employed.
  • Metabolic labeling can also be used to produce labeled proteins and peptides.
  • cells can be grown on a media containing isotope-labeled precursor molecules.
  • an organism can be grown on 15 N-labeled organic or inorganic material, such as urea or ammonium chloride, as the sole nitrogen source. See Example 5.
  • biopolymers are labeled with 15N.
  • the following is a preferred protocol.
  • This protocol may be used to produce 15 N-labeled biomolecules. Due to the fact that the only source of nitrogen is urea, this media lends itself to being a very cost-effective way to label proteins (the cell and all of its components as well) with 15 N. The one caveat is that the host organism must be able to grow and produce the target protein in a defined media. A preferred host is Bacillus subtilis. Purification is made easier because the unwanted proteins are usually at level(s) lower than the target protein reducing the amount of contaminants to separate from this protein.
  • the protocol is as follows:
  • Refrigeration of this media will help storage life, but it has been found that after ⁇ 1.5 to 2 months the MOPS media production level (for protease) decreases.
  • Shake Flask conditions Using sterilized (e.g., autoclaved) shake flasks(bottom baffled are best for aeration of culture) use a 10 to 20% liquid volume(eg 50 mL in a 250 mL shake flask or 300 mL in a 2800 mL Fernbach)). For example, for protease production a 10 to 15% volume works well, for amylase production a 20% volume works well.
  • Inoculation and Growth Cultures should be inoculated from thawed and mixed glycerol stocks (which were made in the Mops/Urea media prior to the labeling experiment) at the level of 150 ⁇ L per 250 mL shake flask or 1 vial(l.5 mL) per 2800 mL shake flask. Once inoculated the cultures should be grown at 37° C. and 325 to 350 rpm for ⁇ 60 hrs (spo ⁇ host, cutinase production), ⁇ 72hrs (spo ⁇ host) for protease production and ⁇ 90 hrs (spo+ host or amylase production), to achieve a maximum yield.
  • the cultures should be harvested as the titers will only decrease and background biopolymers and by products will make the purification/isolation more difficult.
  • the material may be centrifuged at a high rpm (e.g., 12,000 rpm for 250 mL bottles) for 30 minutes. Filter the supernatants through 0.8 micron filters (Nalgene or Corning 1 L units are preferred). Measure the total titer of this supernatant.
  • the cell pellets can be saved, stored at ⁇ 70° C., and used in future experiments as all of this material is labeled with 15 N.
  • This step should be done in a cold room (4° C.) to minimize recovery loss.
  • Use 400 mL stirred cell(s) (Amicon 8400 series, 76 mm diameter membranes) with a 10,000MWCO membrane (PM, polysulfone, is best, but may retain hydrophobic molecules).
  • PM polysulfone
  • Add 350 mL of the supernatant to each of the stirred cells it is assumed that at least 1000 mL of supernatant is available.
  • This volume should be measured and an (activity) assay done to check the concentration of the labeled protein so that the total labeled protein available can be calculated (assays can be done on the permeate(s) to check for loss, also this material can be frozen away because all the protein components are labeled).
  • the concentrated material should be dialyzed into an appropriate buffer system (if not the sample is ready to be run using the desired chromatographic method/system that will give the best yield of pure 15 N biopolymer).
  • This is set up with dialysis tubing of 10,000MWCO (SpectraPor 7, 32 mm), filling the tubing with the concentrate, never more than 75 mL per tube, clamping off the set up and put into a graduated cylinder (in the 4° C. cold room) filled with buffer (20 mM MES, pH 5.5, 1 mM CaCl 2 works well for most applications) on a stir plate (slowly stirring).
  • the quantity of buffer used is between 20 to 50 times the volume of concentrate being dialyzed, and fresh buffer should be used after 4 hours to ensure a good dialysis. It works best to let the sample dialyze overnight in the second buffer exchange. When done the sample should be removed from the dialysis tubing very carefully so that all the protein is recovered. At this point the sample should be filtered with a 0.45micron filter unit, activity assays should be done along with a volume measurement.
  • ion-exchange chromatography is the preferred method used to separate the labeled proteins from their matrix and works best if the PI of the target protein is known.
  • the two pH ranges we have worked with so far is either pH 6.0 or pH 8.0, this involves using a cation exchange resin for binding the target protein and a salt (NaCl) gradient for elution of this protein.
