U.S. patent application number 14/517504 was filed with the patent office on 2015-04-16 for method for analysis of compound-binding ability of protein.
The applicant listed for this patent is EISAI R&D MANAGEMENT CO.. Invention is credited to Hiroyuki Katayama, Yoshiya Oda.
Application Number | 20150105292 14/517504 |
Document ID | / |
Family ID | 37683566 |
Filed Date | 2015-04-16 |
United States Patent
Application |
20150105292 |
Kind Code |
A1 |
Oda; Yoshiya ; et
al. |
April 16, 2015 |
METHOD FOR ANALYSIS OF COMPOUND-BINDING ABILITY OF PROTEIN
Abstract
A method for analyzing a binding ability of protein to a
compound, involves fractionating first and second groups of
proteins into plural fractions using a carrier having the compound
immobilized thereon; combining fractions, analyzing the combined
fractions with mass spectrometry; based on the mass spectrometry
information, obtaining, regarding each fraction, an intensity ratio
between peaks derived from a protein in each of the groups of
fractions; and comparing degrees of the binding ability of the
plural kinds of proteins to the compound.
Inventors: |
Oda; Yoshiya; (Tsukuba-shi,
JP) ; Katayama; Hiroyuki; (Tsukuba-shi, JP) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
EISAI R&D MANAGEMENT CO., |
Tokyo |
|
JP |
|
|
Family ID: |
37683566 |
Appl. No.: |
14/517504 |
Filed: |
October 17, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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11989565 |
Jan 28, 2008 |
8889423 |
|
|
PCT/JP2006/315545 |
Jul 31, 2006 |
|
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14517504 |
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Current U.S.
Class: |
506/9 ;
506/39 |
Current CPC
Class: |
G01N 33/6848 20130101;
G01N 2458/15 20130101; G01N 33/58 20130101; G01N 2030/8411
20130101; Y10T 436/24 20150115; G01N 33/54306 20130101; G01N
2560/00 20130101; G01N 30/72 20130101; H01J 49/0409 20130101; G01N
30/84 20130101; G01N 2030/027 20130101 |
Class at
Publication: |
506/9 ;
506/39 |
International
Class: |
G01N 33/68 20060101
G01N033/68; G01N 33/58 20060101 G01N033/58; G01N 33/543 20060101
G01N033/543 |
Foreign Application Data
Date |
Code |
Application Number |
Jul 29, 2005 |
JP |
2005-222097 |
Claims
1. A method for analyzing a binding ability of protein to a
compound, comprising: (a) fractionating a first group of proteins
into plural fractions using a carrier having the compound
immobilized thereon; (b) adding a certain amount of a second group
of proteins to each of the fractions obtained in step (a); (c)
analyzing the fractions obtained in step (b) with mass
spectrometry; and (d) based on the mass spectrometry information,
obtaining, regarding each fraction, an intensity ratio between a
peak derived from a protein in the fraction obtained in step (a)
and a peak derived from a protein in the second group of proteins,
and comparing degrees of the binding ability of the plural kinds of
proteins to the compound.
2. The method according to claim 1, wherein one of the first group
of proteins and second group of proteins is isotope-labeled.
3. The method according to claim 1 further comprising labeling the
fractions obtained in (a).
4. The method according to claim 3, wherein the fractioning of (a)
comprises changing the strength of an eluting solvent.
5. The method according to claims 4, further comprising identifying
each protein contained in each fraction based on the mass
spectrometry information.
6. The method according to claim 5, wherein the comparing the
degrees of the binding ability of the plural kinds of proteins to
the compound comprises determining that a protein concentrated in a
fraction which is eluted later has a higher binding ability to the
compound.
7. The method according to claim 1, wherein (d) comprises
determining that a protein concentrated in a fraction which is
eluted later has a higher binding ability to the compound that an
earlier eluted protein.
8. The method according to claim 1, wherein the fractioning of (a)
comprises changing the strength of an eluting solvent.
9. The method according to claims 1, further comprising identifying
each protein contained in each fraction based on the mass
spectrometry information.
