WO2017053932A1

WO2017053932A1 - Identification of immunoglobulin free light chains by mass spectrometry

Info

Publication number: WO2017053932A1
Application number: PCT/US2016/053675
Authority: WO
Inventors: David R. Barnidge; David L. Murray
Original assignee: Mayo Foundation For Medical Education And Research
Priority date: 2015-09-24
Filing date: 2016-09-26
Publication date: 2017-03-30
Also published as: AU2016326757B2; EP3353200A1; CN108026164A; US20180267057A1; AU2016326757A1; JP2018536147A; EP3353200A4; JP6968058B2; US11209439B2

Abstract

This document relates to methods for identifying one or more immunoglobulin free light chains in a sample using mass spectrometry. For example, this document relates to a method for identifying one or more immunoglobulin free light chains in a sample that includes (a) providing a sample; (b) subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and (c) identifying the presence of the one or more immunoglobulin free light chains.

Description

Identification of Immunoglobulin Free Light Chains by Mass

Spectrometry

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application Serial No. 62/232, 182, filed on September 24, 2015, the contents of which are incorporated by reference in their entirety.

TECHNICAL FIELD

This document relates to methods for identifying one or more immunoglobulin free light chains in a sample using mass spectrometry.

BACKGROUND

Immunoglobulins (Igs) have a two-fold symmetry with each intact Ig containing two heavy and two light chains. The light chains are subdivided into two main types (kappa and lambda) based on their amino acid sequences in the C terminal constant region. Plasma cells are responsible for synthesis of the heavy and light chains resulting in the production of an intact Ig.

The amino acid sequence of a human immunoglobulin light chain consists of three regions: the N-terminal V region (approximately 107 amino acids for kappa and 110 amino acids for lambda), the J region (12 amino acids), and the C-terminal C region (106 amino acids). Each region is translated from a specific set of genes expressed only in B cells which make and secrete light chains either as part of an intact immunoglobulin or as a free light chain. B-cells are also able to randomly mutate V and J region genes for light chains through the process of somatic hypermutation resulting in a large number of different gene combinations (approximately 1.3 x 10³ for kappa alone) (see, e.g., Lefranc, MP. Cold Spring Harb Protoc 2011; 2011 : 595-603). Since the light chain V and J region gene sequences are created randomly, the Central Limit Theorem (Mukhopadhyay, N and Chattopadhyay, B. Sequential Anal 2012; 31 :265-77) predicts that the amino acid sequence of the expressed light chain repertoire should have a normally distributed molecular mass profile. SUMMARY

Provided herein is a method for identifying one or more immunoglobulin free light chains in a sample. The method includes (a) providing a sample; (b) subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and identifying the presence of the one or more immunoglobulin free light chains.

In some embodiments, the sample is suspected to include an immunoglobulin free light chain.

In some embodiments, the one or more immunoglobulin free light chains are selected from the group consisting of free kappa light chains and free lambda light chains, and mixtures thereof. For example, the immunoglobulin free light chain can be a free kappa light chain.

Additionally, the method can include identifying at least two free kappa light chains. In some embodiments, the immunoglobulin free light chain is a free lambda light chain. For example, the method can include identifying at least two free lambda light chains.

In some embodiments, the one or more immunoglobulin free light chains includes at least one of a glycosylated immunoglobulin free light chain, a cysteinylated immunoglobulin free light chain, and a glutathionylated immunoglobulin free light chain.

In some embodiments, identifying the one or more immunoglobulin free light chains occurs in the presence of a polyclonal background.

In some embodiments, the method further includes measuring the concentration of the one or more immunoglobulin free light chains in the sample.

In some embodiments, the method has a peak area percent variation of less than about 15% when the concentration of at least one immunoglobulin free light chain in the sample is measured 5 to 15 times. For example, the method can have a peak area percent variation of less than about 10% when the concentration of at least one immunoglobulin free light chain in the sample is measured 5 to 15 times.

In some embodiments, the method further includes identifying at least one

immunoglobulin free light chain dimer.

In some embodiments, the method further includes contacting the sample with a reducing agent prior to subjecting the sample to the mass spectrometry technique. The reducing agent can be selected from the group consisting of dithiothreitol (DTT), reduced glutathione, β- mercaptoethanol, tris(2-carboxyethyl) phosphine hydrochloride, cysteine, 2-mercaptoethylamine, 3-mercaptopropionic acid, and mixtures thereof. In some embodiments, the reducing agent is dithiothreitol.

In some embodiments, the method does not include contacting the sample with a reducing agent.

In some embodiments, the method does not include purifying the sample.

In some embodiments, the mass spectrometry technique is LC-MS/MS. The LC-MS/MS technique can include a quadrupole time-of-flight mass spectrometer. In some embodiments, the mass spectrometry technique is a top-down mass spectrometry technique.

In some embodiments, the sample is a serum sample, a urine sample, a cerebrospinal fluid sample, or whole blood.

In some embodiments, the sample is from a single subject and the method further includes diagnosing a disorder in the subject wherein the disorder is a plasma cell dyscrasia. For example, the sample can be from a single subject and the method can further include diagnosing at least one of a multiple myeloma or a light chain amyloidosis.

In some embodiments, the sample is from a subject and the method further comprises diagnosing a disorder in the subject wherein the disorder is at least one of multiple myeloma, monoclonal gammopathy of undetermined significance, B-cell chronic lymphocytic leukemia, Waldenstroms macrogloblinemia, amyloid light chain amyloidosis, or non-secretory myeloma.

In some embodiments, the sample is from a subject and the method further comprises distinguishing an auto-immune response from a monoclonal gammopathy in the subject.

Also provided herein is a method for identifying one or more immunoglobulin free light chains in a sample that includes (a) providing a sample; (b) contacting the sample with a reducing agent; (c) subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and (d) identifying the presence or absence of one or more

immunoglobulin free light chains.

Additionally, provided herein is a method for diagnosing a disorder in a subject. The method includes (a) providing a sample from the subject; (b) subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and (c) identifying the presence or absence of one or more immunoglobulin free light chains.

In some embodiments, the disorder is selected from multiple myeloma, monoclonal gammopathy of undetermined significance, B-cell chronic lymphocytic leukemia, Waldenstroms macrogloblinemia, amyloid light chain amyloidosis, non-secretory myeloma and combinations thereof.

In some embodiments, after diagnosing the subject as having a disorder, the method further includes administering to the subject a therapeutically effective amount of a therapeutic agent to treat the disorder. The therapeutic agent can include one or more of chlorambucil, fludarabine, cyclophosphamide, rituximab, bendamustine, carfilzomib, cyclophosphamide, doxorubicin, vincristine, prednisone, chlorambucil, obinutuzumab, ofatumumab, pentostatin, alemtuzumab, fludarabine, bortezomib, thalidomide, dexamethasone, doxorubicin, ibrutinib, melphalan, adriamycin, lenalidomide, pomalidomide, a bisphosphonate, a glycosaminoglycans, a purine nucleoside analog, and a monoclonal antibody.

In some embodiments, the disorder is monoclonal gammopathy of undetermined significance and the therapeutic agent is a bisphosphonates.

In some embodiments, the disorder is B-cell chronic lymphocytic leukemia and the therapeutic agent is selected from chlorambucil, fludarabine, cyclophosphamide, rituximab, bendamustine, cyclophosphamide, doxorubicin, vincristine, prednisonea, chlorambucil, obinutuzumab, or ofatumumab, pentostatin, alemtuzumab, fludarabine, monoclonal antibody, and combinations thereof.

In some embodiments, the disorder is Waldenstroms macrogloblinemia and the therapeutic agent is selected from bortezomib, thalidomide, fludarabine, dexamethasone, chlorambucil, rituximab, cyclophosphamide, doxorubicin, vincristine, prednisone, a monoclonal antibody, a purine nucleoside analog, ibrutinib, and combinations thereof.

In some embodiments, the disorder is amyloid light chain amyloidosis and the therapeutic agent is selected from a melphalan, prednisone, vincristine, adriamycin, dexamethasone, bendamustine, thalidomide, cyclophosphamide, lenalidomide, pomalidomide, bortezomib, a glycosaminoglycans, and combinations thereof.