  • the load onto the column should be 25 to 35 per cent of the total column capacity, a 25 cv (column volume) wash with the running buffer and a 50 to 100 cv elution gradient where the eluate is collected in fractions. This ensures that the majority of the contaminants are eliminated from the protein sample fractions which will be pooled and assayed. At this point the pool is concentrated using a stirred cell in the cold room (4° C.) and buffer exchanged/diafiltered to make another run using the either the same chromatographic procedure or a complimentary procedure involving conservative fractionation of the eluate.
  • the pooled target biopolymer should be buffer exchanged while concentrating the sample in the buffer system that will be used for sample storage, whether frozen at minus20° C. or formulated for future use.
  • the amount of concentration of the sample is determined by the desired final biopolymer concentration that is needed in future use.
  • the target biopolymer or analog, produced in isotope-labeled form either by synthesis or in vivo, can be purified by any means known in the art.
  • some extracellular alkaline proteases of microbial origin can be obtained in pure form by a single cation exchange chromatography step at pH 7.8 to 8.0 (Christianson and Paech, 1994).
  • extracellular alkaline proteases can be obtained in pure form by cation exchange chromatography at pH 5.5 to 5.8 (Hsia et al., 1996), and yet other enzymes and proteins can be purified using one or more similar or different separation techniques, such as anion exchange, affinity, or hydrophobic interaction chromatography, size-exclusion chromatography, chromatofocusing, preparative isoelectrofocusing, precipitation, ultrafiltration, and others (for overviews see Deutscher, 1990, Scopes, 1994, and Janson and Ryden, 1998).
  • Peptides of specific sequence can be synthesized by standard techniques, purified by reverse-phase chromatography (RP-HPLC).
  • the protein or peptide is purified, a proof of purity can be ascertained, e.g. by SDS-PAGE for proteins, by RP-HPLC for peptides, the protein or peptide concentration can be determined by quantitative amino acid analysis, by total nitrogen analysis, by weight, or by light absorbance of the denatured protein (provided the amino acid sequence is known).
  • a solution of purified protein or peptide of known protein mass content is called a ‘calibrated solution’.
  • the solution can be stabilized, as desired, by refrigeration, freezing, or by additives such as polyols and saccharides (1,2-propanediol, glycerol, sucrose, etc.), salt (sodium chloride, ammonium sulfate, etc.), and buffers adjusted to the pH of optimal stability.
  • additives such as polyols and saccharides (1,2-propanediol, glycerol, sucrose, etc.), salt (sodium chloride, ammonium sulfate, etc.), and buffers adjusted to the pH of optimal stability.
  • the activity used in the practice of the present invention to fragment a protein into smaller fragments can be any enzyme or chemical activity which is capable of repeatedly and accurately cleaving at particular cleavage sites. Such activities are widely known and a suitable activity can be selected using conventional practices.
  • Examples of such enzyme or chemical activities include the enzyme trypsin which hydrolyzes peptide bonds on the carboxyl side of lysine and arginine (with the exception of lysine or arginine followed by proline), the enzyme chymotrypsin which hydrolyzes peptide bonds preferably on the carboxyl side of aromatic residues (phenylalanine, tyrosine, and tryptophan), and cyanogen bromide (CNBr) which chemically cleaves proteins at methionine residues. Trypsin is often a preferred enzyme activity for cleaving proteins into smaller pieces, because trypsin is characterized by low cost and highly reproducible and accurate cleavage sites. Techniques for carrying out enzymatic digestion are widely known in the art and are generally described by Allen, 1989, Matsudaira, 1993, Hancock, 1996, and Kellner et al., 1999.
  • restriction enzymes used herein are commercially available and their reaction conditions, cofactors and other requirements would be known to the ordinarily skilled artisan.
  • 1 ⁇ g of plasmid or DNA fragment is used with about 2 units of enzyme in about 20 ⁇ l of buffer solution.
  • isolating DNA fragments typically 5 to 50 ⁇ g of DNA are digested with 20 to 250 units of enzyme in a larger volume.
  • Appropriate buffers and substrate amounts for particular restriction enzymes are specified by the manufacturer. Incubation times of about 1 hour at 37° C. are ordinarily used, but may vary in accordance with the supplier's instructions. After digestion the reaction is electrophoresed directly on a polyacrylamide gel to isolate the desired fragment.
  • a chromatographic column comprising a chromatographic medium capable of fractionating the peptide digests as they are passed through the column.
