COMPARISON OF PROTEIN SAMPLES
RELATED APPLICATIONS
[00001] This application claims the benefit of priority of U.S. Provisional
Application Ser. No. 61/355,269, filed June 16, 2010 which is incorporated herein by
reference in its entirety.
BACKGROUND OF THE INVENTION
[00002] The present invention relates to an analytical method of comparing two or
more protein samples using bottom-up Liquid Chromatography - Mass Spectroscopy
(LC-MS) with a Stable Isotope - Tagged Reference Standard (SITRS).
[00003] Peptide mapping with mass spectroscopy (MS) detection is used in protein
analytics for confirmation of the primary sequences. Known analytical methods
primarily qualitatively confirm the presence of expected peptides.
SUMMARY OF THE INVENTION
[00004] In one aspect, the invention is directed to a method of characterizing a
protein sample, the method comprising: (i) providing a sample of a first protein, having
a known amino acid sequence, wherein at least one amino acid in the first protein is
replaced with an isotopically labeled amino acid; (ii) providing a sample of a second,
unlabeled protein comprising an unlabeled amino acid corresponding to the isotopically
labeled variant in the first protein; (iii) mixing the first sample and the second sample to
form a mixture; (iv) subjecting the mixture to protein digestion to form a first digest; (v)
subjecting the first digest to bottom-up Liquid Chromatography - Mass Spectroscopy to
form a first spectra including one or more doublet or singlet peaks, each doublet peak
indicating the presence of an isotopically labeled peptide from the first sample and a
corresponding unlabeled peptide from the second sample and each singlet peak
indicating presence of peptide with a mutation, modification, or impurity. In certain
embodiments, the method further comprises the step of (vi) comparing the relative
intensities of the peaks in the doublet to determine the relative amount of each peptide,
wherein a 1:1 peak ratio indicates substantial identity of the first and second peptides
and wherein a differential in peak intensity reflects the presence of a chemically distinct
peptide. In another embodiment, the method further comprising the step of quantifying
the amount of the chemically distinct peptide based in a relative reduction in peak
intensity. In another embodiment, the method further comprising the step of (vii)
subjecting the digest to tandem mass spectroscopy to determine the sequence of a
peptide represented by a singlet peak in the spectra.
[00005] In another aspect, the present invention is a method of qualitatively detecting
the presence of mutations, modifications or impurities in a protein sample. The method
allows comparing two or more protein samples to each other by comparing each sample
to a Stable Isotope-Tagged Reference Standard (SITRS) protein. The method includes
providing a sample of a first protein wherein at least one amino acid in the first protein
(SITRS), having a known amino acid sequence, is replaced with an isotopically labeled
amino acid; providing a sample of an unlabeled protein including an unlabeled amino
acid corresponding to the isotopically labeled amino acid in the first protein, mixing the
first protein and the unlabeled protein standard to form a mixture, subjecting the mixture
to digestion and the subsequent analysis by bottom-up Liquid Chromatography - Mass
Spectroscopy to determine whether a spectra includes a doublet indicating the presence
of that particular peptide in each protein. If the doublet peak is not observed, then a
single peak may correspond to a peptide, resulting from one of the following
possibilities: (1) the peptide does not contain the labeled amino acid; (2) the peptide
contains a modification; (3) the peptide contains a mutation, insertion or deletion; (4) the
peptide corresponds to an impurity, and does not contain amino acid sequence present in
the protein sample. The single peaks can then be analyzed by MS/MS to reveal the
sequence of the peptide and to determine which of the four possibilities listed above are
present.
[00006] In another aspect, the present invention is a method of quantitatively
determining the presence of mutations or modifications in a protein sample. The method
includes providing a sample of a first protein (SITRS), having a known amino acid
sequence, wherein at least one amino acid in the first protein is replaced with an
isotopically labeled amino acid; providing a sample of an unlabeled protein sample
including an unlabeled amino acid corresponding to the isotopically labeled amino acid
in the first protein, mixing the first protein and the unlabeled protein sample to form a
mixture, subjecting the mixture to digestion and the subsequent analysis by bottom-up
Liquid Chromatography - Mass Spectroscopy to determine whether a spectra includes a
doublet indicating the presence of that particular peptide in both the SITRS and the
unlabeled protein samples, and to compare the intensities of the peaks in the doublet to
determine the relative abundances of that particular peptide in each protein. Additional
unlabeled protein samples can be compared among each other by first comparing to the
same SITRS antibody as described above, and then comparing the results among each
unlabeled protein sample.
[00007] These and other aspects of the invention will be understood and become
apparent upon review of the specification by those having ordinary skill in the art.
BRIEF DESCRIPTION OF THE DRAWINGS
[00008] Figure 1 is a schematic diagram of a SITRS experiment in accordance with
the present invention.
[00009] Figure 2 is a representative mass spectrum of MAb-1 peptide generated by
tryptic digest in the presence of its SITRS counterpart in accordance with the present
invention.
[000010] Figure 3 is an extracted ion mass spectra for a SITRS experiment in which
wt mAb-1 was compared to mAb-1 that was spiked with mutant to 20% (the wt HC(255-
273) peptide that is present in both wt and mutant mAb is shown) in accordance with the
present invention.
[000011] Figure 4 is a table of monoisotopic peak intensities for HC(255-273) from
Figure 3 in accordance with the present invention.
[000012] Figure 5 is an extracted ion mass spectra for the SITRS experiment in which
wt mAb-1 was compared to mAb-1 that was spiked with mutant to 20% (the wt HC(218-
247) peptide that is modified in the mutant mAb is shown) in accordance with the
present invention.
[000013] Figure 6 is a table of monoisotopic peak intensities for HC(2 18-247) from
Figure 5 in accordance with the present invention.
[000014] Figure 7 is an extracted ion mass spectra for the SITRS experiment in which
wt mAb-1 was compared to mAb-1 that was spiked with mutant to 20% (the mutated
HC(2 18-247) peptide that is only present in the mutant mAb, and absent from the S RS
sample is shown) in accordance with the present invention.
[000015] Figure 8 is an LC chromatogram demonstrating antibody desalting utilizing
the size exclusion chromatography - high performance liquid chromatography (SEC -
HPLC) in accordance with the present invention.
[00010] Figure 9 is a comparison of mass spectra of a peptide from (A) pure
unlabeled MAb-1 and (B) MAb-1 contaminated with 10% MAb-2. SITRS was mixed
with each in a 1:1 ratio prior to tryptic digest and analysis in accordance with the present
invention.
[00011] Figure 10 is a graph depicting SITRS values for 6 peptides studied in the
quantitation of a MAb-1 sample contaminated with 10% MAb-2 in accordance with the
present invention.
[00012] Figure 11 is a comparison of SV from MAb-1 peptides derived from Human
Embryonic Kidney 293 cells versus Chinese Hamster Ovary cells in accordance with the
present invention.