In some embodiments, the disorder is non-secretory myeloma and the therapeutic agent is selected from thalidomide, bortezomib, lenalidomide, carfilzomib, pomalidomide and combinations thereof. Also, provided herein is a method for diagnosing a monoclonal gammopathy in a subject. The includes: (a) providing a sample from the subject; (b) subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and (c) diagnosing a monoclonal gammopathy in the subject based on the identification of one or more free kappa immunoglobulin light chains or one or more free lambda immunoglobulin light chains.

In some embodiments, the method further includes contacting the sample comprising an immunoglobulin free light chain with a reducing agent prior to subjecting the sample to the mass spectrometry technique.

Additionally, provided herein is a method for monitoring a treatment of a monoclonal gammopathy in a subject. The method includes: (a) providing a first sample of the subject, obtained before the treatment; (b) providing a second sample of the subject obtained during or after the treatment; (c) subjecting the first and second samples to a mass spectrometry technique to obtain a mass spectrum of the first and second samples; (d) determining the concentration of at least one of free kappa immunoglobulin light chain or at least one free lambda

immunoglobulin light chain in the first and second samples; and (e) comparing the concentration of the at least one free kappa immunoglobulin light chain or the at least one free lambda immunoglobulin light chain in the first and second samples.

In some embodiments, the method further includes contacting the first and second samples comprising an immunoglobulin free light chain with a reducing agent prior to subjecting the first and second samples to the mass spectrometry technique.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.

Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims. DESCRIPTION OF DRAWINGS

FIG. 1. Shows the LC-MS/MS spectra (non-deconvoluted, FIG. lA and deconvoluted, FIG. IB), for normal serum spiked with HUMIRA®. FIG. 1 A shows the non-deconvoluted LC- MS/MS spectra for normal serum spiked with HUMIRA®. FIG. IB shows the deconvoluted LC-MS/MS spectra for normal serum spiked with HUMIRA®

FIG. 2. Shows the LC-MS/MS spectra of normal serum spiked with both kappa free light chains and HUMIRA®. FIG 2A shows the retention times for the LC-MS/MS spectra of normal serum spiked with both kappa free light chains and HUMIRA®. Fig 2B shows the summed spectra for the LC-MS/MS spectra of normal serum spiked with both kappa free light chains and HUMIRA®

FIG. 3. Shows the LC-MS/MS spectra for normal serum spiked with both lambda free light chains and HUMIRA®. FIG. 3 A shows the LC-MS/MS spectra for normal serum spiked with HUMIRA®. FIG 3B shows the LC-MS/MS spectra for normal serum spiked with both lambda free light chains and HUMIRA®.

FIG. 4. Shows the LC-MS/MS spectra for normal serum spiked with both lambda free light chains and HUMIRA® and shows the presence of an immunoglobulin free light chain dimer. FIG. 4A shows the summed spectra for normal serum spiked with both lambda free light chains and HUMIRA®. FIG 4B shows the spectra for normal serum spiked with both lambda free light chains and HUMIRA®, which has been deconvoluted to show molecular mass.

FIG. 5. Shows the LC-MS/MS results for serial dilutions of kappa immunoglobulin free light chains and lambda free light chains.

FIG. 6. Shows the LC-MS/MS spectra for serum— that has been treated (FIG. 6A), or has not been treated, with dithiothreitol (FIG. 6B)— taken from a patient diagnosed with a monoclonal gammopathy of undetermined significance.

FIG. 7. Shows the top down mass spectrometry spectra for serum taken from a patient diagnosed with monoclonal gammopathy of undetermined significance. FIG. 7A shows the top down mass spectrometry spectra for serum, which has not been treated with dithiothreitol, taken from a patient diagnosed with monoclonal gammopathy of undetermined significance. FIG. 7B shows the top down mass spectrometry spectra for serum, which has been treated with dithiothreitol, taken from a patient diagnosed with monoclonal gammopathy of undetermined significance FIG. 8. Shows the LC-MS/MS spectra for serum taken from a patient diagnosed with smoldering myeloma. FIG. 8A shows the summed mass spectra for serum taken from a patient diagnosed with smoldering myeloma. FIG. 8B shows the spectra for serum taken from a patient diagnosed with smoldering myeloma, which has been deconvoluted to show molecular mass.

FIG. 9. Shows a mass spectra from pooled serum spiked with both adalimumab (500 mg/L) and purified kappa FLC (100 mg/L). The spectra are as follows: (i) FIG. 9A shows multiply charged ions from the kappa FLC monomer along with its retention time and molecular mass determined by deconvolution of the mass spectrum; (ii) FIG. 9B shows multiply charged ions from the kappa FLC dimer along with its retention time and molecular mass determined by deconvolution of the mass spectrum; and (iii) FIG. 9C shows multiply charged ions from adalimumab (heavy chain and light chain intact) along with its retention time and molecular mass determined by deconvolution of the mass spectrum.

FIG. 10. Shows a total ion chromatograms (TIC) from serum after enrichment using

MELON™ GEL. FIG. lOA is from control serum from a healthy donor. FIG. 10B is from an AL patient. The numbered peaks represent signal from high abundance proteins that are not completely removed by MELON™ GEL, which are presumed to be; 1 - (alpha- 1 -antitrypsin), 2 (transferrin), and 3, an unknown 61 kDa protein. Signal presumed to be from an FLC dimer in the AL patient serum is labeled in TIC B.

FIG. 11. Shows a mass spectrum observed after summing spectra over the retention time of the FLC dimer peak shown in Figure 10. The multiply charged ions were deconvoluted to determine the molecular mass of the dimer shown in the inset.

FIG. 12. Shows a mass spectrum showing the FLC monomer along with the inset that shows the molecular mass found after deconvolution of the mass spectrum. The spectrum also shows the multiply charged ions from Al AT which co-elutes with the lambda monomer.

FIG. 13. Shows a total ion chromatograms (TIC) from the same AL patient MELON™ GEL enriched serum sample reduced with DTT (black trace) and non-reduced (no DTT) red trace; same as Figure 10B. The TIC shows that the response from the monoclonal FLC is not as pronounced in the reduced sample as the non-reduced sample as a result of the substantial increase in the response observed in the mass spectrometer by the polyclonal light chains as they are reduced off of their corresponding heavy chains. FIG. 14. Shows a mass spectrum showing the FLC lambda monomer multiply charged ions from the AL patient serum in its reduced form. The inset shows the molecular mass of the reduced monoclonal lambda light chain after deconvolution. The mass spectrum also shows at m/z = 2100 the polyclonal lambda and kappa +11 charge states with the lambda monoclonal light chain clearly observed in the lambda polyclonal distribution.

FIG. 15. Shows a top-down MS fragment ion mass spectrum showing the C-terminal y-ions from a cysteinylated kappa FLC in its non-reduced form (top) and non-cysteinylated kappa light chain in reduced form (bottom). The y7+cysteinylation fragment ion and yi fragment ion are labeled with an arrow to show the difference in the mass due to cysteinylation of the C-terminal cysteine residue.

FIG. 16. Shows the Linear regression analysis of AL patient FLC. The graphs were generated by plotting the concentration of the FLC by nephelometry against the peak area for the FLC observed in the mass spectrometer. The R² correlation coefficients are listed for kappa and lambda FLC with outliers removed.

FIG. 17. Shows a mass spectrum showing the FLC lambda monomer multiply charged ions from a patient sample including glycosylated FLCs (top). The inset shows the molecular mass of the glycosylated light chain after deconvolution.

FIG. 18. Shows a top-down MS fragment ion mass spectrum showing detection and confirmation of glycosylation of FLCs.

DETAILED DESCRIPTION

Normal plasma cells produce excess kappa and light chains which are excreted into serum (free light chains, FLC). Approximately twice as many kappa to lambda light chains are produced in humans. Each FLC molecule contains approximately 220 amino acids and each molecule is composed of an N-terminal domain that contains the variable (VL) region and a C-terminal domain that contains the constant (CL) region. This methods described herein utilize the unique mass of the VL region as a marker of plasma cell clonality.