  • Preferred chromatographic techniques include, for example, reverse phase, anion or cation exchange chromatography, open-column chromatography, and high-pressure liquid chromatography (HPLC).
  • HPLC high-pressure liquid chromatography
  • Other separation techniques include capillary electrophoresis, and column chromatography that employs the combination of successive chromatographic techniques, such as ion exchange and reverse-phase chromatography.
  • precipitation and ultrafiltration as initial clean-up steps can be part of the peptide separation protocol. Methods of selecting suitable separation techniques and means of carrying them out are known in the art.
  • precipitation, ultrafiltration, and reverse-phase HPLC are preferred separation techniques.
  • any suitable separation technique can be used to resolve the polynucleotide fragments.
  • size-based analysis of polynucleotide samples relies upon separation by gel electrophoresis (GEP).
  • GEP gel electrophoresis
  • Capillary gel electrophoresis (CGE) may also be used to separate and analyze mixtures of polynucleotide fragments having different lengths, e.g., the different lengths resulting from restriction enzyme cleavage.
  • the polynucleotide fragments which differ in base sequence, but have the same base pair length are resolved by techniques known in the art.
  • DGGE denaturing gradient gel electrophoresis
  • DGGC denaturing gradient gel capillary electrophoresis
  • MIPC Matched Ion Polynucleotide Chromatography
  • Any suitable mass spectrometry instrumentation can be used in practicing the present invention, for example, an electrospray ionization (ESI) single or triple-quadrupole, or Fourier-transform ion cyclotron resonance mass spectrometer, a MALDI time-of-flight mass spectrometer, a quadrupole ion trap mass spectrometer, or any mass spectrometer with any combination of source and detector.
  • ESI electrospray ionization
  • MALDI time-of-flight mass spectrometer a quadrupole ion trap mass spectrometer
  • any mass spectrometer with any combination of source and detector for example, an electrospray ionization (ESI) single or triple-quadrupole, or Fourier-transform ion cyclotron resonance mass spectrometer, a MALDI time-of-flight mass spectrometer, a quadrupole ion trap mass spectrometer, or any mass spectrometer with
  • Gapped BLAST is utilized as described in Altschul et al. (Nucleic Acids Res. 25:3389-3402,1997).
  • the default parameters of the respective programs e.g., XBLAST and NBLAST. See http://www.ncbi.nlm.nih.gov.
  • a biopolymer or biopolymer fragment is said to “correspond” to an analog thereof when the biopolymer/fragment and analog have similar chemical and physical properties, but differ in at least one chemical or physical property.
  • an analog of a target polypeptide can comprise a polypeptide having an amino acid sequence identical to that of the target, the analog being formed, however, from amino acids that differ isotopically from those making up the target polypeptide.
  • the polypeptide analog can be isotopically identical to the target in terms of its amino acid content, but have an amino acid sequence that is homologous, but not identical, to the sequence of the target (e.g., the analog can have one or more amino acid substitutions, insertions, or deletions (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 substitutions)).
  • the analog shares at least 90, 95, and/or 98 percent homology with the target biopolymer.
  • the analog can be derivatized (e.g., tagged) in a fashion so as to alter at least one chemical or physical property as compared to the target.
  • the analog differs from the biopolymer is not critical, provided only that the two are capable of producing a pair of peaks that can be distinguished one from the other, yet which occur relatively close to one another, in mass spectrographic analysis (i.e., a peak pair can be identified attributable to the target and analog).
  • a purified, isotope-labeled, calibrated form (analog) of a target protein is added to a solution (e.g., a cell extract) known or believed to contain the target protein.
  • a solution e.g., a cell extract
  • the resulting mixture is subjected in its entirety to rapid protein fragmentation, e.g., by trypsin digestion.
  • the resulting peptides are briefly separated, e.g., by reverse-phase chromatography, and the eluting peptides are monitored by mass spectrometry.
  • the ratio of integrated peak areas of a reconstructed ion current chromatogram of corresponding peptides provides a direct measure for the molar concentration of the unknown concentration of the known protein.
  • Example 1 As detailed in Example 1, the inventors have tested such a method with 15 N- Bacillus lentus subtilisin-N76D-S103A-V104I ( 15 N-subtilisin-DAI), and accurately determined the unknown concentrations of subtilisin-DAI to ⁇ 5%. In other experiments, correct concentrations were obtained with a standard-to-target mass ratio of up to 10:1, with as low as 2 ⁇ g ⁇ ml ⁇ 1 and as little as 2 ⁇ g of target protein (see Table II). In yet another experiment, the fragmentation time was reduced to 1 min, and the total chromatography cycle was limited to 20 min (see FIG. 3).
