# Patent

## Title
Methods and compositions for detecting thyroglobulin in a biological sample

## Abstract

The invention provides a method and reagents for determining the presence and/or amount of human thyroglobulin in a biological sample. In one embodiment, the method comprises (a) digesting a biological sample containing proteins to provide peptide fragments; (b) contacting the digested sample with a binding reagent comprising a plurality of antibodies that are capable of binding to at least one thyroglobulin peptide fragment; and (c) determining the presence and/or amount of the thyroglobulin peptide fragments that are bound to the binding reagent. In some embodiments, the binding reagent comprises a plurality of antibodies capable of binding to at least one thyroglobulin peptide fragment set forth in TABLE 1. In some embodiments, the binding regent comprises a plurality of antibodies capable of binding to at least one thyroglobulin peptide selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application claims the benefit under 35 U.S.C. §119 of U.S. Provisional Application No. 60/943,758, filed Jun. 13, 2007, which is hereby incorporated by reference.


FIELD OF THE INVENTION
This invention relates to methods and reagents for determining the presence and/or amount of human thyroglobulin in a biological sample.
BACKGROUND
This invention relates to methods and compositions for detecting thyroglobulin in a biological sample. Thyroglobulin, which is secreted from functioning thyroid tissue, is very useful as a tumor marker in the diagnosis of recurrent, residual, and metastatic thyroid cancer. The presence of thyroglobulin in the plasma/serum of patients indicates functioning thyroid tissue. Following surgery and treatment with radioactive iodine, patients with thyroid cancer should be free of all functioning thyroid tissue. Detectable thyroid tissue in these patients indicates the need for further therapy.
However, quantitation of thyroglobulin using immunoassays is problematic. Current methods of detection utilizing immunoassays, or antibody-based assays, to quantitate intact protein in patient serum samples are complicated by several limitations. Immunoassays for thyroglobulin are affected by patient autoantibodies to thyroglobulin, patient antibodies to reagent antibodies, reagent antibody saturation with analyte, and lack of standardization (Hoofnagle, A., and M. H. Wener, Clin Lab Int 8:12-14 (2006)). Patient autoantibodies to thyroglobulin bind to thyroglobulin epitopes, or surface features of the protein, and interfere with reagent antibodies binding to the thyroglobulin analyte in the assay, causing falsely low concentrations of thyroglobulin to be measured by traditional “sandwich” immunoassays and falsely high concentrations of thyroglobulin in radioimmunoassays. Some patients have antibodies to reagent immunoglobulins, also called human anti-mammalian antibodies, which can cause an erroneously positive result. For example, approximately 10% of patients have antibodies to thyroglobulin (Tg) that could potentially interfere with immunoassays (Kloos, R. T., et al., J. Clin Endocrinol Metab 90:5047-5057 (2005); Spencer, C. A., Clin Chem 42:661-663 (1996); Spencer, C. A., et al., J. Clin Endocrinol Metab 89:3702-3704 (2004)). The prevalence of Tg autoantibodies increases to 25% in patients with differentiated thyroid carcinoma (Ericsson, U. B., et al., Clin Immonol Immunopathol 37:154-162 (1985); Spencer, C. A., et al., J. Clin Endocrinol Metab 83:1121-1127 (1998); Okosieme, O. E., et al., Clin Chem 52:729-734 (2005)).
In certain cases, very high concentrations of thyroglobulin saturate the reagent antibodies used in immunoassays and prevent formation of tripartite reagent immunoglobulin-antigen complexes, resulting in falsely low concentrations of thyroglobulin to be measured. Lastly, because all immunoassays use different antibodies generated independently by each company, there is suboptimal standardization of thyroglobulin immunoassays, and results from one immunoassay may not be in accord with the results of another.
Therefore, a need exists for improved methods and compositions for the detection of thyroglobulin in order to more accurately detect residual, recurrent, or metastatic disease in patients afflicted with thyroid cancer.
SUMMARY
This summary is provided to introduce a selection of concepts in a simplified form that are further described below in the Detailed Description. This summary is not intended to identify key features of the claimed subject matter, nor is it intended to be used as an aid in determining the scope of the claimed subject matter.
In one aspect, the invention provides a method for determining the presence or amount of human thyroglobulin in a biological sample. The method comprises (a) digesting a biological sample containing proteins to provide peptide fragments; (b) contacting the digested sample with a binding reagent comprising a plurality of antibodies that are capable of binding to at least one thyroglobulin peptide fragment; and (c) determining the presence or amount of the thyroglobulin peptide fragments that bound to the binding reagent. In some embodiments, the binding reagent comprises a plurality of antibodies capable of binding to at least one thyroglobulin peptide fragment set forth in TABLE 1. In some embodiments, the binding reagent comprises a plurality of antibodies capable of binding to at least one thyroglobulin peptide selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5.
In another aspect, the invention provides a composition comprising at least one thyroglobulin peptide fragment consisting of SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:5. In some embodiments, the thyroglobulin peptide fragment is conjugated to keyhole limpet hemocyanin. In some embodiments, the composition further comprises an adjuvant for inducing an immune response in a mammalian subject.
In another aspect, the invention provides an isolated antibody which binds to a thyroglobulin peptide fragment having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5. In some embodiments, the invention provides a composition comprising a combination of a plurality of first antibodies and a plurality of second antibodies, the first and second antibodies capable of binding to a different amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3 and SEQ ID NO:5.
In another aspect, the invention provides a kit comprising (a) a plurality of antibodies that are capable of binding to at least one thyroglobulin peptide fragment; and (b) a reagent comprising trypsin. In some embodiments, the kit further comprises an internal standard reagent. In some embodiments, the kit comprises a plurality of antibodies that are capable of binding to at least one thyroglobulin peptide fragment set forth in TABLE 1.
In another aspect, the invention provides a method for monitoring the efficacy of treatment of a human thyroid cancer patient. The method comprises (a) digesting a biological sample containing protein obtained from the human thyroid cancer patient to provide peptide fragments; (b) contacting the digested sample with a binding reagent comprising a plurality of antibodies that are capable of binding to at least one thyroglobulin peptide fragment; and (c) determining the presence or amount of the thyroglobulin peptide fragments that bound to the binding reagent, wherein the detection of the presence of thyroglobulin peptide fragments indicates the need for further treatment. In some embodiments, the binding reagent comprises a plurality of antibodies capable of binding to at least one thyroglobulin peptide fragment set forth in TABLE 1. In some embodiments, the binding regent comprises a plurality of antibodies capable of binding to at least one thyroglobulin peptide selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3 and SEQ ID NO:5.