Plasma cell immunoglobulin production involves the matching of a light chain (LC) with a heavy chain (HC) via a disulfide bond. The HC-LC dimer is then coupled to another HC-LC dimer through additional disulfide bonds to form an immunoglobulin that is secreted from the cell. During normal immunoglobulin production plasma cells produce excess polyclonal free light chains (FLC) that are secreted into circulation and in healthy individuals these excess FLC are reabsorbed and metabolized in the kidney. However, individuals with a plasmaproliferative disorder have a population of clonal plasma cells that secrete a

monoclonal FLC into circulation at a concentration higher than the normal polyclonal LC repertoire. A clinical application of serum FLC measurements are for patients with

monoclonal gammopathies. In these diseases, a dysregulated or malignant plasma cell clone, or clones, overproduce Igs and FLCs in comparison to the normal polyclonal background, which can be detected by skewed kappa/lambda FLC ratios or by quantitation of an Ig in excess of the poly clonal background.

Currently in clinical medicine, FLC ratios are measured by immunoassays that rely on specific antibodies, which bind to antigenic sites in the FLC. However, current methods are not specific for individual kappa and lambda FLCs and, hence, quantitation of these groups includes the polyclonal background. Accordingly, monoclonality must be inferred from the kappa/lambda ratio. Unfortunately, the reliance on kappa/lambda ratios can be affected by other conditions occurring in the patient. For example, patients who have autoimmune disease may have skewed polyclonal kappa and lambda ratios independent of or in addition to a monoclonal gammopathy.

The methods described herein utilize high mass accuracy to measure FLCs in serum, urine, cerebrospinal fluid (CSF), and other body fluids. The mass accuracy allows for direct quantitation of each kappa and lambda light chain. Thus, a reliance on kappa and lambda ratios alone are not necessary to infer monoclonality.

Provided herein is a method for identifying one or more immunoglobulin free light chains in a sample. The method includes (a) providing a sample; (b) subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and identifying the presence or absence of the one or more immunoglobulin free light chains.

As used herein, the term "immunoglobulin free light chains" refers to the excess kappa and lambda light chains that are excreted from plasma cells into serum (free light chains, FLC). Immunoglobulin free light chains can also refer to dimers of immunoglobulin free light chains.

In some embodiments, the sample is suspected to include an immunoglobulin free light chain. In some embodiments, the one or more immunoglobulin free light chains are selected from the group consisting of free kappa light chains, free lambda light chains, and mixtures thereof. For example, the immunoglobulin free light chain can be a free kappa light chain. Additionally, the method can include identifying at least two free kappa light chains (i.e. kappa light chains having distinct mass or mass to charge ratios). In some embodiments, the immunoglobulin free light chain is a free lambda light chain. Additionally, the method can include identifying at least two free lambda light chains (i.e. lambda light chains having distinct mass or mass to charge ratios).

In some embodiments, the one or more immunoglobulin free light chains include at least one of a glycosylated immunoglobulin free light chain, a cysteinylated immunoglobulin free light chain, and a glutathionylated immunoglobulin free light chain. For example, the one or more immunoglobulin free light chains can include at least one of a glycosylated

immunoglobulin free light chain and a cysteinylated immunoglobulin free light chain. A cysteinylated immunoglobulin free light chain can be identified based on the difference between the mass observed for the immunoglobulin free light chain and the mass calculated for the immunoglobulin free light chain. For example a difference of about 119 Daltons (Da) between the mass observed for the immunoglobulin free light chain and the mass calculated for the immunoglobulin free light chain can indicate the presence of a cysteinylated immunoglobulin free light chain. Similarly, a glutathionylated immunoglobulin free light chain can be identified if the difference between the mass observed for the immunoglobulin free light chain and the mass calculated for the immunoglobulin free light chain. For example, a difference of about 305 Da, which is equal to the mass of a glutathione addition to a cysteine residue, between the mass observed for the immunoglobulin free light chain and the mass calculated for the

immunoglobulin free light chain can indicate the presence of a glutathionylated immunoglobulin free light chain.

Exemplary scans of a sample containing glycosylated immunoglobulin free light chains using the methods described herein is show in Figures 17 and 18.

In some embodiments, the identifying the one or more immunoglobulin free light chains occurs in the presence of a polyclonal background.

In some embodiments, the method further includes measuring the concentration of the one or more immunoglobulin free light chains in the sample. For example, the concentration of the one or more immunoglobulin free light chains can be measured by examining the peak area of the resulting mass spectrometry spectrum and comparing this to a standardized curve. In some embodiments, an internal sample can be included in or added to the sample.

In some embodiments, the method further includes-identifying at least one

immunoglobulin free light chain dimer. For example, a kappa free light chain dimer or a lambda free light chain dimer.

In some embodiments, the method further includes contacting the sample with a reducing agent prior to subjecting the sample to the mass spectrometry technique. The immunoglobulin light chains can be decoupled from immunoglobulin heavy chains by cleavage of the disulfide bonds between the light and heavy chains. Additionally, the reducing agent can decouple immunoglobulin free light chain dimers by reducing disulfide bonds. The reducing agent can be selected from the group consisting of dithiothreitol (DTT), reduced glutathione, β- mercaptoethanol, tris(2-carboxyethyl) phosphine hydrochloride, cysteine, 2-mercaptoethylamine, 3-mercaptopropionic acid, and mixtures thereof. In some embodiments, the reducing agent is dithiothreitol.

In some embodiments, the method does not include purifying the sample prior to subjecting the sample to a mass spectrometry technique. For example, in some embodiments, the method does not include immunopurifying the sample prior to subjecting the sample to the mass spectrometry technique. Similarly, in some embodiments, the method does not include performing chromatography on the sample prior to subjecting the sample to the mass

spectrometry technique. In some embodiments, the method does not include purifying the sample (e.g., immunopurification) prior to subjecting the sample to the mass spectrometry technique but does include centrifuging the sample prior to subjecting the sample to the mass spectrometry technique. In some embodiments, the method does not include immunopurification prior to subjecting the sample to the mass spectrometry technique. In some embodiments, the method includes immunopurification with antibodies (e.g., antibodies specific for

immunoglobulin free light chains). In some embodiments, the method includes purification using a MELON™ GEL.

In some embodiments, prior to subjecting the sample to the mass spectrometry technique, the sample can be purified by affinity purification, (e.g., MELON™ GEL purification, such as mixing the sample with MELON™ GEL beads). Further, the method can include contacting the sample with a non-reducing buffer (e.g., ammonium bicarbonate) prior to subjecting the sample to the mass spectrometry technique.

In some embodiments, the mass spectrometry technique is LC-MS/MS. The LC-MS/MS technique can include a quadrupole time-of-flight mass spectrometer. A quadrupole mass analyzer (Q) consists of four cylindrical rods, set parallel to each other. In a quadrupole mass spectrometer, the quadrupole is the component of the instrument responsible for filtering sample ions based on their mass-to-charge ratio (m/z). The time-of-flight (TOF) analyzer uses an electric field to accelerate the ions through the same potential, and then measures the time they take to reach the detector. If the particles all have the same charge, the kinetic energies are identical, and their velocities depend only on their masses. Lighter ions reach the detector first. Any ESI-Q-TOF mass spectrometer can be used, e.g., the ABSciex TripleTOF 5600 quadrupole time-of-flight mass spectrometer. The mass spectrum, e.g., the mass spectrum of multiply charged intact light chain or heavy chain polypeptide ions, can be analyzed to identify one or more peaks at an appropriate mass/charge expected for the chain. For example, for the light chains, the peaks can occur at about 600 - 2700 m/z, 700 - 2400 m/z, 800 - 2100 m/z, 900 - 1800 m/z, 1000 - 1600 m/z, or about 1000 - 1500 m/z. In some embodiments, the peaks can occur at about 600 - 2500 m/z. Fragment ion peaks can be detected at a range of m/z of 250- 2000. In some embodiments, at least one of a +11 and a +18 charge state is used for a immunoglobulin free light chain monomer. For example, the peak area from an extracted ion chromatogram (EIC) generated using the +18 charge state for the immunoglobulin free light chain monomer can be used to calculate the %CV values. In some embodiments, at least one of a +33 and a +36 charge state is used for an immunoglobulin free light chain dimer. For example, the peak area from an extracted ion chromatogram (EIC) generated using the +36 charge state for the immunoglobulin free light chain dimer can be used to calculate the %CV values. In some embodiments, the source conditions include an IS (ion spray voltage) of about 4500 volts (V) to about 6500 V or about 5000 V to 6000 V, or about 4500 V, 5000 V, 5500 V, 6000 V, or about 6500 V. For example, the source conditions can include an IS of about 5500 V.