[00013] Figure 12 is a SITRS bar graph for the SITRS experiment in which wt
mAb-1 was compared to mAb-1 that was spiked with mutant to 20% in accordance with
the present invention.
[00014] Figure 13 is a SITRS bar graph for the SITRS experiment in which wt
mAb-1 was compared to mAb-1 that was spiked with mutant to 2.5% in accordance with
the present invention.
[00015] Figure 14 is a plot of the amounts of peptides HC(218-247), HC(344-359)
and HC(288-300) in the mutant-spiked antibody relative to that of the wild-type
antibody as measured by the SITRS analysis of various mutant-spiked mAb-1 samples
in accordance with the present invention.
[00016] Figure 15 is a SITRS bar graph for the comparison of batches of MAb- 1
samples produced by two different cell lines using two different processes (CHOproduced
(Figure 15A) and HEK-produced (Figure 15B)) in accordance with the present
invention.
[00017] Figure 16 is table of stable isotope-tagged reference standard (SITRS)
results presented in Figure 15B with conventional analyses in accordance with the
present invention. Selected results of the SITRS analysis (n = 6) of mAb-1 from batch 2
(CHO-produced) and batch 3 (HEK-produced) are compared to the results obtained by
conventional methods (n = 3).
[00018] Figure 17 is a SITRS bar graph for the comparison of mAb-1 samples
mildly stressed in two different formulation buffers in accordance with the present
invention.
[00019] Figure 18 is a SITRS bar graph for the comparison of DTPA-MAb- 1
conjugate to unmodified MAb-1 in accordance with the present invention.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
[00020] Reference now will be made in detail to the embodiments of the invention,
one or more examples of which are set forth below. Each example is provided by way
of explanation of the invention, not limitation of the invention. In fact, it will be
apparent to those skilled in the art that various modifications and variations can be made
in the present invention without departing from the scope or spirit of the invention. For
instance, features illustrated or described as part of one embodiment can be used on
another embodiment to yield a still further embodiment.
[00021] Thus, it is intended that the present invention cover such modifications and
variations as come within the scope of the appended claims and their equivalents. Other
objects, features and aspects of the present invention are disclosed in or are obvious
from the following detailed description. It is to be understood by one of ordinary skill in
the art that the present discussion is a description of exemplary embodiments only, and
is not intended as limiting the broader aspects of the present invention.
[00022] As used herein, the term "protein" or "polypeptide" refers to a polymer of 10
or more amino acids, e.g., 50, 100, 200, 300, 400, 500 or more amino acids. Exemplary
proteins of the invention include, without limitation, recombinant proteins,
biotherapeutic proteins, monoclonal antibodies and other antibodies, antibody-drug
conjugates or other bioconjugates, imaging antibodies, fusion proteins, or PEGylated
proteins.
[00023] As used herein, the term "monoclonal antibody" refers to a class of antibody
proteins that bind to a specific target molecule (antigen) at one specific site (antigenic
site).
[00024] The measurements achieved by the present invention take into account not
only the masses of peptides generated during proteolytic digest, but also the abundance
of each resulting peptide. Measuring of the abundance of peptides by MS is enabled by
utilizing a SITRS sample that is mixed with an unlabeled protein prior to protein digest.
As used herein, the term "SITRS sample" or "SITRS standard" means a protein (e.g., an
antibody) of known sequence, labeled with a stable isotopically labeled variant of at
least one amino acid present in the protein.
[00025] In one aspect, therefore, the present invention is a method of comparing two
samples of proteins (e.g., antibodies) to qualitatively and/or quantitatively identify
differences, such as mutations, modifications or impurities in the samples. The
measurement may be conducted by utilizing a SITRS sample mixed with an unlabeled
protein (e.g., unlabeled antibody) prior to protein digestion and LC-MS.
[00026] Introduction of a stable isotopically-labeled variant as an internal standard
mitigates variation and artifacts from sample handling and MS detection that may affect
quantitation. Examples of potential variations mitigated in accordance with the present
invention include extent of protein digestion, formation of artifacts due to sample
handling and/or variations in the ionization efficiency during MS detection. By utilizing
the present method, such parameters may be normalized with respect to the SITRS
sample.
[00027] In one aspect, the present method includes preparing a labeled protein (the
SITRS sample) and mixing the labeled protein with an unlabeled protein sample. The
mixed sample may then be subjected to bottom-up LC-MS to qualitatively and/or
quantitatively determine low-level mutations, modifications or impurities in the
unlabeled sample. This analysis may also be used to determine poor choice of an
expression cell line, inefficiencies in a growth media, inefficiencies in cell culture
conditions, inefficiencies in a purification process, or inadequacy of a formulation
buffer.
[00028] In one exemplary embodiment, unlabeled antibody is formed in an
experimental growth media or produced by an experimental cell line/clone, the resulting
unlabeled antibody is mixed with a SITRS sample, and then the mixed sample is
subjected to protein digestion and bottom-up LC - MS, which may be used to determine
whether the experimental growth media cell line/clone is acceptable for production of
desired antibodies.
[00029] Under standard Reverse Phase - High Performance Liquid Chromatography
(RP-HPLC) conditions, labeled and unlabeled peptides have nearly identical retention
times and, therefore, migrate together. While not resolvable by chromatography, the
labeled and unlabeled peptides are distinguishable by MS detection, yielding differences
in Daltons (Da) equivalent to the number of labeled residues in the particular peptide.
Accordingly, when the SITRS sample is mixed with an unlabeled antibody or other
protein, doublets indicating a difference in Da will appear in the mass spectra, indicating
incorporation of the labeled amino acids into the SITRS sample, and the presence of the
peptide with the same amino acid sequence in both the SITRS sample and the unlabeled
antibody. A SITRS sample in which the only difference from its unlabeled counterpart
(in a 1:1 mix) is the presence of the labeled amino acids will produce doublets in which
each peak has an identical intensity.
[00030] The SITRS sample may be prepared using methods known in the art in
which heavy amino acids are used in place of standard amino acids. For example, when
preparing a protein that includes arginine and lysine residues, the growth media may
include arginine and lysine residues composed of six 13C atoms instead of the naturally
abundant 12C atoms (Arginine-6 and Lysine-6).
[00031] Heavy isotope-labeled variants known in the art are contemplated as useful
in accordance with the present invention. Those having skill in the art will recognize
that the selection of the heavy isotope-labeled variants will depend on the protein being
formed and the protein digestion that will be conducted on the protein in preparation for
LC-MS detection. For example, when the protein being produced includes arginine
and/or lysine and will be subjected to trypsin digest, a heavy arginine and/or lysine may
be desirable. Similarly, when the protein being produced includes aspartic acid and will
be subjected to endoproteinase AspN digestion, a heavy aspartic acid may be desirable.