DESCRIPTION OF THE DRAWINGS
The foregoing aspects and many of the attendant advantages of this invention will become more readily appreciated as the same become better understood by reference to the following detailed description, when taken in conjunction with the accompanying drawings, wherein:
FIG. 1 shows the protein sequence of human thyroglobulin with representative peptides underlined that are useful for practicing various embodiments of the methods of the invention, as described in Examples 1-6;
FIG. 2 graphically illustrates the quantitation of thyroglobulin in digested human serum in accordance with an embodiment of the method of the invention, as described in Example 3;
FIG. 3 graphically illustrates the results of the experiment carried out to quantify the amount of thyroglobulin in the international certified reference material (BCR-457), as described in Example 4;
FIG. 4A graphically illustrates the elution profile of the internal standard (VIFDANAPV*AVR)(SEQ ID NO:2) where V* represents 13C5, 14N-labeled valine);
FIG. 4B graphically illustrates the fragment ion spectra collected in the linear ion trap of the mass spectrometer for the internal standard (VIFDANAPV*AVR)(SEQ ID NO:2) where V* represents 13C5, 14N-labeled valine);
FIG. 4C graphically illustrates the elution profile of endogenous peptide SEQ ID NO:2 purified from a digest of human serum;
FIG. 4D graphically illustrates the fragment ion spectra collected in the linear ion trap of the mass spectrometer for the endogenous peptide SEQ ID NO:2;
FIG. 4E graphically illustrates the elution profile of endogenous peptide SEQ ID NO:3 purified from a digest of human serum;
FIG. 4F graphically illustrates the fragment ion spectra collected in the linear ion trap of the mass spectrometer for the endogenous peptide SEQ ID NO:3;
FIG. 4G graphically illustrates the elution profile of endogenous peptide SEQ ID NO:5 purified from a digest of human serum;
FIG. 4H graphically illustrates the fragment ion spectra collected in the linear ion trap of the mass spectrometer for the endogenous peptide SEQ ID NO:5, as described in Example 4;
FIG. 5A graphically illustrates the response (peak area of endogenous peptide SEQ ID NO:2/peak area internal standard peptide) detected in a dilution series of a human serum sample containing 319 ng/mL Tg, as described in Example 5;
FIG. 5B graphically illustrates the response (peak area of endogenous peptide SEQ ID NO:3/peak area internal standard peptide) detected in a dilution series of a human serum sample containing 319 ng/mL Tg, as described in Example 5;
FIG. 5C graphically illustrates the response (peak area of endogenous peptide SEQ ID NO:5/peak area internal standard peptide) detected in a dilution series of a human serum sample containing 319 ng/mL Tg, as described in Example 5;
FIG. 6A graphically illustrates a comparison between the Tg detection results obtained from a Beckman Access 2 assay x-axis) and the results obtained from the immunoaffinity enrichment and LC-MS/MS assay for peptide SEQ ID NO:3 (y-axis), as described in Example 6; and
FIG. 6B graphically illustrates the residuals of each data point from the regression line shown in FIG. 6A, wherein the standard error of the residuals (Sy/x) was determined to be 3.914, as described in Example 6.