In some embodiments the source conditions include a temperature of about 350 °C to about 650 °C, about 400 °C to about 600 °C, about 450 °C to about 550 °C, or about 475 °C to about 525 °C, or about 350 °C, 400 °C, 450 °C, 475 °C, 500 °C, 525 °C, 550 °C, 600 °C, or about 650 °C. For example, the source conditions can include a temperature of about 500 °C.

In some embodiments the source conditions include a curtain gas flow (CUR) of about 35 to about 55, or about 40 to about 50, or about 35, 40, 45, 50, or about 55. For example, the source conditions can include a curtain pressure (CUR) of about 45.

In some embodiments the source conditions include an ion source gas 1 (GSl) of about 25 to about 45 or about 30 to about 40, or about 25, 30, 35, 40, or about 45. For example, the source conditions can include an ion source gas 1 (GSl) of about 35.

In some embodiments the source conditions include an ion source gas 2 (GS2) of about 20 about 40 or about 25 to about 35, or about 20, 25, 30, 35, or about 40. For example, the source conditions can include an ion source gas 2 (GS2) of about 30.

In some embodiments the source conditions include a collision energy (CE) (e.g., the potential drop across the collision cell) of 30±5, 40±5, 50±5, 60±5, or 70 50±5. For example, the source conditions can include a CE of 50±5.

In some embodiments the source conditions include an IS of about 5500, a temperature of about 500 °C, a CUR of about 45 psi, a GSl of about 35 psi, a GS2 of about 30 psi, and a CE of 50±5.

In some embodiments, the mass spectrometry technique is a top-down mass spectrometry technique. For example, when a top-down mass spectrometry technique is used the method can include identifying the isotype of an immunoglobulin free light chain.

Additional mass spectrometry techniques are described in PCT/US2015/24379 and PCT/US2014/022475, each of which is incorporated by reference in its entirety.

In some embodiments, the sample is from a single subject and the method further includes diagnosing a disorder in the subject wherein the disorder is a plasma cell dyscrasia. For example, the sample can be from a single subject and the method can further include diagnosing at least one of a multiple myeloma or a light chain amyloidosis. In some embodiments, the sample is a serum sample, a urine sample, a cerebrospinal fluid sample, or a whole blood sample.

In some embodiments, the sample is from a single subject and the method further comprises diagnosing a disorder in the subject wherein the disorder is at least one of monoclonal gammopathy of undetermined significance, B-cell chronic lymphocytic leukemia, Waldenstrom macrogloblinemia, amyloid light chain amyloidosis, or non-secretory myeloma.

In normal serum samples the free kappa light chains can have a range, 3.3-19.4 mg/L and the free lambda light chains can have a range of 5.7-26.3 mg/L. See, e.g., Clin Chem. 2002 Sep; 48(9) pages 1437-44.

In some embodiments, the sample is from a single subject and the method further comprises distinguishing an auto-immune response from a monoclonal gammopathy in the subject.

Also provided here in is a method for identifying one or more immunoglobulin free light chains in a sample that includes (a) providing a sample; (b) contacting the sample with a reducing agent; (c) subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and (d) identifying the presence or absence of one or more

immunoglobulin free light chains.

Additionally, provided herein is a method for diagnosing a disorder in a subject. The method includes (a) providing a sample from the subject; (b) subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and (c) identifying the presence or absence of one or more immunoglobulin free light chain.

In some embodiments, the disorder is a monoclonal gammopathy. In some embodiments, the disorder is selected from multiple myeloma, monoclonal gammopathy of undetermined significance, B-cell chronic lymphocytic leukemia, Waldenstrom's macrogloblinemia, amyloid light chain amyloidosis, non-secretory myeloma and combinations thereof.

In some embodiments, the sample is a serum sample, a urine sample, a cerebrospinal fluid sample, or a whole blood sample.

In some embodiments, after diagnosing the subject as having a disorder, the method further includes administering to the subject a therapeutic agent to treat the disorder (e.g., a therapeutically effective amount). The therapeutic agent can include one or more of

chlorambucil, fludarabine, cyclophosphamide, bendamustine, carfilzomib, cyclophosphamide, doxorubicin, vincristine, prednisone, chlorambucil, pentostatin, fludarabine, bortezomib, thalidomide, dexamethasone, doxorubicin, ibrutinib, melphalan, adriamycin, lenalidomide, pomalidomide, a bisphosphonate, a glycosaminoglycans, a purine nucleoside analog, and a monoclonal antibody (e.g., rituximab, obinutuzumab, and alemtuzumab).

In some embodiments, the disorder is monoclonal gammopathy of undetermined significance and the therapeutic agent is a bisphosphonates. Non-limiting examples of bisphosphonates include alendronate (e.g., BINOSTO®, FOSAMAX®, risedronate (e.g., ACTONEL®, ATELVIA®), ibandronate (e.g., BONIVA®) and zoledronic acid (e.g.,

RECLAST®, ZOMETA®)

In some embodiments, the disorder is B-cell chronic lymphocytic leukemia and the therapeutic agent is selected from chlorambucil, fludarabine (e.g., FLUDARA®),

cyclophosphamide (e.g., CYTOXAN®), bendamustine, cyclophosphamide, doxorubicin, vincristine (e.g., ONCOVIN®), prednisonea, chlorambucil, obinutuzumab, ofatumumab, pentostatin (e.g., NIPENT®), alemtuzumab (e.g., CAMPATH®), fludarabine, a monoclonal antibody (e.g., rituximab), and combinations thereof.

In some embodiments, the disorder is Waldenstroms macrogloblinemia and the therapeutic agent is selected from bortezomib, thalidomide, fludarabine, dexamethasone, chlorambucil, cyclophosphamide, doxorubicin, vincristine, prednisone, a monoclonal antibody (e.g., rituximab), a purine nucleoside analog (e.g., cladribine), ibrutinib, and combinations thereof.

In some embodiments, the disorder is amyloid light chain amyloidosis and the therapeutic agent is selected from a melphalan, prednisone, vincristine, adriamycin, dexamethasone, bendamustine, thalidomide, cyclophosphamide, lenalidomide, pomalidomide, bortezomib, a glycosaminoglycans (e.g., eprodisate), and combinations thereof.

In some embodiments, the disorder is non-secretory myeloma and the therapeutic agent is selected from thalidomide, bortezomib, lenalidomide, carfilzomib, pomalidomide and combinations thereof.

In some embodiments, after diagnosing the subject as having a disorder, the method further includes performing a treatment such as a plasma exchange or a stem cell transplant (e.g., an autologous peripheral blood stem cell transplantation). In some embodiments, after diagnosing the subject as having a disorder, the method further includes administering to the subject a therapeutically effective amount of a therapeutic agent to treat the disorder and one or more of a plasma exchange and a stem cell transplant

Also, provided herein is a method for diagnosing a monoclonal gammopathy in a subject. The method includes: (a) providing a sample from the subject; (b) subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and (c) diagnosing a monoclonal gammopathy in the subject based on the identification of one or more free kappa immunoglobulin light chains or one or more free lambda immunoglobulin light chains.

immunoglobulin light chain in the first and second samples; and (e) comparing the concentration of the at least one free kappa immunoglobulin light chain or the at least one free lambda immunoglobulin light chain in the first and second samples. The first sample obtained before treatment can be obtained before the start of any treatment, before the start of a particular administration regime, or before a single administration. During the monitoring of treatment, a decrease in the peak height or peak area of an identified immunoglobulin free light chain can indicate that the treatment is progressing positively. Likewise, during the monitoring of treatment, a decrease in concentration of an identified immunoglobulin free light chain can indicate that the treatment is progressing positively. During the monitoring of treatment, an increase in the peak height or peak area of an identified immunoglobulin free light chain can indicate that the dosage of therapeutic agent should be increased. Likewise, during the monitoring of treatment, an increase in concentration of an identified immunoglobulin free light chain can indicate that the dosage of therapeutic agent should be increased. In some embodiments, the method further includes contacting the first and second samples comprising an immunoglobulin free light chain with a reducing agent prior to subjecting the first and second samples to the mass spectrometry technique.