  • the methods of the present invention can be applied to unknown (putative) polypeptides, as well. Analysis of such polypeptides can be accomplished, for example, using synthetic isotope-labeled peptides, or by calibrating an isotope-labeled cell extract with peptides of natural abundance atomic composition. In an embodiment of the latter, a putative protein of interest is selected using one or more available databases and software tools.
  • sequence libraries can be used, including, for example, the GenBank database (now centered at the National Center for Biotechnology Information, Bethesda, summarized by Burks et al., 1990), EMBL data library (now relocated to the European Bioinformatics Institute, Cambridge, UK, summarized by Kahn and Cameron, 1990), the Protein Sequence Database and PIR-International (summarized by George et al., 1996), and SWISS-PROT (described in Bairoch and Apweiler, 2000).
  • GenBank database now centered at the National Center for Biotechnology Information, Bethesda, summarized by Burks et al., 1990
  • EMBL data library now relocated to the European Bioinformatics Institute, Cambridge, UK, summarized by Kahn and Cameron, 1990
  • the Protein Sequence Database and PIR-International summarized by George et al., 1996)
  • SWISS-PROT described in Bairoch and Apweiler, 2000.
  • a theoretical fragmentation e.g. trypsin digest
  • MS-Digest for example, (available at http://prospector.ucsf.edu/) allows for the “in silico” digestion of a protein sequence with a variety of proteolytic agents including trypsin, chymotrypsin, V8 protease, Lys-C, Arg-C, Asp-N, and CNBr.
  • the program calculates the expected mass of fragments from these virtual digestions and allows the effects of protein modifications such as N-terminal acetylation, oxidation, and phosphorylation to be considered. From the theoretical fragmentation, a suitable peptide is selected, which can then be synthesized and calibrated. The suitability of the peptide can be checked by querying the genome of interest for redundancy. If the same peptide (string of amino acid residues) occurs on more than one protein then another peptide should be selected.
  • the organism can be grown on isotope-enriched media.
  • the nitrogen content of the media is enriched in 15 N.
  • the calibrated peptide is added to a protein extract from the cells, and the entire mixture is digested rapidly and ‘cleaned up’; for example, and without limitation, by precipitation, ultra-filtration, or ion exchange chromatography.
  • the choice of an optimal technique can be tailored by the skilled artisan to the properties of the peptide (size, charge, hydrophic index, etc.) since these features can be established prior to the use of the peptide as an internal standard.
  • the resulting ‘lean’ solution is passed over a RP-HPLC column attached to a mass spectrometer.
  • the skilled artisan can focus the separation and the mass measurement on a very narrow window, both in time and mass, and thereby tremendously increase the sensitivity of the detection. If the expected peak pair is found (wild-type from internal standard, 15 N from organism), peak area integration yields the absolute concentration of the targeted protein. Preferably, in this embodiment, a series of experiments is carried out, as appropriate, to assure that the fragmentation of the target protein is substantially complete with respect to the peptide of interest.
  • the 15 N-labeled extract can be queried for any number of proteins, even simultaneously, as long as mass and retention times can be properly spaced.
  • the just-described method provides a calibrated 15 N-labeled protein mixture (cell extract) that can be conserved (e.g., in small aliquots) for later use.
  • a calibrated 15 N-labeled cell extract the organism can be grown under defined conditions, and extracts queried for the presence, for an increase or decrease of the absolute concentration of the target protein by mixing it with the calibrated 15 N-labeled aliquot.
  • the digest does not have to be quantitative as long as a little of the fragment of the molecule of interest is formed. Analysis can be carried out by LC/MS as above.
  • any protein other than the target proteins can be quantified relative to the level in the isotope-labeled sample similar to the approach taken by others using isotope labeling (Oda et al., 1999) and reporter groups (Gygi et al., 1999).
  • the teachings herein can be adapted to a number purposes.
  • the selected target can be a polymer of nucleotides, e.g., one or more polynucleotides and/or oligonucleotides.
  • a target oligonucleotide is selected for analysis and an analog of the target oligonucleotide is generated.