DETAILED DESCRIPTION
Unless specifically defined herein, all terms used herein have the same meaning as they would to one skilled in the art of the present invention.
As used herein, the term “peptide fragment” refers to any portion of a protein, such as thyroglobulin, which can be produced by a reproducible fragmentation process, such as digestion with a protease (e.g., trypsin).
As used herein, the term “antibody” refers to any of the classes of immunoglobulin molecules of any species, or any molecules derived therefrom, or any other specific binding agents constructed by variation of a conserved molecular scaffold so as to specifically bind a protein such as thyroglobulin and/or one or more peptide fragment(s) thereof. Exemplary antibodies include polyclonal, monoclonal and recombinant antibodies.
As used herein, the term “anti-peptide antibody” refers to any type of antibody (in the preceding general sense) that binds to a peptide fragment for the purposes of enrichment and/or detection of the peptide fragment from a biological sample or processed sample.
As used herein, the term “bind” or “binding” includes any physical attachment or close association, which may be permanent or temporary.
The human thyroglobulin polypeptide (SEQ ID NO:1, shown in FIG. 1) is a very large macromolecule with an apparent molecular weight of approximately 660 kDa. The predicted mass of one monomer of the homodimeric antigen is only 302 kDa. Post-translational modifications account for the remainder. These post-translational modifications include oxidation and iodination of tyrosine residues, which occurs as thyroglobulin is modified into the thyroid hormones triiodothyronine and thyroxine. Thyroglobulin exists predominantly in the colloid of the thyroid gland where it serves as a reservoir for the thyroid hormones released upon TSH stimulation of the gland. It leaks into the lymphatics surrounding functioning thyroid tissue, which subsequently circulates in the plasma. In addition, thyroglobulin is modified by phosphorylation at serine and tyrosine residues, by sulphation, and by O- and N-linked glycosylation, which may also be sulphated and phosphorylated. Importantly, around 10% of plasma thyroglobulin mass is composed of variable carbohydrate moieties. (Hoofnagle, A., and M. H. Wener, CLI 8:12-14 (2006).)
The present inventors have identified specific peptide fragments of thyroglobulin that can be detected and/or measured individually or in combination as a surrogate for the abundance or concentration of thyroglobulin in a biological sample, such as human serum. The inventors have further demonstrated that the identified specific peptides from thyroglobulin can be directly identified and quantitated as fragment ions with the correct mass that are derived from ions of correct precursor mass of an intact peptide using a suitable mass spectrometer. To help improve the sensitivity of the approach, antibodies have been generated against three of these specific peptide fragments of thyroglobulin, and these anti-peptide antibodies have been used to bind to and enrich the corresponding peptide fragments in a complex mixture of serum/plasma peptides. The use of anti-peptide antibodies to detect thyroglobulin removes the problematic interference of endogenous antibodies. In addition, because thyroglobulin peptide is directly detected using mass spectrometry rather than thyroglobulin protein being detected indirectly using antibodies, this embodiment of the method of the invention solves the problem of standardization and “hook effect” present in traditional immunoassays. Therefore, the methods and compositions provided in accordance with various embodiments of the invention may be used as a reference method for the detection of thyroglobulin in biological specimens that can be as a reference standard for comparison to results of other methods of detection of thyroglobulin and thereby improve the accuracy of detection of residual, recurrent, or metastatic disease in patients afflicted with thyroid cancer.
In accordance with the foregoing, in one aspect the invention provides a method for determining the presence or amount of human thyroglobulin in a biological sample. The method comprises (a) digesting a biological sample containing proteins to provide peptide fragments; (b) contacting the digested sample with a binding reagent comprising a plurality of antibodies that are capable of binding to at least one thyroglobulin peptide fragment; and (c) determining the presence or amount of the thyroglobulin peptide fragments that bound to the binding reagent.
The methods of the invention can be used to detect and/or measure the concentration of human thyroglobulin in any biological sample that contains protein, such as, for example, but not limited to, human blood, serum, plasma, cerebrospinal fluid, ascites, pleural effusions, pericardial effusions, and other biological fluids. In some embodiments of the method, the biological sample is human serum.
In accordance with the methods of the invention, the biological sample is digested into peptide fragments. The sample may be digested with any reagent that reproducibly generates a set of peptide fragments, such as a protease. Exemplary proteases that may be used in the methods of the invention include trypsin, endoproteinase Glu-C, endoproteinase Lys-C, endoproteinase Asp-N, pepsin, and staphylococcus protease V8.
In one embodiment of the invention, the biological sample is digested with trypsin under the appropriate conditions and for a period of time sufficient to generate peptide fragments. Any trypsin capable of reliably cleaving serum/plasma proteins would be sufficient. Trypsin preparations that may be used in the methods of the invention are commercially available, for example, from Sigma-Aldrich, Inc., or Promega, Inc. Prior to digestion, the trypsin may be optionally methylated with a methylating agent in order to render the protease resistant to self-cleavage. In accordance with various embodiments of the invention, TABLE 1 describes an incomplete set of peptide fragments (SEQ ID NOS:2-29) that are obtained from tryptic digestion of human thyroglobulin (SEQ ID NO:1).
In some embodiments, the trypsin digest is carried out in the presence of a non-ionic detergent, such as Tween 20, Tween 40, Tween 80 or Octyl-beta-D-glucopyranoside (ProClin®) at an amount from about 0.05% (w:v) to about 0.005% (w:v). In some embodiments, the trypsin digest is carried out in the presence of from about 0.05% (w:v) to about 0.005% (w:v) of Tween 20.
Once the biological sample is digested to provide peptide fragments, the digested sample is contacted with a binding reagent comprising a plurality of antibodies that are capable of binding to at least one thyroglobulin peptide fragment. In one embodiment, the sample is digested with trypsin, and the binding reagent comprises a plurality of anti-peptide fragment antibodies that bind to one or more peptide fragments set forth in TABLE 1. In another embodiment, the binding reagent comprises a plurality of antibodies capable of binding to at least one thyroglobulin peptide fragment selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5. In another embodiment, the binding reagent comprises a plurality of antibodies capable of binding to at least one thyroglobulin peptide fragment selected from SEQ ID NO:2 and SEQ ID NO:3. In another embodiment, the binding reagent comprises a plurality of antibodies capable of binding to SEQ ID NO:3. In another embodiment, the binding reagent comprises a plurality of first antibodies and a plurality of second antibodies, the first and second antibodies being capable of binding to different thyroglobulin peptide fragments set forth in TABLE 1, such as, for example, SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5. In another embodiment, the binding reagent comprises a plurality of first antibodies, a plurality of second antibodies and a plurality of third antibodies, the first, second and third antibodies being capable of binding to different thyroglobulin peptide fragments set forth in TABLE 1, such as, for example, SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5. In some embodiments, the binding reagent is a solid phase reagent comprising a plurality of attached antibodies that are capable of binding to at least one thyroglobulin peptide fragment.
In accordance with the various embodiments of the methods of the invention, each anti-peptide antibody preparation may be used to directly detect or enrich a peptide fragment with an identified amino acid sequence (e.g., SEQ ID NOS:2-29) in a digested sample containing a mixture of other peptide fragments. In one embodiment, the anti-peptide antibody preparations for use in the methods comprise antibodies that bind to SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:5. In one embodiment, the anti-peptide preparation for use in the methods comprises antibodies that bind to SEQ ID NO:3.
The anti-peptide antibodies may be polyclonal, monoclonal, or an antibody fragment generated using any standard method. For example, a method for generating anti-peptide polyclonal antibodies is described in Example 2.
In one embodiment, the anti-peptide antibodies are monoclonal antibodies with high affinity suitable for improving the limit of detection by recovering the majority of peptides from the digestions and by permitting stringent washes to remove non-specifically bound peptides.
As used herein, the modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogenous population of antibodies and is not to be construed as requiring production of the antibody by any particular method. Monoclonal antibodies can be obtained using any technique that provides for the production of antibody molecules by continuous cell lines in culture, such as the hybridoma method described by Kohler, G., et al., Nature 256:495, 1975, or they may be made by recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567, to Cabilly). Monoclonal antibodies may also be isolated from phage antibody libraries using the techniques described in Clackson, T., et al., Nature 352:624-628, 1991, and Marks, J. D., et al., J. Mol. Biol. 222:581-597, 1991. Such antibodies can be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD and any subclass thereof.
For example, monoclonal antibodies can be obtained by injecting a suitable mammal (e.g., a BALB/c mouse) with a composition comprising a thyroglobulin polypeptide or peptide fragment thereof. After a predetermined period of time, splenocytes are removed from the mouse and suspended in a cell culture medium. The splenocytes are then fused with an immortal cell line to form a hybridoma. The formed hybridomas are grown in cell culture and screened for their ability to produce a monoclonal antibody against thyroglobulin, or the peptide fragment thereof. (See also Current Protocols in Immunology, Vol. 1, John Wiley & Sons, pages 2.5.1-2.6.7, 1991.)
The presence of peptide fragment bound to the anti-peptide antibody may be detected using any suitable method. Exemplary methods include mass spectrometry, capillary gel electrophoresis with mass spectrometric detection, ultraviolet absorbance detection, electrochemical detection, or flow cytometric analysis using a solid phase antibody and a second detection antibody.
In one embodiment, the peptide fragments are eluted from the binding reagent, and the enriched peptides are detected using mass spectrometry. Methods for detection of peptide fragments using mass spectrometry are known in the art and are described in U.S. Patent Publication No. 2004/0072251, to Anderson, hereby incorporated by reference. Any instrument capable of ion fragmentation and reliable quantitation may be used in accordance with the methods of the invention. For example, a triple quadrupole instrument capable of specific selection of ions with correct precursor mass in the first quadrupole, ion fragmentation in the gas phase in the second quadrupole, fragment ion selection in the third quadrupole, and ion detection by photomultiplier tube may be used to detect the enriched peptide fragments.
In some embodiments of the method, an internal standard of the peptide fragment selected for detection (as a surrogate for the parent protein) is added to the digested sample prior to detection. The internal standard may be any altered version of the respective peptide fragment that is recognized as equivalent to the peptide fragment by the appropriate binding reagent and differs from it in a manner that can be distinguished by a mass spectrometer, either through direct measurement or molecular mass, or through mass measurement of fragments (e.g., through MS/MS analysis), or by another equivalent means.
For example, the internal standard may be an isotope-labeled peptide fragment, such as described in Example 4. An isotope-labeled peptide fragment may be generated by chemical synthesis, wherein a peptide fragment identical to the natural one is made by incorporating amino acid precursors that contain heavy isotopes of hydrogen, carbon, oxygen, or nitrogen to introduce the isotopic label. In another example, a particular portion of thyroglobulin may be synthesized in an in vitro synthesis system (using recombinant techniques known to those of skill in the art) for use as an internal standard.
The internal standard is added to the digested sample at a known concentration before contacting the sample with the binding reagent. The binding reagent thus captures and enriches both the natural and the internal standard (labeled peptide) together according to their relative abundances in the sample. Since the internal standard is added at a known concentration, the ratio between the amounts of the natural and labeled forms detected by the final MS analysis allows the concentration of the natural peptide in the sample mixture to be calculated. Thus, the methods of the invention allow for the measurement of the quantity of thyroglobulin in a complex mixture, and because the selected peptide (e.g., SEQ ID NOS:2, 3, and/or 5) is produced by complete digestion of a mixture of proteins, the abundance of the parent protein thyroglobulin (SEQ ID NO:1) in the mixture of proteins can be deduced.
In some embodiments, the method further comprises analyzing one or more external standards, or calibrators, in parallel with the methods for determining the presence or amount of thyroglobulin. The external standard, or calibrators, useful in this embodiment of the method include any solution containing a known amount of human thyroglobulin (SEQ ID NO:1), or a known amount of another polypeptide comprising SEQ ID NO:2, SEQ ID NO:3 and/or SEQ ID NO:5.
In another aspect, the invention provides a method for monitoring the efficacy of treatment of a human thyroid cancer patient. The method comprises (a) digesting a biological sample containing protein obtained from the human thyroid cancer patient to provide peptide fragments; (b) contacting the digested sample with a binding reagent comprising at least one antibody that is capable of binding to at least one thyroglobulin peptide fragment; and (c) detecting and/or measuring the amount of the thyroglobulin peptide fragments that are bound to the binding reagent, wherein the detection of thyroglobulin peptide fragments indicates the need for further treatment.
As described herein and demonstrated in Examples 1-6, the methods of the invention may be used to enrich thyroglobulin peptides from a complex mixture of serum/plasma peptides using immunoglobulins that recognize specific thyroglobulin peptides followed by direct identification and quantitation of the thyroglobulin peptides, for example, by mass spectrometry. Thyroglobulin, which is secreted from functioning thyroid tissue, is useful as a tumor marker in the diagnosis of recurrent, residual and metastatic thyroid cancer. See, e.g., Hoofnagle, et al., CLI 8:12-14 (2006); Whitley, R. J., et al., Clin. Lab. Med. 24:29-47 (2004); and Saghari, M., et al., Nuclear Medicine Communications 27:567-572 (2006).
The treatment for thyroid cancer typically involves the surgical removal of thyroid tissue, followed by treatment with radioactive iodine, which should eliminate all functioning thyroid tissue. Therefore, the presence of thyroglobulin in the plasma/serum of thyroid cancer patients indicates functioning thyroid tissue and the need for further therapy, such as additional surgery or radioiodine ablation. Sensitive detection of thyroglobulin permits prompt treatment of residual, recurrent, or metastatic disease. Over the past few decades, improvements in assay sensitivity have shortened the time to treatment for thyroid cancer survivors, likely leading to improved survival (Whitley, R. J., et al., Clin Lab Med 24:29-47 (2004)).
In another aspect, the invention provides an isolated antibody which binds to a thyroglobulin peptide fragment having an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5. As described in Examples 1-3, tryptic peptide fragments set forth as SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5 of human thyroglobulin were identified using both liquid chromatography-electrospray ionization-tandem mass spectrometry and liquid chromatography-matrix assisted laser desorption ionization-tandem time of flight mass spectrometry. Utilization of both methods ensured that the identified peptide fragments SEQ ID NOS:2, 3, and 5 will be robust in all mass spectrometric methods currently in use. As described in Example 2, antibodies that bind the three peptides (SEQ ID NOS:2, 3, and 5) were generated and used in a detection assay for thyroglobulin, as described in Example 3.
In another aspect, the invention provides a composition comprising at least one thyroglobulin peptide fragment consisting of SEQ ID NOS:2, 3, or 5. In one embodiment, the invention provides a composition comprising at least two thyroglobulin peptide fragments consisting of SEQ ID NOS:2, 3, or 5. In another embodiment, the invention provides a composition comprising thyroglobulin peptide fragments consisting of SEQ ID NOS:2, 3, and 5. In some embodiments, the compositions further comprise an adjuvant for inducing an immune response in a mammalian subject. In further embodiments, at least one thyroglobulin peptide in the composition is conjugated to keyhole limpet hemocyanin. The compositions comprising peptide fragments may be used to generate the anti-peptide antibodies for use in the methods of the invention.
In another aspect, the invention provides a kit comprising (a) a plurality of antibodies that are capable of binding to at least one thyroglobulin peptide fragment; and (b) a reagent comprising trypsin. In some embodiments, the kit further comprises an internal standard reagent. In some embodiments, the plurality of the antibodies in the kit are capable of binding to at least one thyroglobulin peptide fragment set forth in TABLE 1. The kit may further include one or more compositions for use in the methods described herein.
The following examples merely illustrate the best mode now contemplated for practicing the invention, but should not be construed to limit the invention.
EXAMPLE 1
This example describes the identification of the most abundant peptides liberated from human thyroglobulin during digestion of a thyroglobulin containing sample digested with trypsin, as determined using two different mass spectrometric detection techniques.
Methods:
Trypsin Digestion:
Modified trypsin (Promega, Inc.) was used. It was modified with a methylating agent in order to render the protease resistant to self-cleavage and permit more complete digestion with less enzyme.
Human thyroglobulin (Cortex, Biochem Inc., San Leandro, Calif.) was digested with modified trypsin under the following three different conditions:
Digestion 1: Tg was denatured in 3.5 mol/L urea in 100 mmol/L NH4HCO3, reduced with 5 mmol/L dithiothreitol (DTT), alkylated with 15 mmol/L iodacetamide, and then digested for 18 hours at 37° C. with modified sequencing grade trypsin (Promega, Madison, Wis.) at 100 μg Tg per mL (trypsin:Tg ratio of 1:20 w/w)
Digestion 2: Tg was digested under the same conditions as described in Digestion 1, but without reduction and alkylation;
Digestion 3: Tg was digested under the same conditions as Digestion 1, except that Tg was supplemented with normal human serum (2 μg Tg per 126 μg human serum proteins: 1.28 mg protein per mL).
The resulting thyroglobulin peptides from each trypsin digestion were purified using a hydrophilic lipophilic binding (HLB) solid phase extraction cartridge (1 mL bed volume, Waters, Milford, Mass.). After washing twice with 1 mL 0.1% formic acid in water, peptides were eluted with 80% acetonitrile, 0.3% formic acid, dried down under nitrogen, and reconstituted in 100 μl of 5% acetonitrile, 0.3% formic acid in water.
Peptides were identified using two complementary techniques:
(i) microelectrospray ionization liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a Thermo-Finnigan LTQ ion trap analyzer (Waltham, Mass.). The detection of peptides was carried out using an instrument from Thermo Electron, Inc. (LTQ), which is an ion trap instrument capable of ion fragmentation in the gas phase. Ions were introduced to the mass spectrometer using a nanoflow liquid chromatography system with flow splitting to achieve stable gradients at low flow rates; and
(ii) off-line HPLC-plate spotting followed by matrix assisted laser desportion ionization-tandem time of flight mass spectrometry (MALDI-TOF-TOF) with an Applied Biosystems 4700 mass analyzer (Foster City, Calif.).
For LC-TOF-TOF experiments, peptides were separated using nanoflow liquid chromatography on a system comprised of a FAMOS autosampler, Switchos column switching device, and a PROBOT MALDI plate spotting robot (Applied Biosystems, Inc.). The peptides were then identified on an ABI 4700 tandem time-of-flight instrument (Applied Biosystems, Inc.).
Results:
The results of the mass spectrometric analysis of the human thyroglobulin peptides are shown in TABLE 1.