When the protein being produced includes a glutamic acid and will be subjected to
endoproteinase GluC digestion, a heavy glutamic acid may be desirable. When the
protein being produced includes a chain of aspartic acid - aspartic acid - aspartic acid -
aspartic acid - lysine and will be subjected to enterokinase digestion, a heavy aspartic
acid and/or heavy lysine may be desirable. When the protein being produced includes a
chain of isoleucine - glutamic acid or aspartic acid - glycine - arginine and will be
subjected to Factor Xa digestion, a heavy isoleucine, glutamic acid, aspartic acid,
glycine, and/or arginine may be desirable. When the protein being produced includes a
chain of arginine - X - X - arginine and will be subjected to furin digestion, a heavy
arginine may be desirable. When the protein being produced includes a histidine -
tyrosine linkage and will be subjected to genease I digestion, a heavy histidine and/or
tyrosine may be desirable. When the protein being produced includes an amino acid
having an aromatic side chain and will be subjected to chymotrypsin digestion, a heavy
amino acid having an aromatic side chain may be desirable. When the protein being
produced includes a lysine and will be subjected to Lys-C or Lys-N digestion, a heavy
lysine may be desirable. When the protein being produced includes a methionine and
will be subjected to CNBr digestion, a heavy methionine may be desirable. When the
protein being produced includes an arginine and will be subjected to endoproteinase
ArgC digestion, a heavy arginine may be desirable. The invention is not intended to be
limited to particular isotopically labeled variants or particular methods of protein
digestion and the isotopically labeled variants and methods can be varied depending on
the protein.
[00032] The present invention may further include a protein purification step.
Protein purification methods known in the art are contemplated as useful in accordance
with the present invention and may be utilized. A protein purification step may be
conducted prior to protein digestion and, in some embodiments, it may be desirable to
conduct a protein purification step prior to mixing the samples. In other embodiments, it
may be desirable to conduct a protein purification step after mixing samples, but prior to
protein digestion.
[00033] In some embodiments, it may be desirable to denature, reduce, and/or
alkylate the mixed sample prior to protein digestion. The denaturation, reduction and
alkylation steps may be conducted by methods known in the art. For example, the
denaturation step may be conducted with the use of dialysis, off-line solid-phase
extraction (SPE), on-line SPE, or liquid chromatography (LC), such as Size Exclusion
Chromatography - High Performance Liquid Chromatography (SEC-HPLC) or Reverse
Phase - High Performance Liquid Chromatography (RP-HPLC). In the on-line SPE or
LC method, flow-rate may be controlled, the ultra-violet (UV) signal may be monitored,
and the fraction collection may be timed to collect only the purified protein and not any
residual buffer or other contaminants from the growth process or sample treatment.
[00034] Figure 1 provides a schematic SITRS analysis. Figures 3 and 5 show mass
spectra from the SITRS analysis for two mixed samples, including an unlabeled MAb
and its corresponding SITRS standard (no modification or mutation). As can be seen, a
SITRS standard and an unlabeled MAb were mixed in a 1:1 ratio, subjected to protein
(tryptic) digest, and then subjected to bottom-up LC-MS. The resulting mass spectra of
peptides common to both the unlabeled sample and the SITRS standard are unique in
that the mass to charge (m/z) peaks appear as doublets, due to the presence of labeled
amino acids in the SITRS standard. Thus, a peptide that is identical in chemical
composition to its SITRS counterpart and is present in the same amount as its SITRS
counterpart will have an intensity that is equal to that of the standard (in a 1:1 mix) (see,
e.g., Figure 3).
[00035] Peptides whose population is partially composed of point mutants or sitespecifically
modified molecules, such as, for example, deamidation, N-terminal
pyroglutamate, or differential glycosylation, will have a mass spectra where the intensity
of the peak from the unlabeled sample is reduced compared to a SITRS standard by an
amount that reflects the abundance of the chemically distinct peptide as can be seen in
Figure 5. Accordingly, by mixing a SITRS standard with an unlabeled protein
preparation and subjecting the mixed sample to protein digestion and bottom-up LC-MS,
the presence of mutations, modifications and/or site- specifically modified molecules in
the unlabeled protein preparation may be identified and quantitated.
[00036] Antibody preparations from different cell lines may be compared utilizing
the strategy described above. For example, the methods of the invention may be
employed to qualitatively identify the presence of mutations and/or modifications in an
unlabeled antibody grown in an experimental growth media or produced by an
experimental clone/cell line. In this embodiment, a standard sample including at least
one isotopically labeled amino acid (the "SITRS standard") is mixed with an unlabeled
antibody produced by an experimental cell line. The mixed sample may then be
subjected to protein digestion and bottom-up LC - MS to determine whether the
experimental cell line is acceptable for production of desired antibodies.
[00037] Similarly to the embodiment discussed above, if the unlabeled antibody and
the SITRS standard differ only in the presence of the labeled amino acid in the SITRS
standard, then the two samples will migrate together through the MS and the only
significant differences in the mass spectra will appear in the form of doublets indicating
the presence of the labeled amino acids in the SITRS standard.
[00038] If the doublet peak is not observed, then a single peak may correspond to a
peptide resulting from one of the following possibilities: (1) the peptide does not contain
the labeled amino acid; (2) the peptide contains a modification; (3) the peptide contains
a mutation, insertion or deletion; (4) the peptide corresponds to an impurity and does not
contain the amino acid sequence present in the antibody sample. The single peaks can
then be analyzed by MS/MS to reveal the sequence of the peptide and to determine
which of these four possibilities is present. Figure 7, for example, shows the presence
of the mutant peptide, which does not have a sister doublet. Accordingly, by mixing a
SITRS standard with an unlabeled antibody and subjecting the mixed sample to protein
digestion and bottom-up LC-MS, the presence of mutations, modifications and/or sitespecifically
modified molecules in the unlabeled antibody may be identified. Several
unlabeled MAbs prepared by different cell lines can then be compared utilizing the same
strategy described above in order to select the best clone.
[00039] In another aspect of the invention, the labeled SITRS standard enables
quantitation of a protein by mass spectrometry, via comparison of the intensity of the
m/z peak of each labeled SITRS standard peptide relative to that of its corresponding
unlabeled peptide of unlabeled sample in each doublet. This in turn allows the
comparison of all peptides spanning nearly an entire protein sequence. Several
unlabeled proteins can then be compared to each other utilizing the strategy described
above.
[00040] In this aspect of the invention, an unlabeled protein is prepared.
Additionally, a SITRS standard corresponding to the unlabeled MAb is obtained. The
unlabeled protein and the SITRS standard should be substantially identical and, if
mixed, should show a 1:1 doublet in the MS, such as that seen in Figure 1. To quantify
the presence of any mutations or modifications in the unlabeled protein, the
corresponding SITRS standard is mixed with an unlabeled sample. The mixture of the
corresponding SITRS standard and unlabeled sample may then be subjected to protein
digest and bottom-up LC-MS. The resulting spectrum may then be analyzed to
determine whether the intensities of the doublet peaks are the same.