  • the target oligonucleotide can be, for example, an oligonucleotide that is known to be in a mixture, a putative oligonucleotide (e.g., derived from a genome database search) that is potentially present in a mixture, or a known or putative oligonucleotide segment or fragment.
  • the analog of the target oligonucleotide can be the target oligonucleotide itself or a unique segment or fragment of the target oligonucleotide.
  • One or the other of the target oligonucleotide and analog is labeled, using methods known in the art (e.g., 32 P labeling), so that the two can be distinguished from one another in subsequent mass analysis.
  • the analog is purified and its absolute quantity is determined in a solid quantity or in a solution by standard techniques (the analog is now said to be ‘calibrated’), and a known amount is employed as an internal standard in the solution to be assayed.
  • the oligonucleotides of the mixture are treated with a fragmenting activity (e.g., an endonuclease), and the oligonucleotide fragments of the mixture are then resolved.
  • Corresponding oligonucleotide fragment pairs are then analyzed by selected ion monitoring of a mass spectrometer. Peak area integration of such pairs provides a direct measure for the amount of target oligonucleotide in the crude solution.
  • the present teachings can be adapted for the identification of a target biopolymer fragment in a crude solution or mixture.
  • a fragment of a target protein is identified in a solution otherwise not including such fragment (i.e., the fragment to be identified is not natively present in the solution)
  • a selected fixed ratio of an analog of the target protein and the target protein are added to the solution.
  • the target protein and analog are then subjected to fragmentation, e.g., by treatment with a fragmenting activity, thereby generating a plurality of corresponding peptide pairs.
  • the peptide fragments are then resolved, e.g., by way of a suitable chromatographic technique.
  • Mass spectrometric analysis is then employed to identify those fragment pairs corresponding to the target protein that exhibit the selected ratio.
  • the fragments that arose from the target protein are identified via their characteristic (selected) mass ratio.
  • the fragment pairs exhibiting the selected ratio can then be sequenced using any suitable technique, e.g., utilizing further mass spectrometric analysis, database query, etc. (see, e.g., Lahm and Langen, 2000; Corthals et al., 1999).
  • Bacillus lentus subtilisin-N76D-S103A-V104I (subtilisin DAI) was expressed by Bacillus subtilis grown on minimal media and 15 N-urea as nitrogen source. The protein was purified (Goddette et al., 1992; Christianson and Paech, 1994) and calibrated by amino acid analysis and by active site titration (Hsia et al., 1996) as described previously.
  • FIG. 1 UV traces of a tryptic co-digest of 15 N-subtilisin DAI and subtilisin. Peptides are numerated in the order of occurrence beginning with the N-terminus (see Table I).
  • FIG. 2 (A) Integrated total ion current (TIC) chromatogram of peptide 3 of subtilisin (indexed (s)) and 15 N-subtilisin DAI (indexed ( 15 N). (B) TIC of peptides 5, 6 and 9 of 15 N-subtilisin DAI and subtilisin. The results of area integration for both TIC and UV peaks are summarized in Table I. Note that sequence differences of subtilisin and subtilisin-DAI reside on peptide 5 (N74D) and 6 (S101I, V102A). Amino acid sequence numbering is linear.
  • Table I Sequence comparison, m/z values, and ratios of integrated TIC peak areas and UV absorbance peak areas for chromatograms in FIG. 1.
  • concentration measured by the co-digest technique for subtilisin and subtilisin-DAI was 8.15 and 7.13 mg/ml, respectively, while the given concentration (established by independent methods) was 7.99 and 7.03 mg/ml, respectively.
  • FIG. 4(A) shows an SDS-PAGE gel of the composition of the sample.
  • FIG. 4(B) displays the peptide map, and
  • FIG. 5 gives a few examples of TIC traces. The data show that the sample contains an alkaline serine protease closely related to subtilisin BPN′, and in this case, specifically at 0.54 mg ⁇ ml ⁇ 1 .
  • subtilisin-DAI Randomly generated variants of subtilisin-DAI were expressed by cultures grown on minimal media in microtiter plates. Aliquots of cell-free supernatants were probed for the presence of subtilisin-DAI variants by co-digests with 15 N-labeled subtilisin-DAI. In separate experiments the catalytic activity was measured. In yet another experiment, the ratio of specific concentration to activity (referred to as ‘conversion factor’ f) was measured by active site titration with a mung bean inhibitor (MBI) solution calibrated in the same experiment with a previously standardized solution of subtilisin-DAI (Hsia et al., 1996). The data shown in Table II show convincingly the accuracy of the peptide mapping method for protein concentration measurements.