TABLE 1







DETERMINATION OF THE BEST PEPTIDES FOR ANTIBODY PRODUCTION IN RABBITS.A









Peak area (Ion trap) or peak height (TOF-TOF)











MALDI-
















SEQ

Linear Ion Trap
TOF-TOF


















ID

Digestion
Digestion
Digestion
Digestion
Hydro-



Peptide
NO:
m/za
1
2
3
1
phobicity


















VIFDANAPVAVR
2
1272.48
58,210,204
81,447,918
194,201
51030
−0.3



 


LGDQEFIK
3
950.07
55,335,595
53,930,998
34,267
8,802
0.4


 


SHGQDSPAVYLK
4
1302.42
47,082,888
123,119
5,659
5,368
0.0


 


FPLGESFLVAK
5
1208.43
44,489,374
65,300,983
111,541
11,170
−0.4


 


GGADVASIHLLTAR
6
1381.56
42,916,756
41,942,023
118,664
17,907
−0.2


 


FLQGDHFGTSPR
7
1362.48
40,413,027
64,930,010
55,123
39,950
−0.1


 


FLAVQSVISGR
8
1177.38
37,065,560
55,773,419
0
18,100


 


FPDAFVTFSSFQR
9
1549.71
33,791,534
42,267,723
75,971
14,392
−0.4


 


WESQLPQPR
10
1141.26
30,972,286
56,904,484
0
20,485


 


SQAIQVGTSWK
11
1205.35
22,604,066
3,943,502
3,572
4,616


 


KVPTFATPWPDFVPR
12
1759.04
22,157,262
13,653,736
55,741
6,121


 


TSGLLSSWK
13
979.11
17,249,237
3,423,684
0
1,571


 


LALQFTTNPK
14
1133.32
16,877,659
17,944,078
70,315
5,354


 


LRNEDLGLPPLFPPR
15
1735.02
16,390,867
15,413,817
98,462
5,648


 


AVLM#GGSALSPAAVISHER
16
1883.16
12,210,274
7,198,321
4,955
4,510


 


AGGENYKEFSELLPNR
17
1824.97
10,408,136
9,727,929
0
15,093


 


AVLMGGSALSPAAVISHER
18
1867.16
7,280,1332
4,535,058
0
5,511


 


TAFYQALQNSLGGEDSDAR
19
2044.13
5,816,139
10,528,062
109,692


 


NEAGLQC*DQNGQYR
20
1653.77
4,599,373
719,823
0


 


RAVLM#GGSALSPAAVISHER
21
2039.35
4,308,195
1,608,455
0


 


LEDIPVASLPDLHDIER
22
1933.15
3,722,758
8,297,059
68,482
2,904


 


IMQYFSHFIR
23
1342.59
2,551,140
8,873,673
0
3,920


 


ELFVDSGLLRPMVEGQSQQFS
24
3152.57
2,069,760
7,314,594
31,510


VSENLLK


 


KPGISLLSYEASVPSVPISTHGR
25
2396.73
1,893,836
5,039,748
19,749
3,170


 


RFSPDDSAGASALLR.S
26
1563.70
1,798,745
2,111,330
0
512


 


R.SHGQDSPAVYLKK.G
27
1430.59
1,515,236
491,341
0
675


 


R.LAAQSTLSFYQR
28
1385.55
1,413,785
2,014,669
0
14,309


 


ETEEIVSASNSSR
29
1409.44
66,054
0
0
675





ACommercially available human thyroglobulin was digested under three different conditions and resulting peptides were separated with liquid chromatography. The peptides were then analyzed using either electrospray ionization tandem mass spectrometry with a linear ion trap mass spectrometer or matrix assisted laser desorption ionization tandem mass spectrometry with a tandem time-of-flight instrument. Peptides were selected based on the total peak area and peak height on both instruments and hydrophobicity near 0.5 or −0.5.


aAverage mass/charge is listed for the MH+ ion of each peptide.