EXAMPLES

Example 1. Detecting kappa FLC in a spiked sample.

Two spiked samples were made using normal pooled serum. Sample A was spiked with 0.5g/dL HUMIRA® (a monoclonal IgG kappa therapeutic antibody) while sample B was spiked with both HUMIRA® and commercially available kappa light chains at 0.125 g/dL. Next, 50 μΐ. of each spiked serum was diluted to with 450 μΐ_^ of MELON™ Gel buffer and added to a spin column and mixed for 5 minutes.

After centrifuging, a 2 μΐ_^ injection of the purified samples was made onto a 1.0 x 75 mm Poroshell 300SB-C3, 5 μπι column flowing at 25 μΕ/ιηίηυΐε. A 15 minute gradient was started at 80%A / 20%B, held for 0.5 minutes, ramped to 70%A / 30%B over 1 minute, then ramped to 60%A / 40%B over 4 minutes, then ramped to 5%A / 95%B over 5 minutes, held for 2.5 minutes, then ramped to 80%A / 20% over 1 minute, then equilibrating at 80%A / 20% for 1 minute.

Spectra were collected on an ABSciex TripleTOF 5600 quadrupole time-of- flight mass spectrometer (ABSciex, Vaughan ON, CA) in ESI positive mode with a Turbo V dual ion source with an automated calibrant delivery system (CDS). Source conditions were: IS: 5500, Temp: 500, CUR: 45, GS1 : 35, GS2: 30, CE: 50±5. TOF MS scans were acquired from m/z 600-2500 with an acquisition time of 100 ms. Fragment ion scans were acquired from m/z 350- 2000 with an acquisition time of 100 ms. The instrument was calibrated every 5 injections through the CDS using calibration solution supplied by the manufacturer.

The resulting mass distribution demonstrates the ability to this method detect kappa free light chains (FLCs) from intact monoclonal Igs (HUMIRA®) which is not dependent on the ratio of kappa/lambda FLCs. Figure 1 shows the results (non-deconvoluted and deconvoluted) of the normal serum spike with HUMIRA® only and demonstrates the detection of the intact Ig.

Figure 2 shows the results of the normal serum spiked with both kappa FLCs and HUMIRA® and demonstrates the methods ability to detect the FLC in the presence of the Intact Ig.

Example 2. Detecting kappa FLC in a spiked sample.

Two spiked samples were made using normal pooled serum. Sample A was spiked with 0.5g/dL HUMIRA® (a monoclonal IgG kappa therapeutic antibody) while sample B was spiked with both HUMIRA® and commercially available lambda light chains at 0.125 g/dL. The samples were subjected to the analysis procedure as described in Example 1.

The resulting mass distribution demonstrates the ability to this method detect lambda free light chains (FLCs) from intact monoclonal Igs (HUMIRA®), which is not dependent on the ratio of kappa/lambda FLCs. Figure 3 shows the results of the normal serum spiked with both lambda FLCs and HUMIRA® and demonstrates the ability to detect FLC in the presence of intact Ig. In this example, as shown in Figure 4, the method was able to confirm not only the presence of the FLC but also demonstrate that the light chain was circulating as a dimer.

Example 3. Measuring FLC Quantities in Serum.

Serial dilutions of the kappa and lambda FLCs were made by diluting normal human serum spike with kappa and lambda free light chains. Quantitation of the amount of free light chain was performed using the procedure described in Example. Figure 5 shows that the peak area of the FLC is directly proportional to the concentration of FLC in serum.

Example 4. Precision of FLC measurement.

Human serum was spiked with 0.125 g/dL kappa FLC and was repeatedly measured 12 times using the procedure described in Example 1. The peak area percent variation was determined to be 8.8%. This amount of variation is acceptable for clinical practice.

Example 5. Detecting FLC in a patient with a monoclonal gammopathy.

Serum from a 77 year old MGUS (monoclonal gammopathy of undetermined

significance) patient (A) with an IgG kappa monoclonal gammopathy with an associated abnormal kappa/lambda FLC ratio of 3.81 by nephelometry was examined using the procedure described in Example 1. A second sample from the same patient was treated with DTT

(dithiothreitol) reducing agent to separate the light and heavy chains prior to Ig isolation and measurement.

The resulting spectra are shown in figures 6A and 6B and demonstrate that kappa FLC has a slightly different mass than the kappa clone associated with the intact IgG kappa. Figure 7 shows that by using top-down mass spectrometry, the fragmentation pattern reveals a kappa constant region for each ion.

Example 6.

Serum from a 70 year old smoldering myeloma patient (A) with an IgG lambda monoclonal gammopathy with an associated abnormal kappa/lambda FLC ratio of 0.483 by nephelometry was examined using the procedure described in Example 1. The resulting spectra are shown in figure 8 and demonstrate the presence of multiple lambda based clones. The ability to detect multiple FLC is unique to this method.

Example 7

Materials

Serum samples: Fifteen serum samples from patients with AL were obtained under patient informed consent associated with the amyloid biobank IRB protocol 521-93 at the Mayo Clinic in Rochester Minnesota. An additional fifteen serum samples from patients with AL were obtained under patient informed consent associated with the amyloid biobank (Giampaolo please fill in the IRB number) at IRCCS Policlinico San Matteo in Pavia, Italy.

Reagents: Ammonium bicarbonate, dithiothreitol (DTT), and formic acid were purchased from Sigma-Aldrich (St. Louis, MO). Water, acetonitrile, and 2-propanol were purchased from Honeywell Burdick and Jackson (Muskegon, MI).

Monoclonal Immunoglobulins: The therapeutic monoclonal immunoglobulin adalimumab (Humira) was purchased from Abbott Laboratories (Chicago, IL). Lambda and Kappa immunoglobulin light chain standards were purchased from Bethyl Laboratories (Montgomery, TX). The standards were purified from the urine of patients with multiple myeloma who consented to have their urine used as a source for a monoclonal immunoglobulin light chain standard. The concentration of each standard was confirmed using The Binding Site FLC nephelometric assay. Bradwell AR, Carr-Smith HD, Mead GP, et al. "Highly sensitive, automated immunoassay for immunoglobulin free light chains in serum and urine. " Clinical chemistry. 2001;47(4):673-680.

Serum FLC Preparation: A volume of 20 μΕ of serum was mixed with 200 μΕ of MELON™ GEL bead slurry in a 1.5 mL microcentrifuge tube (Thermo-Fisher Scientific, Waltham MA). The serum and beads were mixed on a shaker for 5 minutes at room temperature after which the beads were allowed to settle. A volume of 20 μL· of MELON GEL supernatant containing the FLC was removed and mixed with 20 μΕ of 50 mM ammonium bicarbonate and then analyzed by microLC-ESI-Q-TOF MS. MELON™ GEL purified samples were also analyzed after reduction with DTT. In this case a volume of 20 μΕ of MELON™ GEL supernatant was mixed with 20 μΕ of 50 mM ammonium bicarbonate 10 μΕ of 200 mM DTT and allowed to reduce at 55°C for 15 minutes before being analyzed by microLC-ESI-Q-TOF MS.

LC Conditions: An Eksigent Ekspert 200 microLC (Dublin, CA) was used for separation;

mobile phase A was water+0.1% FA, and mobile phase B was 90% acetonitrile+10% 2- propanol+0.1% FA. A 2 μΕ injection was made onto a 1.0 x 75 mm Poroshell 300SB-C3, 5 μπι column heated to 60 and flowing at 25 μΕ/πήηυΐε. A 25 minute gradient was started at 80%A / 20%B, held for 1 minute, ramped to 75%A / 25%B over 1 minutes, then ramped to 65%A / 35%B over 10 minutes, then ramped to 50%A / 50%B over 4 minutes, then ramped to 95%A / 5%B over 2 minutes held for 5 minutes, then ramped to 80%A / 20% over 1 minute, then equilibrating at 80%A / 20% for 1 minute.