[00041] Additionally, to verify that the unlabeled MAb and the SITRS standard are
identical with the exception of the isotopically labeled variants in the SITRS standard,
the unlabeled MAb and the SITRS standard may be mixed together, subjected to protein
digestion, and subjected to bottom-up LC-MS. The resulting mass spectral pattern
should result in a substantially 1:1 peak as seen in Figure 1. Peptides whose population
is partially composed of point mutants or site- specifically modified molecules (such as
deamidation, N-terminal pyroglutamate or differential glycosylation) however, will have
a mass spectrum where the intensity of the peak from the unlabeled standard sample is
reduced compared to the SITRS standard by an amount that reflects the abundance of
the chemically distinct peptide (Figure 1).
[00042] When comparing two unlabeled protein samples to each other, for example
unlabeled sample A to unlabeled sample B, it might be necessary to further minimize
variations that may arise from pipetting errors and MS detection. In order to minimize
these variations, the ratios of the unlabeled sample A to the SITRS standard may be
compared with those of the unlabeled sample B to the SITRS standard, as shown in
Equation 1. The resultant value is called the SITRS Value (SV).
[00043]
„ I A , I B IA , ISITRS - B
S V = / X C = — * X C
ISITRS - A ISITRS - B I B ISITRS - A (Eq. 1)
In Equation 1, IA the peak intensity of the unlabeled sample A, ISETRS-A the peak
intensity of the SITRS standard mixed with the unlabeled sample A, I B is the peak
intensity of the unlabeled standard sample B , and ISETRS-B s the peak intensity of the
SITRS standard mixed with the unlabeled standard sample B . The peak intensity ratio
of the unlabeled sample A to the unlabeled standard sample B is converted to a
percentage of the expected signal by multiplying by c, a constant that is experimentally
determined by obtaining the average of the most similar ratios of [(IA/ISETRS-A)/(IB/ISETRSB)]
according to equation 2. Common peptides between the two runs will have similar
ratios while peptides bearing differences will have different ratios.
c= 10 0 / {(IA/IsrrRS -A)/(lB /ISETRS-B )}most similar (Eq. 2)
[00044] Alternatively, the ratios of the unlabeled sample A to the SITRS standard
may be compared with those of the unlabeled sample B to the SITRS standard, as shown
in Equation 3:
xl 00 (Eq. 3)
In Equation 3, A and B are the relative amounts of a peptide in sample A and the same
peptide in sample B , respectively. IA, IB, ISETRS-A and ISETRS-B are intensities of m/z ion
peaks for the same peptide in samples A, B , SITRS standard mixed with sample A and
SITRS standard mixed with sample B , respectively. Constant c is a normalization factor
that accounts for possible unequal addition of SITRS standard to sample A versus
sample B. Specifically, c is a trimmed mean of B/A values that exclude outliers outside
of the 95% confidence interval of B/A values for a set of peptides that typically do not
undergo post-translational modifications. Thus, multiplication of IA/IS RS-A by c
produces a result equal to the ratio of IB/IS RS-B for the majority of the peptides
quantitated.
[00045] Thus, a single quantitation experiment may involve running at least two
protein digests, one containing unlabeled sample A (for example, a well characterized
reference antibody) and the SITRS standard and the other containing the unlabeled
sample B (for example, an antibody sample in question) plus the SITRS standard.
[00046] The following examples describe exemplary embodiments of the invention.
Other embodiments within the scope of the claims herein will be apparent to one skilled
in the art from consideration of the specification or practice of the invention as disclosed
herein. It is intended that the specification, together with the examples, be considered to
be exemplary only, with the scope and spirit of the invention being indicated by the
claims which follow the examples.
Examples
[00047] Unless otherwise indicated, the following materials and equipment were
utilized in the present examples. The methods described herein are not, however,
limited to methods utilizing only these materials and/or equipment:
[00048] Materials used for Chinese Hamster Ovary (CHO) cell media and amino
acids include:
• Lys/Arg dropout media, available from Invitrogen, Carlsbad, California;
• L-Arginine (Arg-6) monohydrochloride, available from Cambridge Isotope
Laboratories, Andover, MA, cat# CLM-2265-0.25 (MW 216.62);
• L-Lysine (Lys-6) dihydrochloride, available from Cambridge Isotope
Laboratories cat# CLM-2247-0.25 (MW 225.07);
• L-Arginine monohydrochloride, available from Sigma, Milwaukee, WI, cat#
A5131-1G (MW 210.66); and
• L-Lysine monohydrochloride, available from Sigma, Milwaukee, WI, cat#
L5626-1G, (MW 182.65)
• Milli-Q Water or equivalent.
[00049] Materials used for Protein A purification include:
• rProtein A Sepharose Fast Flow, available from GE Healthcare, Wauwatosa, WI
cat# 17-1279-03;
• 1M tris buffered saline (Tris), pH 8.5;
• IX phosphate buffered saline (PBS), pH 7.4;
• Acetic acid;
• Sodium chloride;
• Poly-Prep Chromatography Columns; available from Bio-Rad, Hercules, CA cat
#731-1550;
• Vacuum manifold;
• UV-Vis Spectrophotometer, model: Cary 50; available from Varian, Palo Alto,
CA; and
• Microcon YM-30, available from Millipore, Billerica, MA cat# 42410.
[00050] Materials used for trypsin digestion in peptide mapping include:
• Iodoacetic acid (IAA), available from Sigma; cat #14386- 10G;
• Dithiothreitol (DTT), available from Sigma; cat# D-9163;
• Trypsin, available from Worthington, Lakewood, NJ cat #TRSEQZ, 4.61 u/mgP;
• 1M Tris-HCl, pH 8.0;
• 1M Tris-HCl, pH 7.5;
• Guanidine hydrochloride (Gua-HCl), available from Calbiochem, Gibbstown,
NJ; cat# 369075;
• 5N hydrochloric acid (HC1); JT Baker, Phillipsburg, NJ; cat# 5618-02; and
• 0.22 mih (CA) sterile filter disposable unit, available from Corning Life Sciences;
cat# 430015.
[00051] SEC-HPLC system used for gel filtration to remove denaturants and other
impurities:
• Agilent 1200 Quaternary HPLC system, available from Agilent Technologies,
Santa Clara, CA;
• Agilent reservoir tray, available from Agilent;
• Agilent G13 11A quaternary pump, available from Agilent;
• Agilent G1322A degasser (in-line), available from Agilent;
• Agilent G1367B HiP-ALS high performance autosampler, available from
Agilent;
• Agilent G1316A TCC column compartment with temp control, available from
Agilent;
• Tosoh TSK-Gel SW3000XL guard column, 6.0mm ID x 40 mm L, 7 mih particle,
available from Tosoh, Tokyo, Japan, cat# 08543;
• Agilent G1364C Analytical fraction collector, available from Agilent;
• Agilent G1330B temp controller for fraction collector, available from Agilent;
• Agilent G1365D MWD (UV-VIS detector), available from Agilent; and
• Agilent Chemstation data acquisition system with computer, available from
Agilent.