10. The method according to claim 3, wherein the comparing the
degrees of the binding ability of the plural kinds of proteins to
the compound comprises determining that a protein concentrated in a
fraction which is eluted later has a higher binding ability to the
compound.
11. The method according to claim 2, wherein the comparing the
degrees of the binding ability of the plural kinds of proteins to
the compound comprises determining that a protein concentrated in a
fraction which is eluted later has a higher binding ability to the
compound.
12. The method according to claim 1, wherein the comparing the
degrees of the binding ability of the plural kinds of proteins to
the compound comprises determining that a protein concentrated in a
fraction which is eluted later has a higher binding ability to the
compound.
13. A method for analyzing a binding ability of protein to a
compound, comprising: (a1) fractionating a first group of proteins
into plural fractions using a carrier having the compound
immobilized thereon; (a2) analyzing the fractions obtained in (a1)
with mass spectrometry; (a3) identifying each of the proteins in
the fractions obtained in (a1) based on the mass spectrometry
information obtained in (a2); (a4) quantitating each of the
proteins in the fractions obtained in (a1); (b1) analyzing a second
group of proteins with mass spectrometry; (b2) identifying each
protein in the second group of proteins based on the mass
spectrometry information obtained in (b1); (b3) quantitating each
protein in the second group of proteins; and (c) obtaining,
regarding each fraction obtained in (a1), a ratio between the
protein quantity obtained in (a4) and the protein quantity obtained
in (b3), and comparing degrees of the binding ability of the plural
kinds of proteins to the compound.
14. The method according to claim 8 wherein each of the
quantitating comprises calculating an EMPAI of each of the proteins
in the fractions; and the ratio is the ratio between the
EMPAIs.
15. The method according to claim 9, wherein the comparing the
degrees of the binding ability of the plural kinds of proteins to
the compound comprises determining that a protein concentrated in a
fraction which is eluted later has a higher binding ability to the
compound.
16. A system for analyzing a binding ability of protein to a
compound, comprising: (a) a fractionator for fractionating a first
group of isotope-labeled proteins into plural fractions using a
carrier having the compound immobilized thereon; (b) a fractionator
for fractionating a second group of proteins into one or plural
fractions using a carrier having the compound immobilized thereon;
(c) a mixer for adding a certain amount of the one fraction
obtained by fractionator (b), or a certain amount of a mixture of
all the fractions or a mixture of plural contiguous fractions among
the fractions obtained by fractionator (b), to each of the
fractions obtained by fractionator (a); (d) an analyzer for
analyzing the fractions obtained by fractionator (c) with mass
spectrometry; and (e) a comparer for, based on the mass
spectrometry information, obtaining, regarding each fraction, an
intensity ratio between a peak derived from a protein in the
fraction obtained by fractionator (a) and a peak derived from a
protein in the fraction obtained by fractionator (b), and comparing
degrees of the binding ability of the plural kinds of proteins to
the compound.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a division of application Ser. No.
11/989,565, filed Jan. 28, 2008, which was a U.S. National Phase
Application of PCT International Application No. PCT/JP2006/315545,
filed on Jul. 31, 2006, which claims priority to Japanese Patent
Application No. 2005-222097, filed Jul. 29, 2005, all of which are
hereby incorporated herein by reference.
TECHNICAL FIELD
[0002] The present invention relates to a method for analyzing a
binding ability of protein to a compound using mass
spectrometry.
BACKGROUND OF THE INVENTION
[0003] Analysis of protein-protein binding gives us a lot of useful
information for studying functions of each protein. Analysis of
binding between a compound available for a drug and protein gives
us important information for revealing influences of such a
compound on living organisms.
[0004] For analyzing the binding between a substance and protein,
not only the specificity of the protein which binds to the
substance, and but also the binding ability between the substance
and protein (also referred to as the "binding activity"), are also
important indicators.
[0005] For example, when an inhibitor against an enzyme is
developed, if the binding ability of the inhibitor to the enzyme is
lower than the binding ability of the original substrate of the
enzyme to the enzyme, the inhibitor cannot fully function as an
inhibitor.
[0006] The binding ability between molecules is generally
represented by the binding constant (or dissociation constant).