M# - refers to oxidized methionine (increased mass of 16 Da)


C* - refers to carbamidomethylated cysteine






Peptide Analysis and Selection for Antibody Production
As shown in TABLE 1, a total of 28 different peptides were detected using both mass spectrometric analysis methods in the tryptic digestion of human thyroglobulin protein (SEQ ID NO:1, shown in FIG. 1). The length of the peptides range from nine amino acid residues up to 29 amino acid residues. TABLE 1 shows the results for the human thyroglobulin peptide resulting from the trypsin digestion as the peak area (as determined from digestions 1-3 analyzed by the ion trap mass spectrometer) or the peak height (as determined from Digestion 1 analyzed by the MALDI-TOF-TOF mass spectrometer). The number of times each peptide sequence was detected is the sum of the number of columns in which the peak area is greater than zero. The peptides were identified with database searching using Xcaliber software and the Sequest searching algorithm (from Thermo Electron, Inc.).
Selection of Peptides for Use as Antigens:
Peptides for use as antigens to raise antibodies for use in a thyroglobulin detection assay, as described in Example 2, were selected based on the total peak area and peak height on both instruments. Peptides were also selected with a preferred hydrophobicity value of between −0.3 to −0.5, or between 0.3 to 0.5.
The three most abundant peptides detected in a trypsin digest of human thyroglobulin are determined using both liquid chromatography-tandem mass spectrometry with a linear ion trap instrument and liquid chromatography-matrix assisted laser desorption ionization-tandem time of flight mass spectrometry, with the desired hydrophobicity values were:

    
    
        LGDQEFIK (SEQ ID NO:3)(precursor mass 949.50 Da);
        VIFDANAPVAVR (SEQ ID NO:2)(precursor mass 1271.71 Da); and
        FPLGESFLVAK (SEQ ID NO:5)(precursor mass 1207.67 Da).
    
    


These peptides were used as antigens to generate anti-peptide antibodies as described in Example 2.
The three peptides selected for use as antigens (SEQ ID NO:2, SEQ ID NO:3 and SEQ ID NO:5) were selected as the three most reliably abundant peptides on both ESI-ion trap and MALDI-TOF-TOF platforms. The fourth most abundant peptide from Digestion 1 (SEQ ID NO:5) was selected, because the third most abundant peptide (SEQ ID NO:4) was not well recovered when digested without reduction and alkylation or in the presence of serum proteins. The most abundant peptide across platforms and digestions tested, SEQ ID NO:2, was chosen as the internal standard peptide and a stable isotope-labeled peptide was synthesized, as described in more detail in Example 4.
EXAMPLE 2
This example describes the generation of rabbit anti-human thyroglobulin antibodies against selected thyroglobulin peptides for use in an assay to detect human thyroglobulin in a biological sample.
Methods:
Human Thyroglobulin Peptides
The following three peptides from human thyroglobulin described in Example 1 were selected for use as antigens to generate anti-peptide antibodies for use in an assay to detect human thyroglobulin:

    
    
        LGDQEFIK (SEQ ID NO:3)(precursor mass 949.50 Da);
        VIFDANAPVAVR (SEQ ID NO:2)(precursor mass 1271.71 Da); and
        FPLGESFLVAK (SEQ ID NO:5)(precursor mass 1207.67 Da).
    
    