ESI-Q-TOF MS: Spectra were collected on an ABSciex TripleTOF 5600 quadrupole time-of- flight mass spectrometer (ABSciex, Vaughan ON, CA) in ESI positive mode with a Turbo V dual ion source with an automated calibrant delivery system. Source conditions were: IS: 5500, Temp: 500, CUR: 45, GSl : 35, GS2: 30, CE: 50±5. TOF MS scans were acquired from m/z 600- 2500 with an acquisition time of 100 ms. The instrument was calibrated every 5 injections through the CDS using calibration solution supplied by the manufacturer.

MS Data Analysis: Analyst TF vl .6 was used for instrument control. Data were viewed using Analyst TF vl .6 and Peak View vl .2.0.3. Multiply charged ion peak centroids were used to calculate average molecular mass and the peak area value used for quantification through BioAnalyst software provided with Analyst TF. Multiple ion deconvolution was performed using the Bayesian Protein Reconstruct software package in BioAnalyst. The following settings were used: Start mass (Da) = 22,000, Stop mass (Da) = 65,000Da, Step mass (Da) = 1, S/N threshold = 20, Minimum intensity% = 0, Iterations = 20, Adduct: Hydrogen. All masses are reported as average molecular mass.

Results.

Purified FLC and adalimumab in normal serum as a model system

It has previously been shown that the therapeutic mAb adalimumab works well as a standard for simulating a monoclonal immunoglobulin in serum. In the set of experiments presented here, adalimumab and purified kappa FLC was spiked into serum pooled from healthy individuals. Figure 9 shows three mass spectra acquired from pooled serum spiked with both adalimumab at a concentration of 500 mg/L and purified kappa FLC at a concentration of 100 mg/L. The mass spectrum labeled A was generated by summing mass spectra over a retention time of 6.0 to 6.5 minutes and clearly shows the multiple charge states for the monomer form of the kappa FLC between m/z = 1,000 to 1,500 Da. There is also a heterogeneous set of other multiply charged ions observed above m/z = 1,500. The most abundant ions are associated with a protein having a molecular mass of 45,056.5 Da, which is likely the most common glycoform of alpha-1- antitrypsin (Al AT). These peaks are also found in normal pooled serum. The mass spectrum labeled B was generated by summing mass spectra over a retention time of 6.8 to 7.3 minutes and clearly shows the dimer form of the kappa FLC between m/z = 1,000 to 1,500 Da. The mass spectrum labeled C shows the intact adalimumab at a retention time of 7.4 to 8.0 minutes where the multiply charged ions from the mAb are found between m/z = 2,500 to 3,500 Da. The other multiply charged ions observed between m/z = 1,800 to 2,200 have a calculated molecular mass of 79,551.9 Da and is likely transferrin (Tf) which is present in normal pooled serum without kappa FLC. It is known that MELON™ GEL does not completely deplete transferrin from serum. Imprecision in the microLC-ESI-Q-TOF MS portion of the methodology was examined by performing 20 replicate injections from the same well of 100 mg/L kappa FLC spiked into normal pooled serum. The peak area from the extracted ion chromatogram (EIC) generated using the +18 charge state for the monomer (Figure 9A, m/z = 1,316.78 Da) and the +36 charge state for the dimer (Figure 9B, m/z = 1,310.11 Da) were used to calculate the %CV values. The %CV's were; 5.6 for the monomer, 3.5 for the dimer, and 6.6 for the ratio of dimer to monomer. Serial dilutions (100, 50, 25, 12.5, 6.25. 3.12) were also prepared starting with the 100 mg/L kappa FLC spiked into normal pooled serum diluted with normal serum. Linear regression analysis of the monomer and dimer were performed using the EIC peak areas. The monomer linear regression analysis of the serial dilutions had an R² = 0.996 while the dimer linear regression analysis had an R² = 0.993. The monomer was detected from 6.25 mg/L to 100 mg/L while the dimer was detected from 3.12 mg/L to 100 mg/L. The molecular masses for the kappa FLC monomer and dimer and the adalimumab are also listed in Figure 9. The calculated molecular mass of the monomer found by dividing the dimer by two and adding the mass of a proton is 23,565.3 Da. The difference in the mass between the observed monomer mass and the calculated monomer mass (23,684.3 - 23,565.3) equals 119.0 Da. This mass matches the molecular mass of a cysteinylated cysteine residue. After adding DTT to the sample the dimer was no longer observed and the molecular mass of the monomer was 23,565.3 Da. Imprecision was also examined on 20 replicate injections from the same well of a 100 mg/L purified lambda FLC spiked into normal pooled serum. In these spectra only the dimer of the lambda FLC was observed. To generate the EIC the +33 charge state of the dimer {m/z = 1,373.56 Da) was used and a %CV of 6.9 was found for the peak areas from the replicate injections.

AL Patient Cohort Comparison

After demonstrating that FLC could be enriched from serum using MELON™ GEL, a cohort of 30 patients with confirmed cases of amyloidosis (15 from the Pavia biobank and 15 from the Mayo biobank) was examined. All patient samples were examined in their non-reduced (no DTT; FLC present) and reduced (with DTT; all light chains observed) forms using the same methodology as described for the model FLC preparations. The process of determining the FLC and non-FLC light chains in patient samples is presented in below for an AL patient with a known lambda FLC.

An example of a total ion chromatogram (TIC) from non-reduced serum is shown in Figure 10 where the normal serum TIC is labeled A and the patient with AL serum TIC is labeled B. The TICs have three peaks labeled 1, 2, and 3 presumed to be alpha- 1 -antitrypsin (Al AT), transferrin (Trf), and an unknown 61 kDa protein, respectively. However, the TIC from the AL patient shows a peak that is not observed in the control at a retention time of 6.3 minutes. Figure 11 shows the mass spectrum observed after summing mass spectra over the retention time of this peak. The mass spectrum clearly shows a series of multiply charged ions and the inset shows the deconvoluted spectrum for these ions with the calculated molecular mass of 45,388.4 Da. These ions were assumed to be a dimer comprised of two FLC lambda monomers each with a monomer molecular mass of 22,699.2 Da (45,388.4 / 2 + 1H (reduced cysteine that formed the dimer) + 4H (reduced internal disulfide bonds). The monomer form of the FLC was not readily apparent by observing the TIC alone. To identify the monomer, mass spectra were summed over 30 second retention time windows and manually searched. The FLC monomer was found to coelute with peak 1 with a retention time of 5.5 to 6.6 minutes. The isotype of the FLC was confirmed to be lambda using top-down MS. Figure 12 shows the mass spectrum generated over this retention time which shows that the peak contains two different sets of multiply charged ions. Deconvolution of the ions within the range m/z = 1,000 to 1,600 resulted in a single peak with a molecular mass of 22,813.9 Da as shown in the inset to Figure 12. Deconvolution of the ions within the range m/z = 1,700 to 2,400 resulted in multiple ions that matched the Al AT isoforms observed in the normal control serum.

Since the calculated molecular mass of the monomer did not match the observed mass of the monomer, the sample was reduced with DTT. The goal of this experiment was to; 1) determine if the dimer would be reduced into two monomers; and 2) determine if the molecular mass of the resulting monomer matched the molecular mass of the FLC monomer. Figure 13 shows an overlay of the TIC's from the same sample before (red trace) and after (black trace) the addition of DTT. The intensity of the TIC from the reduced sample in Figure 13 is over two-fold higher than the TIC shown in Figure 10 from the non-reduced samples. This is due to the contribution to the overall ion current from the polyclonal kappa and lambda light chains and their corresponding heavy chains that are now observed by the mass spectrometer since they are in their reduced form where the multiply charged ions from these species are now within the m/z scan range window of the experiment. An FLC monomer was observed after manually summing mass spectra in 30 second retention time intervals and was found to have a retention time of 6.2 to 6.7 minutes. The multiply charged ions found in this retention time window are shown in Figure 14. The calculated of molecular mass of these multiply charged ions was found to be 22,698.9 Da as seen in the inset. The isotype of the monoclonal light chain was confirmed to be lambda by top-down MS 4. There is only a 0.3 Da mass difference from the calculated molecular mass of the lambda light chain monomer and the observed molecular mass from Figure 14.