  • conversion factor conversion factor
  • a further advantage of the technique is that the protein variants can be queried for similarities and approximate location of mutations. Because all peptides of the internal standard are known, each can be checked for the presence of the unlabeled counterpart. If not present the target protein has a mutation on that sequence. Next one would search for a peptide of closely related mass and verify that it exists in the quantity, anticipated from the quantity of those peptides identical in sequence with the internal standard, using the UV trace.
  • This example describes a method for the batch preparation of a 15 N-labeled protease.
  • the Mops/Urea shake flask protocol (described above) was used with all of the chemicals, except for the urea, purchased from Sigma chemical in highest purity available.
  • 15 N 2 Urea(99 atom %) was purchased from Isotec,Inc.
  • a 1.8 L batch of media was prepared with chloramphenicol at 25 ppm and sterile filtered. 300 mL was added aseptically to each of the 6 sterilized 2.8 L bottom baffled fernbachs.
  • the inoculation was done by adding the thawed and mixed glycerol stocks, protease hyper producer prepared previously in the Mops/urea media and frozen, at 1vial(1.5 mL) per shake flask.
  • the shake flasks were put into a New Brunswick shaker/incubator, after inoculation, and run at 37° C. and 350 rpm for 78 hours.
  • MPF activity assays were done on the samples and titers ranged from 0.7 g/L to 1 .4 g/L.
  • the contents from the shake flasks were pooled together, pH adjusted to 5.5 with acetic acid and centrifuged in 250 mL bottles at 12,000 rpm for 30 minutes.
  • the supernatants were filtered with a 0.8 micron Nalgene 1 L filter unit.
  • the pool was assayed at 1.1 g/L for 1700 mL with the total 15 N protease being 1.9 gms.
  • the supernatant was concentrated in the cold room (@4° C.) to 135 mL, using 3 Amicon 8400 stirred cells and PM10 (10,000MWCO) membranes. There was no loss of protein in the concentration step.
  • Dialysis was done using 20 mM MES, pH 5.4, 1 mM CaCl 2 buffer in a 15 L graduated cylinder on a stir plate in the cold room, with the sample being added in two 67.5 mL aliquots respectively to 10,000MWCO Spectra Por 7 dialysis tubing, clamped off and placed into the cylinder with buffer. After the overnight dialysis the samples were removed from the graduated cylinder, the clamps removed from the dialysis tubing and the contents poured into and filtered using a 0.45 micron Nalgene 500 mL filter unit. Assays run at this time showed no loss of protein at 1.9 gm total available in 250 mL.
  • protease protein was purified using a low pH buffer system with a cation exchange column because the PI of the enzyme is around 8.6.
  • An Applied Biosystems Vision was used to do the purification along with a 16 ⁇ 150 mm (32 mL) column of POROS HS 20 (Applied Biosystems cation exchange resin).
  • the program used to do the purification is as follows: Equilibrate the column at 50 mL/minute with 20 cv's (colume volumes) of 20 mM MES, pH 5.4, 1 mM CaCl 2 buffer, load the sample (150 mL) onto the column at 15 mL/minute, wash the column at 50 mL/minute with a gradient from the 20 mM MES, pH 5.4, 1 mM CaCl 2 buffer to 20 mM MES, pH 6.2, 1 mM CaCl 2 buffer in 25 cv's.
  • the labeled protease was concentrated from 1.8 L to 150 mL using an Amicon stirred cell with a 10,000MWCO PM membrane, with a buffer exchange/diafiltration to 20 mM MES, pH 5.4, 1 mM CaCl2 to prepare the sample for another run on the same system with the same method. Some of the labeled protease was lost because of the cuts made on the fractions collected, with the total available 15 N protease down to 1 .4 gm. After three more runs the purification was done. There was a pool of purified material with a 1.3 L total volume.
  • the present invention is useful where only very dilute concentrations of biopolymer are available for analysis.
  • quantity for example, the present invention can be employed to determine the absolute quantity of a selected protein in a solution containing less than 25, less than 20, less than 15, less than 10, less than 5, and down to about 2 micrograms, or less, of such protein.
  • concentration the present invention can be employed to determine the absolute quantity of a selected protein in a solution containing less than 25, less than 20, less than 15, less than 10, less than 5, and down to about 2 micrograms/ml, or less, of such protein.

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