Conjugation of Peptides
Synthetic peptides were generated for each sequence (SEQ ID NOS:2, 3, and 5) and were conjugated to keyhole limpet hemocyanin (KLH) for immunization of rabbits as follows:
Four different reactions were carried out to conjugate the three peptides to keyhole limpet hemocyanin in order to guarantee presentation of both ends of the selected peptides to the rabbits' immune system. For the two peptides that had lysine at the carboxyl terminus (SEQ ID NO:3 and SEQ ID NO:5), gluteraldehyde was used to conjugate both the peptide amino terminus and the lysine at the carboxyl terminus of the peptides to keyhole limpet hemocyanin (KLH).
Keyhole limpet hemocyanin (KLH, Calbiochem, Gibbstown, N.J.) was suspended in PBS (138 mmol/L, NaCl 2.7 mmol/L, KC: 10 mmol/L, phosphate pH7.4), sonicated and vortexed extensively. The mixture was then dialyzed against PBS (3.5 kDa molecular weight cut-off (MWCO)). The solution was then clarified by centrifugation, and the supernatant was used for peptide conjugation. Peptide (2 mg) dissolved in dimethylsulfoxide was added to the KLH solution. The mixture was then brought up to 1 mmol/L glutaraldehyde and incubated for 16 hours at 4° C. with rotation. The reactions were terminated with a few grains of sodium borohydride.
1-Ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride (EDAC, Sigma, St. Louis, Mo.) was used to conjugate KLH to the carboxyl terminus of SEQ ID NO:2, according to the manufacturer's instructions. Gluteraldehyde was used to conjugate KLH to the amino terminus of SEQ ID NO:2.
Efficiency of conjugation was >65% for each reaction, as assessed by MS/MS quantification of peptide that passed through a 10 kDa MWCO Microcon filter (Milipore, Bedford, Mass.). The peptide-KLH conjugates were combined and used to immunize New Zealand rabbits, as described below.
It will be understood by those of skill in the art that the methods are not limited to the use of KLH, and that other peptides (e.g., ovalbumin, albumin, modified albumin and the like) may be conjugated to SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5 in order to stimulate an immune system of a mammalian subject to generate antibodies that bind to the thyrogloublin peptides.
Immunization
The four conjugation reactions containing the three human thyroglobulin peptides SEQ ID NOS:2, 3, and 5 conjugated with KLH as described above were pooled and used to immunize two New Zealand White rabbits using the standard protocol (Pacific Immunology, Ramona, Calif.). The peptide-conjugate pool containing all three peptides (SEQ ID NOS:2, 3, and 5) was injected superficially into two New Zealand White rabbits with complete Freund's adjuvant. Subsequent booster immunizations were carried out with incomplete Freund's adjuvant for a total of four immunizations. Blood was collected at four-week intervals.
The anti-peptide antibodies were purified from the rabbit serum using the three peptides conjugated to bovine serum albumin (generated as described above, by replacing KLH with bovine serum albumin) cross-linked to a cyanogen bromide-activated sepharose solid phase (Sepharose CNBr-4B GE Lifesciences, Piscataway, N.J.), according to the manufacturer's instructions.
After the anti-peptide antibodies were bound to the solid phase, the sepharose was washed until the wash returned to baseline absorbance (at 280 nm), then the anti-peptide antibodies were eluted with 200 mM glycine pH 2.8 into neutralization buffer. After dialysis in phosphate buffered saline (PBS), the antibodies were stored at 4° C. in the presence of sodium azide (as a preservative).
Coupling Anti-Peptide Antibodies to Paramagnetic Beads
The anti-peptide antibodies were chemically cross-linked to paramagnetic beads (from Invitrogen, Inc.) using activated tosyl groups on the surface of the beads. Following the same procedures as described above for KLH, peptides were conjugated to bovine serum albumin (BSA). Peptide-BSA conjugate was then covalently bound to CNBr-activated Sepharose 4B (0.32 g, GE Lifesciences, Piscataway, N.J.), according to the manufacturer's instructions. Protein concentration of the supernatant confirmed >63% conjugate binding to the beads (Commassie Plus, Pierce, Rockford, Ill.). Peptide-BSA Sepharose conjugate was incubated with 10 mL rabbit serum (16 h, 4° C.). Beads were washed with phosphate buffered saline (PBS) and antibodies were eluted in 870 μl. fractions with 200 mmol/L glycine, pH 2.80 into tubes containing 27 μl 3 mol/L Tris, pH 8.6 and 100 μl 3 mol/L KCL. Peak fractions were pooled. The yield was 2-6 mg per 10 mL rabbit serum. Affinity purified antibody was covalently bound to tosyl-activated Dynal M-280 beads (Invitrogen, Carlsbad, Calif.) according to the manufacturer's instructions. Reactions resulted in 2.3 (symbol for +−) 0.12 (SD) pmol binding sites/μl paramagnetic beads (2×109 beads/μL).]
Using a magnet provided by the manufacturer, thyroglobulin peptides in a trypsin digested biological sample that are bound to the anti-peptide antibodies can be isolated from other peptides in the trypsin digest, as described in more detail in EXAMPLE 3.
EXAMPLE 3
This example describes the enrichment and quantitation of thyroglobulin in human serum using the anti-peptide antibodies generated in Example 2.
Methods:
Digestion of Human Serum/Plasma
200 μL of human serum was diluted with 300 μL 100 mM ammonium bicarbonate/0.05% (w:v) Tween 20 (both from Sigma-Aldrich, Inc.). The proteins were reduced with 5 mM dithiothreitol (Bio-Rad, Inc.) for one hour at 37° C. rotating end-over-end. The reduced reactive thiol groups were alkylated with iodoacetamide (from Bio-Rad, Inc.) at room temperature for 30 minutes. The proteins were then digested with 5 μg of modified trypsin (Promega, Inc.) at 37° C. rotating end-over-end for 16 hours, followed by the addition of another 5 μg modified trypsin (Promega, Inc.) at 37° C. rotating end-over-end for four hours.
Enrichment of Selected Thyroglobulin Peptides
20 μL of washed paramagnetic beads with bound anti-peptide antibody raised against thyroglobulin peptides SEQ ID NOS:2, 3, and 5, generated as described in Example 2, were resuspended in the serum digest. The 20 μl of washed paramagnetic beads contained one picomole of antibody binding sites per one microliter of bead suspension (beads were generated according to manufacturer's instructions, from Invitrogen, Inc.). Internal standard peptides, generated as described below, were added to 100 μM each. The mixture was incubated overnight at 4° C. rotating end-over-end. The beads were washed twice with 1 mL 100 mM ammonium bicarbonate and once with 1 mL deionized water. The bound peptides were eluted with 10 μL 2% (v:v) acetic acid, rotating end-over-end for 30 minutes at 37° C.
Detection of Peptides by Liquid Chromatography-Tandem Mass Spectrometry
Using standard C18 reverse phase nanoflow liquid chromatography, peptides were separated from one another during a one hour 0-30% acetonitrile/0.2% formic acid gradient. Eluted peptides were introduced into the mass spectrometer with electrospray ionization and the responses of the endogenous sample peptides normalized to the exogenous internal standard peptides were used to measure the concentration of thyroglobulin in the original human serum sample.
Detection of peptides was carried out using an Applied Biosystems Inc. 4000 Q-TRAP, which is a triple quadrupole instrument capable of specific selection of ions with correct precursor mass in the first quadrupole, ion fragmentation in the gas phase in the second quadrupole, fragment ion selection in the third quadrupole, and ion detection by photomultiplier tube. Ions were introduced to the mass spectrometer using an Eksigent ID liquid chromatography system and electrospray ionization (from Thermo Electron, Inc.).
Results:
FIG. 2 graphically illustrates the results of the immunoaffinity purification of the thyroglobulin peptide VIFDANAPVAVR (SEQ ID NO:2), demonstrating the ability to detect peak areas to 10 ng/ml of thyroglobulin in a human serum dilutional series.
Prior to using the antibody-based method to immunoaffinity purify peptides from the complex matrix of a human serum digest, experiments were carried out that demonstrated the ability to immunoaffinity purify thyroglobulin peptides diluted in buffer, thyroglobulin peptides spiked into digested human serum, and a digest of serum with thyroglobulin spiked into it (data not shown).
Conclusion:
This example demonstrates that peptides from thyroglobulin can be enriched from a complex mixture of serum/plasma peptides using immunoglobulins that recognize specific thyroglobulin peptides followed by direct identification and quantitation of the thyroglobulin peptides by mass spectrometry.
The use of anti-peptide antibodies to detect thyroglobulin removes the problematic interference of endogenous antibodies. For example, interfering antibodies, either autoantibodies to thyroglobulin itself, or non-specific antibodies to immunoglobulins used in traditional immunoassays, are eliminated during enzymatic digestion. In addition, because thyroglobulin peptide is directly detected using mass spectrometry rather than thyroglobulin protein being detected indirectly using antibodies, this embodiment of the method of the invention solves the problem of standardization and “hook effect” present in traditional immunoassays.
The “hook effect” is characterized by the production of artificially low results from samples that have extraordinarily high concentrations of antigen, far exceeding the concentration of the upper standard in the assay concerned. See, e.g., Hoofnagle and Wener, CLI 8:12-14 (2006); and Selby, C., Ann. Clin. Biochem. 36:704-721 (1999). For these reasons, this method may be used as a reference method for the detection of thyroglobulin in biological specimens that can be used as a reference standard for comparison to results of other methods of detection of thyroglobulin and thereby improve the accuracy of detection of residual, recurrent or metastatic disease in patients afflicted with thyroid cancer.
EXAMPLE 4
This example describes another experiment demonstrating the enrichment and quantitation of thyroglobulin in human serum using the anti-peptide antibodies generated in Example 2.
Methods:
Internal Standard Peptide:
A stable-isotope labeled internal standard peptide (VIFDANAPV*AVR)(SEQ ID NO:2) was synthesized, where V* represents 13C5, 14N-labeled valine, was synthesized by Anaspec (San Jose, Calif.). Isotopic purity of the peptide was 99.9%.
Human Samples:
All human samples were used in accordance with guidelines established by the Human Subjects Committee of the University of Washington.
Digestion of Human Serum/Plasma:
100 μl of human serum was diluted with 400 μl of 100 mM NH4HCO3, 0.005% Tween 20 (w:v) and reduced with 5 mM DTT for 60 minutes at 37° C., with rotation. The samples were alkylated in the dark with 15 mM iodoacetamide (15 to 120 minutes) and digested in two steps: first with 4.5 μg trypsin for four hours at 37° C., with rotation); and second with 4.5 μg trypsin for 16 hours at 37° C., with rotation. 20 μl of washed paramagnetic beads with anti-peptide antibody raised against thyroglobulin peptides SEQ ID NOS:2, 3, and 5, (containing 46 pmol of peptide binding sites) generated as described in Example 2, were resuspended in the serum digest. 10 μl of internal standard peptide (15 nmol/L), synthesized as described above, was also added to the serum digest, followed by incubation for 16 hours at 4° C.
The beads were washed twice with 500 μl 100 mmol/L ammonium acetate and then washed twice with 500 μl water. Bound Tg peptides were eluted with 15 μl 2% acetic acid (incubated for 1-2 hours at room temperature, with rotation). Human serum calibrators were analyzed in parallel with clinical specimens.
Liquid Chromatography-Tandem Mass Spectrometry:
Eluted peptides (6 μl) were loaded in duplicate onto a peptide trapping column (1 mm×5 mm, Acclaim PepMap100 C18, Dionex, Sunnyvale, Calif.) and washed with 100% buffer A (2% acetonitrile, 0.1% formic acid in water) before being eluted onto a 0.15×150 mm 5 μm 200 Å C18AQ analytical column (Micron, Auburn, Calif.), with a gradient to 35% buffer B (98% acetonitrile, 0.1% formic acid) over eight minutes at 1,000 nL/min using a Tempo 1D-plus nanoflow liquid chromatography system.
Peptides were analyzed in multiple reaction monitoring mode (MRM) with an Applied Biosystems API 4000 QTRAP using the following transitions:
636.4/1059.6, 636.4/541.3 for SEQ ID NO:2;
475.3/836.4, 475.3/779.4 for SEQ ID NO:3;
604.3/850.5, 604.3/963.5 for SEQ ID NO:5;
639.8/1065.6, 639.4/547.3 for the internal standard peptide.
Peak areas for the transitions were summed for each peptide. Endogenous peptide peak areas were normalized to the peak area of the internal standard peptide.
Quantification of International Tg Reference Material:
The international certified reference material BCR-457 was generated in 1992 from pooled human thyroglobulin isolated from cadaveric thyroid tissue and has been used to provide traceable commercial immunoassays (Feldt-Rasmussen, U., et al., Ann Biol Clin 54:343-8 (1996)). The concentration of thyroglobulin in this reference material has been quantified using the Lowry method, which has been shown to be less precise than methods of direct detection (Barr, J. R., et al., Clin Chem 42:1676-82 (1996)).
With the stable-isotope labeled internal standard (VIFDANAPV*AVR)(SEQ ID NO:2) where V* represents 13C5, 14N-labeled valine), the amount of thyroglobulin in the international Tg reference material was quantified as follows.