When two substances to be bound together are in an antigen-antibody
relationship, the binding constant can be calculated by ELISA or
RIA. Even when two substances to be bound together are in a
relationship other than the antigen-antibody relationship, the
binding constant can be obtained by equilibrium dialysis,
fluorescence quenching, atomic force microscope, quartz vibrator,
surface plasmon resonance, frontal affinity chromatography or other
methods (see document (1) document (2)). However, in order to use
these methods, it is required that both of the substances should be
already known and that both of the substances should be purified
and isolated before measurement. Therefore, these methods cannot be
used for studying the binding ability of a substance to each of
proteins contained in a mixture of plural kinds of unknown
proteins.
[0007] (1) Borch, J., Roepstorff, P., Anal. Chem. 2004, 76,
5243-5248.
[0008] (2) Zhang, B., Palcic, M. M., Schriemer, D. C.,
Alvarez-Manilla, G., Pierce, M., Hindsgaul, O., Anal. Biochem.
2001, 299, 173-182.
DISCLOSURE OF THE INVENTION
[0009] The present invention has an object of providing a method
and a system for analyzing a binding ability of protein to a
compound using a labeling method or a protein quantitation method
and mass spectrometry.
[0010] As a result of active studies performed to solve the
above-described problems, the present inventor found that a binding
ability of protein to a compound can be analyzed (compared) as
follows. Protein bound to a compound immobilized on a carrier is
fractionated into plural fractions. Performing fractionation
separately, one fraction, or a mixture of all the fractions or a
mixture of plural contiguous fractions, is prepared as an internal
standard fraction. A certain amount of the internal reference
fraction is added to each of the above-obtained fractions, and each
of the fractions is analyzed with mass spectrometry. Then, a peak
intensity ratio is detected based on the mass spectrometry
information. By this, the binding ability of protein to the
compound can be analyzed (compared). Thus, the present inventor
completed the present invention.
[0011] The present invention is directed to the following. [0012]
(1) A method for analyzing a binding ability of protein to a
compound, comprising the steps of [0013] (a) fractionating a first
group of isotope-labeled proteins into plural fractions using a
carrier having the compound immobilized thereon; [0014] (b)
fractionating a second group of proteins into one or plural
fractions using a carrier having the compound immobilized thereon;
[0015] (c) adding a certain amount of the one fraction obtained in
step (b), or a certain amount of a mixture of all the fractions or
a mixture of plural contiguous fractions among the fractions
obtained in step (b), to each of the fractions obtained in step
(a); [0016] (d) analyzing the fractions obtained in step (c) with
mass spectrometry; and [0017] (e) based on the mass spectrometry
information, obtaining, regarding each fraction, an intensity ratio
between a peak derived from a protein in the fraction obtained in
step (a) and a peak derived from a protein in the fraction obtained
in step (b), and comparing degrees of the binding ability of the
plural kinds of proteins to the compound. [0018] (2) A method for
analyzing a binding ability of protein to a compound, comprising
the steps of: [0019] (a) fractionating a first group of proteins
into plural fractions using a carrier having the compound
immobilized thereon; [0020] (b) fractionating a second group of
isotope-labeled proteins into one or plural fractions using a
carrier having the compound immobilized thereon; [0021] (c) adding
a certain amount of the one fraction obtained in step (b), or a
certain amount of a mixture of all the fractions or a mixture of
plural contiguous fractions among the fractions obtained in step
(b), to each of the fractions obtained in step (a); [0022] (d)
analyzing the fractions obtained in step (c) with mass
spectrometry; and [0023] (e) based on the mass spectrometry
information, obtaining, regarding each fraction, an intensity ratio
between a peak derived from a protein in the fraction obtained in
step (a) and a peak derived from a protein in the fraction obtained
in step (b), and comparing degrees of the binding ability of the
plural kinds of proteins to the compound. [0024] (3) A method for
analyzing a binding ability of protein to a compound, comprising
the steps of [0025] (a) fractionating a first group of proteins
into plural fractions using a carrier having the compound
immobilized thereon; [0026] (b) fractionating a second group of
proteins into one or plural fractions using a carrier having the
compound immobilized thereon; [0027] (c) labeling the fractions
obtained in step (a); [0028] (d) adding a certain amount of the one
fraction obtained in step (b), or a certain amount of a mixture of
all the fractions or a mixture of plural contiguous fractions among
the fractions obtained in step (b), to each of the fractions
labeled in step (c); [0029] (e) analyzing the fractions obtained in
step (d) with mass spectrometry; and [0030] (f) based on the mass
spectrometry information, obtaining, regarding each fraction, an
intensity ratio between a peak derived from a protein in the
fraction obtained in step (a) and a peak derived from a protein in
the fraction obtained in step (b), and comparing degrees of the
binding ability of the plural kinds of proteins to the compound.