[00052] Materials used for peptide mapping by RP-HPLC with MS detection
include:
• Triflouroacetic acid (TFA); available from JT Baker; cat# 9470-00;
• Formic acid (FA); available from EMD Chemicals; cat# FX0440-5; and
• Acetonitrile (ACN), HPLC-grade, available from Honeywell Burdick and
Jackson, Morris Township, NJ, cat# AH015-4.
[00053] LC-MS system used for peptide mapping by RP-HPLC with MS detection:
• Agilent reservoir tray, available from Agilent;
• Agilent G1376A capillary binary pump, available from Agilent;
• Agilent G1379B micro vacuum degasser (in-line), available from Agilent;
• Agilent G1377A Micro WPS autosampler, available from Agilent;
• Agilent G1330B FC/ALS Therm autosampler thermostat, available from Agilent;
• Agilent G1316B TCC SL column compartment with temp control, available
from Agilent;
• Agilent G65 10A - 6510 Q-TOF LC/MS system, available from Agilent;
• Higgins Analytical Proto 200 C18, 5 mpi, 250x1.0 mm, cat# RS-2501-D185,
available from Higgins Analytical, Mountain View, CA serial# 157337;
• Agilent MassHunter data acquisition system with computer, available from
Agilent;
• Agilent MassHunter Workstation Software Qualitative Analysis; Version
B.03.00; with Bioconfirm, available from Agilent; and
• Microsoft Excel 2003 software; available from Microsoft.
Example 1
[00054] In the present example, unlabeled and labeled monoclonal antibodies
(MAbs) were produced in a chemically defined media that lacked arginine and lysine
amino acids. The media was then supplemented with either unlabeled or labeled LArginine
(Arg) and L-Lysine (Lys) to 3.97 mM and 5.95 mM, respectively. The
unlabeled and labeled versions of an antibody were produced using standard methods
known in the art, then stored at -80 °C until needed.
Protein A purification of labeled MAb-1 (SITRS) and unlabeled MAb-1:
Column Packing
[00055] rProtein A Sepharose Fast Flow was used to purify MAb-1 (labeled and
unlabeled). The resin was resuspended by vigorous shaking. The Sepharose (1.65 mL,
about 1.2 mL of resin) was transferred into a Bio-Rad Poly Prep column that contained
10 mL of IX PBS (the bottom of the column was capped).
[00056] The resin was allowed to settle to the bottom. The cap was then opened and
the buffer was allowed to flow through, but was stopped just before reaching the bed of
the resin.
Protein A Purification
[00057] The resin was equilibrated by passing 20 mL of IX PBS (about 2 column
volumes) at a rate of -3-5 mL/min. Sample (10 mL -10 mg) was applied onto the
column at a rate of - 1 mL/min. 10 mg of labeled MAb-1 and 10 mg of unlabeled MAb-
1 were processed.
[00058] The column was then rinsed with 4 x 10 mL (about 2 column volumes) of
IX PBS at a rate - 3-5 mL/min and the sample was eluted with 5 mL of 0.1 M acetic
acid, 0.15M sodium chloride, pH 3.5 by gravity flow.
Sample Reconstitution
[00059] The A2 o of eluted MAb-1 was measured on a 10X dilution of the eluate.
Specifically, 20 mΐ of protein was diluted to 200 mΐ by addition of 180 of 10 mM
Tris, pH 8.0 buffer. The extinction coefficient of MAb-1 was 1.43 mL/mg*AU.
[00060] Eluted MAb- 1 (5 mL) was neutralized with 0.5 mL of 1M Tris, pH 8.5,
which brought the pH into 7-8 range and raised the final concentration of Tris in the
sample to 100 mM.
[00061] The purified MAb-1 was further concentrated using a Microcon YM-30
centrifugal filter. Because the capacity of the filter was 0.5 mL, the concentration was
performed in two stages. The samples were centrifuged for 10 to 15 minutes at 10,000 g
to reduce the volume to about 0.25 mL (4x concentration). The final sample
concentrations were 6.07 mg/mL for the unlabeled and 5.63 mg/mL for the labeled
MAb-1. Samples were then frozen at -80 °C.
Sample preparation for the SITRS experiment:
[00062] Samples were prepared according to the following procedures:
• Unlabeled MAb- 1, MAb-2 (double-point mutant of MAb- 1), HEK-derived
MAb-1 and labeled MAb-1 samples were diluted with Milli-Q water to 4
mg/mL.
• MAb- 1 (4 mg/mL) was mixed with its double-point mutant MAb-2 (4 mg/mL) to
yield 20%, 10%, 5%, 2.5%, 1.25% and 0.625% MAb-2 mutant-spiked samples
of MAb-1.
• MAb-1 and the mutant- spiked MAb-1 samples (25 mΐ of 4 mg/mL) were mixed
with 25 of 4 mg/mL labeled MAb-1.
• MAb-1, (HEK-derived, 25 mΐ of 4 mg/mL) was mixed with 25 mΐ of 4 mg/mL
labeled MAb-1.
Denaturation, reduction and alkylation of samples
[00063] Each SITRS-spiked sample (25 m ) was added to 75 of 8M Guanidine-
HC1, 0.1M Tris, pH 8.0. The samples were incubated at room temperature for 15
minutes.
[00064] Reduction was carried out by adding 1 of 1M DTT to each sample,
followed by incubation at 37 °C for 30 min.
[00065] The samples were alkylated by adding 5 mΐ of 0.5M IAA, and then
incubating at 37 °C for 30 min under a foil cover. After the incubation, excess IAA was
inactivated by adding 1.5 mΐ of 1M DTT to each sample.
Gel filtration of denatured, reduced and alkylated samples using SEC-HPLC
[00066] The following conditions and materials were used for SEC-HPLC:
• Column: Tosoh TSKgel SW3000XL guard column, 6.0mm ID x 40 mm L, 7 mih
particle
• Mobile Phase A: 10 mM Tris, pH 7.5
• Gradient: isocratic
• Flow rate: 0.25 mL/min, constant
• Autosampler and FC cooler temp: 4°C
• Column oven temp: ambient
• Wavelength: 280 nm
• Total run time: 6 minutes
• Injection vol: 100 mΐ (about 100 mg)
• Fraction collection: based on time, collecting one fraction between 2 and 3
minutes at room temperature
Gel filtrations by SEC-HPLC
[00067] 100 mΐ of each sample were injected, with washing steps in-between, into
the SEC-HPLC. A typical chromatogram is shown in Figure 8. 250 mΐ of purified
sample was recovered by fraction collection; therefore the final concentration was about
0.4 mg/mL assuming that no sample loss occurred during the purification.