After reduction and alkylation with iodoacetamide, triplicate dilution series of the certified reference preparation of Tg (BCR-457, Sigma, St. Louis, Mo.) were digested for two hours at 37° C. using 0.5 μg sequencing grade modified trypsin in 0.1% Rapigest (Waters, Milford, Mass.). Peptides were then lyophilized and reconstituted in 5% acetonitrile, 0.1% formic acid. Suspended peptides were mixed with an equal volume of isotope-labeled internal standard peptide (15 nmol/L) and analyzed with LC-MS/MS.
Results:
FIG. 3 graphically illustrates the results of the experiment carried out to quantify the amount of thyroglobulin in the international certified reference material (BCR-457). As described above, triplicate dilutions of the certified reference material were digested with trypsin and the concentration of SEQ ID NO:2 peptide was determined from the ratio of endogenous to spiked internal standard peptide. Each replicate dilution series in FIG. 3 is represented with different symbols. The curve representing the average of the data points was fit to an equation of the form y=Axn, which was used to determine the dilution necessary to achieve a response of 1.0 (i.e., solving for the dilution (x) where the response (y) equals 1.0). Data shown in FIG. 3 are representative of three independent experiments.
As shown in FIG. 3, the concentration of thyroglobulin in the international reference material BCR-457 using the methods described in this experiment was determined to be 317±7 μg/mL (mean+/SD; N=3), which is very similar to that previously reported for the BCR-457 preparation (324±18 μg/mL).
The goal of this study was to quantify endogenous serum thyroglobulin (Tg) using LC-MS/MS to directly detect specific peptides in tryptic digests of human serum. Polyclonal antibodies were generated in rabbits and covalently bound to a paramagnetic solid phase to enrich Tg peptides from proteolytic digests. Stable-isotope labeled internal standard peptide was included in the immunoaffinity enrichment to help control variability due to sample handling and mass spectrometer performance, and external standards were used to calibrate the response of the endogenous analyte.
With regard to the trypsin digestion, in order to avoid solid phase extraction, which could increase variability due to added specimen manipulation, an alternative approach was used by adding the non-ionic detergent Tween 20 to help denature proteins and to provide stringency in the immunoaffinity purification step. After testing various concentrations of Tween 20, it was determined that reduction and alkylation of 20% serum led to a cloudy solution that was reproducibly cleared with trypsin in the presence of 0.005% (w:v) Tween 20, but not without. Therefore, Tween 20 was included in the trypsin digestions.
It was also determined that sequencing grade trypsin was the only preparation capable of clarifying all human samples tested (N=10).
LC-MS/MS Analysis of Endogenous Thyroglobulin
Enriched Tg peptides were bound to a C18 trapping column and washed prior to being eluted with an acetonitrile gradient and resolved on an analytical column. FIGS. 4A-4G illustrate the ion current chromatograms for the internal standard and the endogenous peptides. Immunoaffinity purified peptides were first loaded onto a peptide trapping column before being resolved with a C18 analytical column, ionized using microelectrospray ionization, and analyzed using multiple reaction monitoring (MRM). Elution profiles of peptides purified from a digest of human serum are shown for each peptide in FIGS. 4A, 4C, 4E, and 4G. Fragment ion spectra were collected in the linear ion trap of the mass spectrometer simultaneously with the collection of MRM data, and are shown for each peptide in FIGS. 4B, 4D, 4F, and 4H.
FIG. 4A graphically illustrates the elution profile of the internal standard (VIFDANAPV*AVR)(SEQ ID NO:2) where V* represents 13C5, 14N-labeled valine).
FIG. 4B graphically illustrates the fragment ion spectra collected in the linear ion trap of the mass spectrometer for the internal standard (VIFDANAPV*AVR) (SEQ ID NO:2) where V* represents 13C5, 14N-labeled valine).
FIG. 4C graphically illustrates the elution profile of endogenous peptide SEQ ID NO:2 purified from a digest of human serum.
FIG. 4D graphically illustrates the fragment ion spectra collected in the linear ion trap of the mass spectrometer for the endogenous peptide SEQ ID NO:2.
FIG. 4E graphically illustrates the elution profile of endogenous peptide SEQ ID NO:3 purified from a digest of human serum.
FIG. 4F graphically illustrates the fragment ion spectra collected in the linear ion trap of the mass spectrometer for the endogenous peptide SEQ ID NO:3.
FIG. 4G graphically illustrates the elution profile of endogenous peptide SEQ ID NO:5 purified from a digest of human serum.
FIG. 4H graphically illustrates the fragment ion spectra collected in the linear ion trap of the mass spectrometer for the endogenous peptide SEQ ID NO:5.
As shown in FIG. 4C (SEQ ID NO:2), FIG. 4E (SEQ ID NO:3) and FIG. 4G (SEQ ID NO:5), peptides SEQ ID NO:2 and SEQ ID NO:3 elute earlier than peptide SEQ ID NO:5 and have a significantly narrower peak width.
As shown in FIGS. 4B, 4D, 4F, and 4H, tandem mass spectra can be collected in parallel with the MRM transitions using the linear ion trap of the 4000 Q-TRAP mass spectrometer. Therefore, these results demonstrate that interpretable MS/MS spectra can be acquired for each peptide tested in serum samples with as little as 100 ng/mL endogenous Tg.
EXAMPLE 5
This example describes an experiment to determine the performance of the three peptides (SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5) in an assay to detect Tg in human serum.
Methods:
To further determine the performance of the three peptides (SEQ ID NO:2, SEQ ID NO:3 and SEQ ID NO:5) in an assay to detect Tg in human serum, human serum containing 319 ng/mL endogenous thyroglobulin was diluted serially with serum that contained no Tg. The samples were reduced, alkylated and digested with trypsin, as described in Example 4. The resulting peptides were enriched for thyroglobulin peptides using paramagnetic beads coated with antibodies to Tg peptides, as described in Example 4. Peptides eluted from the anti-peptide beads were analyzed with LC-MS/MS, as described in Example 4.
Results:
FIG. 5A-5C graphically illustrate the response (peak area of endogenous peptide/peak area internal standard peptide) for each peptide (FIG. 5A: SEQ ID NO:2; FIG. 5B: SEQ ID NO:3; FIG. 5C: SEQ ID NO:5), detected in a dilution series of a human serum sample containing 319 ng/mL Tg. The internal standard peptide (VIFDANAPV*AVR)(SEQ ID NO:2) where V* represents 13C5, 14N-labeled valine, is chemically identical to SEQ ID NO:2 peptide and differs only in mass. As shown in FIGS. 5A-5C, the three peptides (SEQ ID NO:2, SEQ ID NO:3, and SEQ ID NO:5) behaved differently.
When analyzed for peak areas only (data not shown), peptide SEQ ID NO:3 performed the best of the three peptides, with a minimal detectable concentration of 3 ng/mL. Peptide SEQ ID NO:2 had a significant background signal, likely resulting from a peptide that populated antibody binding sites after affinity purification of the antibody, and was different from the zero calibrator at 30 ng/mL. Peptide SEQ ID NO:5 also included high background signal, suffered from greater variability, and had a minimal detectable concentration of 100 ng/mL.
As described above, internal standard peptide was added after digestion to control for variability in the volume of immunoglobulin-coated beads added and to control for variability in sample volume injection and ionization. As shown in FIGS. 5A-5C, after normalization to the internal standard peptide, the responses of peptide SEQ ID NO:2 and the peptide SEQ ID NO:3 had similar characteristics to their respective peak areas, but the response of peptide SEQ ID NO:5 was more erratic.
Discussion of Results
Of the three peptides tested in this experiment, peptide SEQ ID NO:3 allowed for the most sensitive detection of endogenous thyroglobulin. As described in Example 6, good intra-assay precision was demonstrated for peptide SEQ ID NO:3 at 3.8 ng/mL (12 fmol/L) in human serum.
With regard to the other two peptides, it appears that peptide SEQ ID NO:5 may have elicited a poorer antibody response as compared with the other peptides tested, as evidenced by its high limit of detection. Although peptide SEQ ID NO:2 was the most abundant peptide detected by digesting purified human thyroglobulin, as shown in TABLE 1, it was determined that during the generation of the albumin-peptide conjugate used for affinity purification, this peptide non-covalently associated with albumin and bound to CNBr-activated beads directly. The ester linkage formed between conjugate and bead is known to slowly hydrolyze over time, leading to background interference. It is believed that the use of other strategies to generate affinity-purified, highly specific polyclonal antibodies, which are known to those of skill in the art, would alleviate the problem encountered with this peptide. Alternatively, the use of monoclonal antibodies to the peptides would not require affinity purification, and would therefore eliminate the problems related to the affinity purification process.
EXAMPLE 6
This example describes the use of peptide SEQ ID NO:3 for quantitation of Tg in human serum specimens.
Methods:
Given the superior performance of peptide SEQ ID NO:3, it was used for quantitation in subsequent human serum specimens using the peptide response calculated as the peak area of analyte divided by the peak area of the internal standard.
Human serum calibrators were chosen after comparing thyroglobulin spiked into albumin, various dilutions of fetal calf serum, and 100% human serum. It was determined that human calibrators provided the least bias as compared with immunoassay (data not shown). The human serum calibrators used in this experiment were human serum samples (known to be negative of thyroglobulin) with purified thyroglobulin (SEQ ID NO:1) spiked into the serum at known concentrations, or the concentration of spiked in thyroglobulin was determined by another methodology using known immunoassay detection techniques.
Human calibrators were analyzed in parallel with other human serum specimens (0, 2, 5, and 20 ng/mL). The assay for Tg using SEQ ID NO:3 had an intra-assay precision of 13.7% at 22.3 ng/mL Tg, 22.5% at 5.5 ng/mL Tg, and 21.4% at 3.8 ng/mL Tg. Interassay precision was 17.4% at 6.0 ng/mL Tg. The lower limit of detection of Tg, defined as the concentration corresponding to mean+2 SD of the zero calibrator, was 2.6 ng/mL Tg. At 5.5 ng/mL Tg, the mean signal-to-noise ratio was 5.7 (95% CI 3.0-8.3).
Recovery of thyroglobulin spiked into five Tg negative human serum samples at 21.6 ng/mL ranged from 85.0% to 99.6% (mean±SD was 93.0±5.4%). As calculated using peak area determinations, the mean carryover was 0.8%±0.8% (SD). Using the above-described configuration, 14 samples and four calibrators can be analyzed at a time in a three day time period.
The assay with peptide SEQ ID NO:3 was then compared to a currently available immunoassay. To evaluate comparability, 33 samples were analyzed that had been previously quantified using the Beckman Access 2 assay for Tg (Beckman Coulter, Fullerton, Calif.), spanning a range of 3.0 ng/mL to 33.2 ng/mL Tg. The results obtained using the Beckman Access 2 Tg assay were compared with the results using immunoaffinity purification of peptide SEQ ID NO:3 from tryptic digests with external calibration. FIG. 6A graphically illustrates a comparison between the Beckman Access 2 assay results x-axis) and the results obtained from the LC-MS/MS assay with peptide SEQ ID NO:3 (y-axis). As shown in FIG. 6A, the equation of the Deming regression (Analyse-It, Leeds, England, UK) had a slope (95% confidence interval) of 1.032 (0.850-1.216) and an intercept of −1.837 (−4.929-1.256). The Pearson correlation coefficient (r2) was 0.81. The residuals of each data point from the regression line shown in FIG. 6A are shown in FIG. 6B, wherein the standard error of the residuals (Sy/x) was 3.914.
Therefore, it has been demonstrated that the immunoaffinity enrichment and LC-MS/MS assay performs well in comparison with an established immunoassay for Tg detection, even at the low picomolar range in human serum. This result is significant in that this level of detection has not been demonstrated for LC-MS/MS quantification of Tg or other endogenous proteins in human serum or plasma. For example, previous attempts at the quantification of proteins in endogenous human serum have included the direct detection of peptides from Zn-α2 glycoprotein, which was successfully quantified with a sensitivity of  ̃3 μg/mL (90 nmol/L)(Sapin, R., Clin Chem 53:810-2 (2007)). Therefore, this study is the first time, as far as is known, in which a peptide immunoaffinity purification method has been successfully used to measure an endogenous low abundance protein in human serum, such as Tg, with a sensitivity of 9 pmol/L.
It is also important to note that trypsin digestion has an inherent advantage over immunoassay in that it destroys endogenous antibody interferences due either to anti-analyte autoantibodies or non-specific heterophilic antibodies. In addition, by directly detecting an analyte such as an endogenous peptide in reference to a stable-isotope labeled internal standard peptide, mass spectrometry has the advantage of being more easily standardized across laboratories, especially when a standard reference preparation is already available, such as is the case for Tg. Therefore, it is believed that the methods of detecting low abundance Tg in serum provides an alternative diagnostic approach to the methods currently available that are plagued by interference and lack of standardization.
While illustrative embodiments have been illustrated and described, it will be appreciated that various changes can be made therein without departing from the spirit and scope of the invention.