The molecular mass of the monomer in the non-reduced sample is 116 Da greater in mass than the monomer observed in the reduced sample, which is close to the known post-translation modification due to cysteinylation (addition of + 119 Da) of the C-terminal cysteine as previously described by others. Several of the AL patients in the cohort examined using the methods disclosed herein (e.g., monoclonal immunoglobulin Rapid Accurate Mass Measurement - miRAMM) had kappa FLC. Top-down MS was performed on non-reduced and reduced kappa FLC monomers that displayed a mass difference of +119 Da indicative of cysteinylation. Figure 15 shows top-down MS mass spectra from a non-reduced (top) and reduced (bottom) kappa FLC monomer. Monoclonal kappa light chains produce predominantly C-terminal y-ions by top-down MS 4 and as a result, each C-terminal fragment ion from the non-reduced FLC is +119 Da greater in mass compared to the reduced FLC since the cysteinylation takes place at the C- terminal cysteine. This observation confirms the position of the cysteinylation in the kappa FLC monomer and is the first report using top-down MS to characgterize cysteinylation in a monoclonal light chain.

Results from the AL patient cohort examined using the methods disclosed herein are listed in Table 1. The table lists the non-reduced FLC molecular mass, the occurrence of monomer and/or dimers, observed post-translational modifications (PTM), the reduced FLC molecular mass, and the FLC isotype. The table highlights the extraordinary specificity of the methods disclosed herein for identifying FLC in serum as evident by the accurate molecular mass data. However, the methods disclosed herein also provide information on the presence of dimers and/or monomers and PTM's in the same analysis. For example, the sample Pavia 7 had two monomer and two dimer FLC isoforms along with PTM's cysteinylation and

glutathionylation. The glutathionylation was presumed to be present since the mass difference between the two distinct monomers and dimers in the non-reduced sample was 305 Da which is equal to the mass of a glutathione addition to a cysteine residue 21. This mass difference is also observed in the monomers in the reduced sample which suggests that the PTM is stable under the reducing conditions used 22. The cysteinylation PTM was assumed since the observed mass difference between the FLC monomers in the non-reduced sample and the reduced sample is 117 Da, which would equate to the loss of cysteinylation (+119 Da) followed by the loss of 2 hydrogens after interdisulfide bond reformation. Patients that showed a loss in the range of -116 to -119 Da between the non-reduced sample and the reduced sample were labeled as having evidence for cysteinylation. Several of the patients had FLC that exhibited glycosylation as evidenced by the increased molecular mass of the FLC and the oligoclonal nature (2 to 4 glycoforms) of the LC mass speaks that differed by a hexose (162 Da) that were conserved in both the non-reduced and reduced samples and only the most abundant glycoforms are listed in Table 1

Table 1

Non-Reduced Non-Reduced FLC Reduced

Biobank Molecular Mass isoform PTM Molecular Mass Isotyp

Pavia 1 50,550 Dimer g!ycosy!ation 25,280 L

Pavia 2 22,815 + 45.338 Dimer- Monomer cysteinytation 22,699 L

Pavia 3 23,463 Monomer cysteinyiation 23,344 K giycosyiatiori +

Pavia 4 26.371+ 52,504 Dimer+Monomer cysteinytation 26,252 K

Pavia 5 46,960 Dimer 23,484 L

Pavia 6 22.804-22_;922 Monomer cysteinyiation 22,804 L

22,814 + 23,119 / cysteinyiation +

Pavia 7 45,694 + 45,999 Dimer+Monomer giutat ionyiation 22,697 + 23,002 I

Pavia 8 22,664 Monomer 22,731 L

Pavia 9 No FLC's observed 24,264 K

Pavia 10 45,480 Dimer 22,745 L

Pavia 11 47,140 Dimer 23,572 K

Pavia 2 45,290 Dimer 22,584 + oligo L

Pavia 13 44,612 Multiple Dimers 22,310 I

Pavia 4 23,333 Monomer cysteinyiation 23,214 L

Pavia 5 45,247 Dimer 22,764 L

Mayo 1 23,730 + 47,220 Dimer+Moncmet" 23,546 K

Mayo 2 23,055 + 45,866 Dimer+Monomer cysteinyiation 22,937 L

Mayo 3 23,486 Monomer 23,331 K

Mayo 4 26,126 Monomer glyeosy!ation 23,578 K

Mayo 5 45,488 Monomer 22,748 L

Mayo 8 No FLC's observed 22,655 L

Mayo 7 46,059 + 46,221 Dimer glycosylation 23,031 ÷ 23,193 L

Mayo 8 23,345 + 46,449 Dimer+Monomer cysteinyiation 23,226 L

Mayo 9 23,471 ÷ 46,701 Dimer+Monomer cysteinyiation 23,355 K

Mayo 10 23,589 + 46,938 Dimer+Monomer 23,473 K

Mayo 11 45,938 Dimer 22,837 L

Mayo 12 47,643 ÷ 47,805 Dimer glycosyiation 23,056 + 23,218 L

Table 2 displays each patient's FLC listed by isotype (kappa first followed by lambda) along with the kappa/lambda ratio, isotype specific FLC concentration (mg/L), and the corresponding peak area (counts per seconds) of each monoclonal FLC observed in the mass spectrometer. The peak areas listed in the table were found using the same method used to determine linearity and precision for the purified FLC spiked into normal serum. The table shows that the isotype specific FLC concentrations are much higher in the Pavia patient cohort as compared to the Mayo cohort and that the FLC concentrations are present over several orders of magnitude. A linear regression analysis was performed to determine the correlation between the peak areas of each patient's monoclonal FLC found using the methods disclosed herein with the concentration of FLC determined using nephelometry and the results are shown in Figure 16. The linear regression marked Kappa FLC has 2 outliers removed out of a total of 8; patients Pavia 4 and Mayo 10. The linear regression marked Lambda FLC has 4 patient outliers removed out of a total of 15; patients Pavia 7, Pavia 13, Pavia 14, and Pavia 15..

Table 2

FLC MS Peak

Biobank Isotype k λ ratio (mg/rnL) Areas (q

Pavia 3 K 845 1420 49650

Pavia 4 K 73.4 1350 6062

Pavia 11 K 118 1710 63680

Mayo 1 K 7.49 8 4190

Mayo 3 K 11.9 28 3408

Mayo 4 K 27.7 43 1573

Mayo 9 K 51.9 34 6919

Mayo 10 K 42.1 69 38884

Pavia 1 L 0.05 248 11510

Pavia 2 L 0.07 695 86320

Pavia 6 L 0.02 429 47500

Pavia 7 L 0.01 1140 59150

Pav a 0 L 0.08 228 22450

Pavia 12 L 0.07 132 16500

Pavia 13 L 0.017 477 94520

Pavia 14 L 0.01 98 31390

Pavia 15 L 0.04 733 1284

Mayo 2 L 0.01 15 4372

Mayo 5 L 0.03 43 16650

Mayo 7 L 0.01 77 7500

Mayo 8 L 0.11 11 1300

Mayo 11 L 0.02 14 490

Mayo 12 L 0.05 13 2711

Discussion

Example 7 demonstrates that microLC-ESI-Q-TOF mass spectrometry can provide accurate molecular mass information on intact FLC and quantitative information for a specific monoclonal FLC. Furthermore, information on post-translation modifications can also be defined using mass spectrometry. This combination of powerful analytical features makes mass spectrometry a comprehensive platform for monitoring monoclonal FLC. Further, example 7 demonstrates that the methods disclosed herein can readily identify a monoclonal FLC from the polyclonal background and identify the isotype of the light chain by top-down MS eliminating the need for reference ranges to determine if a monoclonal FLC is present. Further, example 7 demonstrates that the methods disclosed herein can be used to monitor dimer/monomer ratios as well as PTM's.