[00068] A column wash was performed between each sample run, by injecting 100
m of cleaning solution (6M Gua-HCL in 75mM Tris, pH 8.0). The column wash
method was the same as above, except the flow rate was at 0.4 mL/min for 6 min and no
fractions were collected.
Trypsin digestion
[00069] 8 m of 0.25 mg/mL trypsin (resuspended in 1mM HCl) were added to 200
mΐ (80 mg) of SEC-HPLC purified sample (1:40 enzyme to sample ratio by weight).
Then, the mixture was incubated for 30 minutes at 37 °C. After incubation, the reaction
was quenched by addition of 4 m of 1M HCl, to a final concentration of 20 mM. 20 mΐ
(or about 8 mg) of sample were loaded onto HPLC for MS analysis.
LC-MS analysis of trypsin-digested antibodies
[00070] The following conditions and materials were used for LC-MS:
• Column: Higgins Analytical Proto 200 C18 RP column (5 mih, 200 A, 1 x 250
mm)
• Mobile Phase A: 0.02% TFA, 0.08% formic acid in water
• Mobile Phase B: 0.02 % TFA, 0.08% formic acid in ACN
• Gradient: binary
• Flow rate: 50 mI h h, constant
• Initial conditions: 2% B
• Autosampler cooler temp: 4°C
• Column oven temp: 60°C
• Total run time: 120 min
• Injection vol: 20 mΐ (8 mg of sample)
• Binary gradient program:
[00071] The method diverted the eluent into waste for the first four minutes, and then
directed it into the mass spectrometer. No MS/MS information was collected during the
run to improve quantitation of the results.
[00072] The quantitation of peak intensities in each doublet was performed and
corresponded to combined sequence of peptides spanning nearly the entire sequence of
the antibody. Data was presented in a form of a "SITRS bar graph" as shown in Figures
10, 11, 12 and 13.
[00073] As can be seen from the above examples, the use of SITRS enables mining
of MS-generated data for both qualitative and quantitative comparison of protein
samples.
[00074] The above examples utilized the previously-discussed gel filtration by SEC
- HPLC to remove denaturants and other impurities. As can be seen in Figure 8, the
eluent was monitored with an end result of a purified and less-dilute antibody sample
than available in traditional desalting techniques. In addition, the nearly-complete
elimination of guanidine salt from the sample permitted the significant shortening of the
trypsin digestion time and, therefore, minimized sample-handling artifacts that could be
introduced by prolonged incubation.
[00075] Three injections of MAb- 1 onto the SEC - HPLC column were made to
remove the guanidine and other contaminants. Absorbance at 280 nm was monitored
throughout the run. Arrows in Figure 8 indicate the start and the end of sample
collection. The antibody was baseline resolved from the guanidine and other
contaminants.
[00076] Digesting a MAb-1 sample after removal of the guanidine and other
contaminants in the presence of an equimolar amount of the SITRS standard resulted in
mass spectra of peptides characterized by the expected doublets of appropriate signal
intensity. Figure 2 shows a typical mass spectrum of a peak from a tryptic digest of
MAb-1, mixed in an equimolar ratio with the SITRS standard. In addition to the
expected m/z peak of 899.9418 ([M+2H]+2 peak corresponding to peptide 127-142 of
LC), plus monoisotopic peaks from naturally- occurring 13C-containing peptides for the
unlabeled peptide, there is an additional set of peaks from the SITRS. The expected
ratio of the peak intensities of MAb-1:SITRS is 1. The experimental ratio measurement,
made by summing the peak heights of all relevant peaks, is 0.81 1. Calculation of the
ratio for 11 peaks from the light chain in the chromatogram results in an average ratio of
0.823 + 0.014. This number was consistent across all 42 peptides examined, with a
standard deviation of 2%. Without being bound by theory, it is believed the deviation
from the expected ratio of 1 is likely due to a systematic factor such as pipetting errors in
the initial protein concentration.
[00077] Figure 3 shows another typical mass spectrum of a peak from a tryptic
digest of MAb-1, mixed in an equimolar ratio with the SITRS standard. In addition to
the expected m/z of 1070.5085 [M+2H]2+ for the peptide 255-273 of heavy chain, plus
monoisotopic peaks from naturally- occurring 13C-containing peptides for the unlabeled
peptide, there is an additional set of peaks from the SITRS (m/z of 1073.5184 [M+2H]2+
plus monoisotopic peaks from naturally-occurring 13C-containing peptides). The
expected ratio of the peak intensities of MAb-1:SITRS is 1 (if samples were mixed 1:1
ratio and no modification of that particular peptide has occurred). The experimental
ratio measurement, made by summing the peak heights of all relevant peaks, is 1.07
(Figure 4). The same ratio was obtained for the same peptide HC(255-273) in 20%
mutant-spiked MAb-1. This number was consistent across the majority of the peptides
examined. However, when peptide HC(218-247) was examined (m/z of 835.15), the
relative abundance of peak intensities corresponding to the unlabeled peptide in the 20%
mutant-spiked MAb-1 was decreased relative to the labeled peptide of the same
sequence in the SITRS standard (Figure 5). The apparent change in peak intensity ratio
has been quantitated and presented in Figure 6. The experimental ratio measurement,
made by summing the peak heights of all relevant peaks in the wild-type MAb sample
(0% mutant), is 1.11, while the same measurement for the 20% mutant-spiked MAb-1 is
0.87. This decrease in the relative intensity of the unlabeled peptide HC(21 8-247) from
the 20% mutant-spiked MAb-1 is consistent with this peptide being modified in the
mutant of MAb-1 (MAb-2 sample).
[00078] In addition to quantitative data obtained from the SITRS experiment
described above, qualitative information about the sample can also be obtained. Figure
7 shows a set of monoisotopic peaks without a doublet. This peak corresponds to a
peptide HC(2 18-247) from MAb-2 (double-point mutant of MAb-1) that is not present
in a wild-type MAb- 1.
Example 2
[00079] The presence of m/z peaks from the SITRS standard enables the quantitation
of differences in abundance of a given peptide. This example details quantitation of the
level of contamination of a sample of MAb-1 by an antibody other than MAb-1, e.g.,
MAb-2 antibody that has an amino acid sequence that does not fully match the sequence
of MAb-1.
[00080] In one experiment, a sample of MAb-1 was spiked with MAb-2 to a final
concentration of 10% (90% MAb-1 + 10% MAb-2). This experiment was intended to
simulate samples that contain varying amounts of an antibody that bears point mutations,
a plausible scenario that may arise by accident or through natural biological processes
during manufacturing. Being highly homologous, most peptides generated by tryptic
digest are common between the two antibodies and were expected to yield a STIRS
value (SV) of 100%. Six such peptides were selected for study. There are a few
however, which differ by 1 or more amino acids and were expected to have an SV of
90%. Figure 9 shows two mass spectra from one such "mutant" peptide. The first
spectrum is from the unlabeled antibody standard (no contaminating MAb-2 was added)
mixed with SITRS (Figure 9A) and the second spectrum is from the unlabeled,
contaminated sample containing 10% MAb-2 mixed with SITRS (Figure 9B). The
observed SV for this mutation-bearing peptide is approximately 93.3%. More broadly,
peptides that are different between MAb-1 and MAb-2 have an average SV of 93%,
while the common peptides had the expected value of approximately 100% (Figure 10).