## Claims

1. A composition comprising at least one synthetic or recombinant thyroglobulin peptide consisting of SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:5.

2. The composition of claim 1, wherein the composition comprises SEQ ID NO:2 and SEQ ID NO:3.

3. The composition of claim 2, wherein the composition further comprises SEQ ID NO:5.

4. The composition of claim 1, wherein the at least one synthetic or recombinant thyroglobulin peptide is conjugated to a peptide that stimulates an immune system of a mammalian subject.

5. The composition of claim 1, wherein the at least one peptide is conjugated to keyhole limpet hemocyanin.

6. The composition of claim 1, wherein the at least one synthetic or recombinant thyroglobulin peptide consists of SEQ ID NO:2.

7. The composition of claim 1, wherein the at least one synthetic or recombinant thyroglobulin peptide consists of SEQ ID NO:3.

8. The composition of claim 1, wherein the at least one synthetic or recombinant thyroglobulin peptide consists of SEQ ID NO:5.

9. The composition of claim 1, wherein the composition further comprises an adjuvant for inducing an immune response in a mammalian subject.

10. A composition comprising at least one thyroglobulin peptide consisting of SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:5, wherein the at least one peptide is conjugated to keyhole limpet hemocyanin.

11. The composition of claim 10, wherein the composition further comprises an adjuvant for inducing an immune response in a mammalian subject.