OTHER EMBODIMENTS

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

Claims

WHAT IS CLAIMED IS: 1. A method for identifying one or more immunoglobulin free light chains in a sample, the method comprising:

a. providing a sample;

b. subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and

c. identifying the presence of the one or more immunoglobulin free light chains.

2. The method of claim 1, wherein the sample is suspected to comprise an immunoglobulin free light chain.

3. The method of claim 1, wherein the one or more immunoglobulin free light chains are selected from the group consisting of free kappa light chains, free lambda light chains, and mixtures thereof.

4. The method of claim 1, wherein the immunoglobulin free light chain is a free kappa light chain.

5. The method of claim 1, wherein the method comprises identifying at least two types of free kappa light chains.

6. The method of claim 1, wherein the immunoglobulin free light chains is a free lambda light chain.

7. The method of claim 1, wherein the method comprises identifying at least two types of free lambda light chains.

8. The method of claim 1, wherein the one or more immunoglobulin free light chains comprises at least one of a glycosylated immunoglobulin free light chain, a cysteinylated immunoglobulin free light chain, and a glutathionylated immunoglobulin free light chain.

9. The method of claim 1, wherein the identifying the one or more immunoglobulin free light chains occurs in the presence of a polyclonal background.

10. The method of claim 1, wherein the method further comprises measuring the

concentration of the one or more immunoglobulin free light chains in the sample.

11. The method of claim 1, wherein the method further comprises identifying at least one immunoglobulin free light chain dimer.

12. The method of claim 1, further comprising contacting the sample with a reducing agent prior to subjecting the sample to the mass spectrometry technique.

13. The method of claim 12, wherein the reducing agent is selected from the group consisting of dithiothreitol (DTT), reduced glutathione, β-mercaptoethanol, tris(2-carboxyethyl) phosphine hydrochloride, cysteine, 2-mercaptoethylamine, 3-mercaptopropionic acid, and mixtures thereof.

14. The method of claim 12, wherein the reducing agent is dithiothreitol.

15. The method of claim 1, wherein the method does not include contacting the sample with a reducing agent.

16. The method of claim 1, wherein the method does not include purifying the sample.

17. The method of claim 1, wherein the mass spectrometry technique is LC-MS/MS.

18. The method of claim 17, wherein the LC-MS/MS technique comprises a quadrupole time-of-flight mass spectrometer.

19. The method of claim 1, wherein the mass spectrometry technique is a top-down mass spectrometry technique.

20. The method of claim 1, wherein the sample is a serum sample, a urine sample, a cerebrospinal fluid sample, or a whole blood sample.

21. The method of claim 1, wherein the sample is from a single subject and the method further comprises diagnosing a disorder in the subject wherein the disorder is a plasma cell dyscrasia.

22. The method of claim 1, wherein the sample is from a single subject and the method further comprises diagnosing a disorder in the subject wherein the disorder is at least one of a multiple myeloma or a light chain amyloidosis.

23. The method of claim 1, wherein the sample is from a single subject and the method further comprises diagnosing a disorder in the subject wherein the disorder is at least one of multiple myeloma, monoclonal gammopathy of undetermined significance, B-cell chronic lymphocytic leukemia, Waldenstroms macrogloblinemia, amyloid light chain amyloidosis, or non-secretory myeloma.

24. The method of claim 1, wherein the sample is from a single subject and the method further comprises distinguishing an auto-immune response from a monoclonal gammopathy in the subject.

25. A method for identifying one or more immunoglobulin free light chains in a sample, the method comprising:

a. providing a sample;

b. contacting the sample with a reducing agent;

c. subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of the sample; and

d. identifying the presence of one or more immunoglobulin free light chains.

92 26. A method for diagnosing a disorder in a subject, the method comprising:

93 a. providing a sample from the subject;

94 b. subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of

95 the sample; and

96 c. identifying the presence of one or more immunoglobulin free light chain.

97

98 27. The method of claim 26, wherein the disorder is selected from multiple myeloma,

99 monoclonal gammopathy of undetermined significance, B-cell chronic lymphocytic leukemia,00 Waldenstroms macrogloblinemia, amyloid light chain amyloidosis, non-secretory myeloma and01 combinations thereof.

02

03 28. The method of claim 26, wherein the sample is a serum sample, a urine sample, a

04 cerebrospinal fluid sample, or a whole blood sample.

05

06 29. The method of claim 26, wherein after diagnosing the subject as having a disorder, 07 further comprises administering to the subject a therapeutic agent to treat the disorder.

08

09 30. The method of claim 29, wherein the therapeutic agent is comprises one or more of a1 0 bisphosphonate, chlorambucil, fludarabine, cyclophosphamide, rituximab, bendamustine, 1 1 carfilzomib, cyclophosphamide, doxorubicin, vincristine, prednisone, chlorambucil,

12 obinutuzumab, ofatumumab, pentostatin, alemtuzumab, fludarabine, bortezomib, thalidomide, 1 3 dexamethasone, doxorubicin, ibrutinib, melphalan, adriamycin, lenalidomide, pomalidomide, a14 glycosaminoglycans, a purine nucleoside analog, and a monoclonal antibody.

1 5

16 31. The method of claim 29, wherein the disorder is monoclonal gammopathy of

1 7 undetermined significance and the therapeutic agent is a bisphosphonate.

1 8

1 9 32. The method of claim 29, wherein the disorder is B-cell chronic lymphocytic leukemia20 and the therapeutic agent is selected from chlorambucil, fludarabine, cyclophosphamide,

21 rituximab, bendamustine, cyclophosphamide, doxorubicin, vincristine, prednisonea, 122 chlorambucil, obinutuzumab, ofatumumab, pentostatin, alemtuzumab, fludarabine, a monoclonal

123 antibody, and combinations thereof.

124

125 33. The method of claim 29, wherein the disorder is Waldenstroms macrogloblinemia and the

126 therapeutic agent is selected from bortezomib, thalidomide, fludarabine, dexamethasone,

127 chlorambucil, rituximab, cyclophosphamide, doxorubicin, vincristine, prednisone, a monoclonal

128 antibody, a purine nucleoside analog, ibrutinib, and combinations thereof.

129

1 30 34. The method of claim 29, wherein the disorder is amyloid light chain amyloidosis and the

1 31 therapeutic agent is selected from a melphalan, prednisone, vincristine, adriamycin,

1 32 dexamethasone, bendamustine, thalidomide, cyclophosphamide, lenalidomide, pomalidomide,

1 33 bortezomib, a glycosaminoglycans, and combinations thereof.

1 34

1 35 35. The method of claim 29, wherein the disorder is non-secretory myeloma and the

1 36 therapeutic agent is selected from thalidomide, bortezomib, lenalidomide, carfilzomib,

1 37 pomalidomide and combinations thereof.

1 38

1 39 36. A method for diagnosing a monoclonal gammopathy in a subject, the method comprising:

140 a. providing a sample from the subject;

141 b. subjecting the sample to a mass spectrometry technique to obtain a mass spectrum of

142 the sample; and

143 c. diagnosing a monoclonal gammopathy in the subject based on the identification of one

144 or more free kappa immunoglobulin light chains or one or more free lambda immunoglobulin

145 light chains.

146

147 37. The method of claim 36, further comprising contacting the sample comprising an

148 immunoglobulin free light chain with a reducing agent prior to subjecting the sample to the mass

149 spectrometry technique.

1 50

1 51 38. A method for monitoring a treatment of a monoclonal gammopathy in a subject

1 52 comprising: 153 a. providing a first sample of the subject obtained before the treatment;

154 b. providing a second sample of the subject obtained during or after the treatment;

155 c. subjecting the first and second samples to a mass spectrometry technique to obtain a

156 mass spectrum of the first and second samples;

157 d. determining the concentration of at least one of free kappa immunoglobulin light

158 chain or at least one free lambda immunoglobulin light chain in the first and second samples; and

159 e. comparing the concentration of the at least one free kappa immunoglobulin light chain

160 or the at least one free lambda immunoglobulin light chain in the first and second samples.

161

162 39. The method of claim 38, further comprising contacting the first and second samples

163 comprising an immunoglobulin free light chain with a reducing agent prior to subjecting the first

164 and second samples to the mass spectrometry technique.

165