The discrepancy was unaccounted for but, without being bound by theory, may be
explained by errors in pipetting or concentration. Thus, the SITRS method was
successfully used to identify point mutations in molecules at a level of 10% of total
protein.
[00081] Figure 11 and Table 1 show data from a SITRS experiment using material
derived from CHO and from 293 cell lines. 293-derived material has 20% less
agalactosylated glycoform (NGA2F) glycosylation in the heavy chain than MAb-1 from
CHO. Furthermore, the two batches also differ in the amount of C-terminal lysine on
the heavy chain, as well as the amount of N-terminal pyroglutamate formation. Peptides
bearing these modifications were readily apparent in the SITRS experiment by their
dramatic differences in SV (columns marked with an asterisk in Figure 11).
Furthermore, peptides that were predicted to show no difference in levels of abundance
(that is, all the common peptides) were similar in their SITRS ratios, with an average
standard deviation for unmodified peptides of 1.4% (ranging from 0.22 to 6.31%).
Table 1. A comparison of modifications identified by SITRS versus standard methods
[00082] As can be seen, therefore, a novel method was devised using a stable
isotope-tagged protein as an internal reference standard to quantitate differences
amongst batches of a given protein. Uniform incorporation of lysine-6 and arginine-6
into MAb-1 was achieved by producing MAb-1 in a cell culture using lysine- and
arginine-deficient chemically-defined media supplemented with the labeled amino acids.
A comparison of unlabeled MAb- 1 with its SITRS standard counterpart by mass
spectrometry demonstrated that the data generated by this method is consistent, with a
standard deviation of 2%. Application of the method to MAb-1 produced by a HEK 293
cell line correctly identified the peptides bearing differences in levels of modification,
such as N-terminal pyroglutamate, C-terminal lysines, and NGA2F levels. Furthermore,
the method was successfully used to identify the peptides bearing 1 amino acid
difference between MAb-2 and MAb-1 at a level of approximately 10%.
Example 3
[00083] In another experiment, a sample of MAb- 1 was spiked with mutant MAb- 1
containing 2 point mutations (MAb-2). Specifically, one mutation resides in peptide HC
(218-247) and the other in HC (344-349). The mutant was added to a final
concentration ranging from 20% (90% MAb-1 + 20% mutant MAb-1, Figure 12) to 2%
(98% MAb-1, 2% mutant MAb-1, Figure 13). Figures 12 and 13 show that peptides
which are common to both wild type and mutant MAb-1 have the expected value of
approximately 100%. The two mutant peptides have the expected value of
approximately 80% (Figure 12) or 98% (Figure 13). Glycopeptide HC (GOF-288-300)
and HC (439-446) are also different between the two samples. This was expected as it
was known that the glycopeptides and the C-terminal peptide in the two samples differed
in their oligosaccharide composition and C-terminal lysine content, respectively. Figure
14 shows the percent difference in levels of wild type peptides HC(218-247), HC(344-
349) and HC(G0F-288-300) for various amounts of mutant MAb-1 spiked into wild-type
MAb as measured by SITRS. The method responds linearly to the amount of mutant
present and has a method detection limit of 2.4%.
Example 4
[00084] To further test the ability of the SITRS method to discriminate between
samples, a change in manufacturing process was simulated by producing the mAb-1 in a
HEK cell line. The SITRS analysis of the CHO- and HEK-derived mAb is shown in
Figures 15A and Figure 15B, respectively. Three peptides immediately stand out from
the analysis. First, HC(l-39), which bears an N-terminal pyroglutamate residue, is more
abundant in the HEK sample by 7.1%. Consistent with this result, HC(l-39) bearing an
N-terminal uncyclized glutamine residue is more abundant by 74% in the CHO-derived
mAb. The second site of differentiation is in the C-terminal heavy chain peptide
HC(439-446). This was due to minor differences in proteolytic processing of Lys446, a
common post-translational event in mAbs. The third significant difference is in the
relative abundance of various glycopeptides.
[00085] To verify these differences, the MAbs were deglycosylated with PNGase F
and the oligosaccharides were quantitated by HPLC after labeling with 2-aminobenzoic
acid. The differences in oligosaccharide content as determined by the SITRS method
versus enzymatic digestion are summarized in Figure 16. Also included in Figure 16 is
a comparison of the levels of N-terminal glutamine conversion and C-terminal lysine
removal between the SITRS and label-free MS analyses, as determined by comparison
of the intensities of de-charged and de-isotoped peaks via the MassHunter with
Bioconfirm software package from Agilent. The results of these two orthogonal
methods agree reasonably well, particularly for abundant peptides.
[00086] In contrast, two batches of the mAb that were produced by the same
manufacturing process in CHO cells were shown to be very similar (Figure 15A). Less
than 3% difference was observed in the amount of N-terminal pyroglutamate in peptide
HC(l-39). Similarly, the relative difference in HC(392-445) was only 3.3%. Unlike the
batch produced in HEK cells, the two CHO-derived batches also showed comparable
glycosylation patterns, a result that is supported by oligosaccharide profiling.
Example 5
[00087] The SITRS method was also successfully used to assess the effect of stress
on an antibody. A comparison of peptides derived from a mAb stored for 6 months or
12 months at 4C in two different buffers seemed to reveal only minor differences
between the two samples (Figure 17). Nevertheless, these minor differences could be
quantitated. For example, there was a 6.2% increase in the amount of pyroglutamate in
HC(l-39) for the 12 month sample. This result correlated with the loss of HC(l-39)
containing N-terminal Gin to 26.8% of that of the 6 month sample. In addition,
HC(370-391) decreased by 4.7% This decrease was attributable to increased
deamidation, as the deamidated peptide was in greater abundance in the 12 month
sample by 231%. The partially digested peptide HC(60-72) (Figure 17) was observed
in the 12 month sample at 9 11% greater abundance over what was observed in the 6
month sample. This result correlated with a concomitant decrease in HC(60-65),
HC(66-72), and HC(68-72).
Example 6
[00088] The SITRS method was also used to monitor bioconjugation experiments of
small molecules, drugs or imaging agents to the protein. For example, Figure 18 shows
data from a SITRS experiment in which the metal-chelating imaging agent, CHX-A"-
DTPA, was conjugated to lysine residues of the antibody. In principle, there are 92
possible reaction sites in the mAb. The SITRS experiment however, reveals that only 3
sites (peptides marked with arrows) react to an extent of > 20%. These reaction sites are
distinguished by the fact that the neighboring C-terminal peptide also decreases in its
relative abundance by an approximately equal amount as the N-terminal peptide that was
modified. This phenomenon is due to the fact that a trypsin cleavage site is lost upon
conjugation with CHX-A"-DTPA.
[00089] All references cited in this specification, including without limitation, all
papers, publications, patents, patent applications, presentations, texts, reports,
manuscripts, brochures, books, internet postings, journal articles, and/or periodicals are
hereby incorporated by reference into this specification in their entireties. The
discussion of the references herein is intended merely to summarize the assertions made
by their authors and no admission is made that any reference constitutes prior art.
Applicants reserve the right to challenge the accuracy and pertinence of the cited
references.
[00090] These and other modifications and variations to the present invention may
be practiced by those of ordinary skill in the art, without departing from the spirit and
scope of the present invention, which is more particularly set forth in the appended
claims. In addition, it should be understood that aspects of the various embodiments
may be interchanged in whole or in part. Furthermore, those of ordinary skill in the art
will appreciate that the foregoing description is by way of example only, and is not
intended to limit the invention so further described in such appended claims. Therefore,
the spirit and scope of the appended claims should not be limited to the description of
the versions contained therein.
What is claimed is:
1. A method of characterizing a protein sample, the method comprising:
(i) providing a sample of a first protein, having a known amino acid
sequence, wherein at least one amino acid in the first protein is replaced with an
isotopically labeled amino acid;
(ii) providing a sample of a second, unlabeled protein comprising an
unlabeled amino acid corresponding to the isotopically labeled variant in the first
protein;
(iii) mixing the first sample and the second sample to form a mixture;
(iv) subjecting the mixture to protein digestion to form a first digest;
(v) subjecting the first digest to bottom-up Liquid Chromatography - Mass
Spectroscopy to form a first spectra including one or more doublet or singlet peaks, each
doublet peak indicating the presence of an isotopically labeled peptide from the first
sample and a corresponding unlabeled peptide from the second sample and each singlet
peak indicating presence of peptide with a mutation, modification, or impurity,
thereby characterizing the second protein sample.
2. The method of claim 1, further comprising the step of (vi) comparing the
relative intensities of the peaks in the doublet to determine the relative amount of each
peptide, wherein a 1:1 peak ratio indicates substantial identity of the first and second
peptides and wherein a differential in peak intensity reflects the presence of a chemically
distinct peptide.
3. The method of claim 1 or 2, further comprising the step of quantifying
the amount of the chemically distinct peptide based in a relative reduction in peak
intensity.
4. The method of any one of the previous claims, further comprising the
step of (vii) subjecting the digest to tandem mass spectroscopy to determine the
sequence of a peptide represented by a singlet peak in the spectra.
5. The method of any one of the previous claims, wherein substantially all
equivalent amino acids in the first protein are isotopically labeled.
6. The method of any one of the previous claims, wherein the isotopically
labeled amino acid comprises at least one heavy isotope.
7. The method of any one of the previous claims, wherein the protein
digestion and the isotopically labeled amino acid are selected from the group consisting
of:
(a) trypsin digestion and one or more of heavy arginines, heavy lysines, and
combinations thereof;
(b) endoproteinase GluC digestion and heavy glutamic acid.
(c) enterokinase light chain digestion and the isotopically labeled variant is
selected from one or more of heavy aspartic acids, heavy lysines, and combinations
thereof.
(d) Factor Xa digestion and one or more of heavy isoluecines, heavy
glutamic acids, heavy aspartic acids, heavy glycines, heavy arginines, and combinations
thereof;
(e) furin digestion and heavy arginine;
(f) genease I digestion and one or more of heavy histidines, heavy tyrosines,
and combinations thereof;
(g) chymotrypsin digestion and a heavy aromatic amino acid
(h) Lys-C or Lys-N digestion and heavy lysine; and
(i) endoproteinase ArgC digestion and heavy arginine.
8. The method of any one of the previous claims, further comprising the
step of purifying the labeled protein and the unlabeled protein prior to protein digestion.
9. The method of any one of the previous claims, wherein the protein is
selected from the group consisting of a recombinant protein, a biotherapeutic protein, an
antibody, a monoclonal antibody, an antibody drug-conjugate, an imaging antibody, a
fusion protein, and a pegylated protein.
10. The method of any one of the previous claims, wherein the protein is an
antibody.
11. The method of any one of the previous claims, wherein the digest
comprises a population of peptides having a combined sequence representing at least
10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more of the complete amino acid
sequence of the protein.
12. The method of claim 11, wherein the combined sequence comprises the
complete amino acid sequence of the protein.
13. The method of any one of the previous claims, further comprising the
steps of:
(i) providing a sample of a third, unlabeled protein comprising an unlabeled
amino acid corresponding to the isotopically labeled variant in the first protein;
(ii) mixing the first sample and the third sample to form a second mixture;
(iii) subjecting the second mixture to a second protein digestion to form a
second digest; and
(iv) subjecting the second digest to bottom-up Liquid Chromatography -
Mass Spectroscopy to form a second spectra including one or more doublet or singlet
peaks, each doublet peak indicating the presence of an isotopically labeled peptide from
the first sample and a corresponding unlabeled peptide from the third sample and each
singlet peak indicating presence of peptide with a mutation, modification, or impurity,
thereby characterizing the third protein sample.
14. The method of claim 13, further comprising the step of (v) comparing the
relative intensities of the doublet peaks in the spectra from the second digest to
determine the relative amount of each peptide.
15. The method of claim 13 or 14, further comprising comparison of the
results of the first and second digests to determine any differences between the second
and the third protein samples.
16. The method of any one of claim 13-15, wherein said comparison
comprises comparing a peak signal ratio of the spectra from the first digest with a
corresponding peak signal ratio of the spectra from the second digest.
17. The method of any one of the previous claims, wherein the first protein
sample is an innovator biologic and the second protein sample is a biosimilar of the
innovator biologic.
18. The method of any one of the previous claims, wherein the first protein
sample is an unconjugated protein and the second protein sample is a conjugated protein.
19. The method of any one of the previous claims, wherein the first and
second protein samples are produced in different cell lines, different cell types or
different manufacturing processes.
20. The method of any one of the previous claims, wherein the first and
second protein samples have been stored under different storage conditions.
21. The method of any one of the previous claims, wherein said method is
employed to detect a mutation, modification or impurity in the second protein sample.
22. The method of claim 21, wherein the mutation, modification or impurity
is selected from the group consisting of altered oligosaccharide content, a N-terminal
glutamine conversion, C-terminal lysine removal, altered pyroglutamate content, and
increased deamidation or oxidation.
23. The method of any one of the previous claims, wherein the first and
second samples are substantially homogenous protein preparations.
24. The method of any one of the previous claims, wherein the first and
second samples are pharmaceutical compositions.