[0031] (4) A method for analyzing a binding ability of protein to a
compound, comprising the steps of: [0032] (a) fractionating a first
group of proteins into plural fractions using a carrier having the
compound immobilized thereon; [0033] (b) fractionating a second
group of proteins into one or plural fractions using a carrier
having the compound immobilized thereon; [0034] (c) labeling the
one fraction obtained in step (b), or a mixture of all the
fractions or a mixture of plural contiguous fractions among the
fractions obtained in step (b); [0035] (d) adding a certain amount
of the fraction or the mixture labeled in step (c) to each of the
fractions obtained in step (a); [0036] (e) analyzing the fractions
obtained in step (d) with mass spectrometry; and [0037] (f) based
on the mass spectrometry information, obtaining, regarding each
fraction, an intensity ratio between a peak derived from a protein
in the fraction obtained in step (a) and a peak derived from a
protein in the fraction obtained in step (b), and comparing degrees
of the binding ability of the plural kinds of proteins to the
compound. [0038] (5) The method according to any one of (1) through
(4), wherein step (a) of fractioning and/or step (b) of fractioning
is the step of performing the fractioning by changing the strength
of an eluting solvent. [0039] (6) The method according to any one
of (1) through (5), further comprising the step of identifying each
protein contained in each fraction based on the mass spectrometry
information.
[0040] In (1) through (6) above, the second group of proteins may
be added in a certain amount to each of the fractions derived from
the first group of proteins without being fractionated into one or
plural fractions using the carrier having the compound immobilized
thereon.
[0041] In (1) through (6) above, the binding ability of protein to
the compound may be analyzed by using a protein quantitation method
or by using an EMPAI of the protein as an index, instead of using a
protein labeling method. [0042] (7) A system for analyzing a
binding ability of protein to a compound, comprising: [0043] (a)
means for fractionating a first group of isotope-labeled proteins
into plural fractions using a carrier having the compound
immobilized thereon; [0044] (b) means for fractionating a second
group of proteins into one or plural fractions using a carrier
having the compound immobilized thereon; [0045] (c) means for
adding a certain amount of the one fraction obtained by means (b),
or a certain amount of a mixture of all the fractions or a mixture
of plural contiguous fractions among the fractions obtained by
means (b), to each of the fractions obtained by means (a); [0046]
(d) means for analyzing the fractions obtained by means (c) with
mass spectrometry; and [0047] (e) means for, based on the mass
spectrometry information, obtaining, regarding each fraction, an
intensity ratio between a peak derived from a protein in the
fraction obtained by means (a) and a peak derived from a protein in
the fraction obtained by means (b), and comparing degrees of the
binding ability of the plural kinds of proteins to the compound.
[0048] (8) A system for analyzing a binding ability of protein to a
compound, comprising: [0049] (a) means for fractionating a first
group of proteins into plural fractions using a carrier having the
compound immobilized thereon; [0050] (b) means for fractionating a
second group of isotope-labeled proteins into one or plural
fractions using a carrier having the compound immobilized thereon;
[0051] (c) means for adding a certain amount of the one fraction
obtained by means (b), or a certain amount of a mixture of all the
fractions or a mixture of plural contiguous fractions among the
fractions obtained by means (b), to each of the fractions obtained
by means (a); [0052] (d) means for analyzing the fractions obtained
by means (c) with mass spectrometry; and [0053] (e) means for,
based on the mass spectrometry information, obtaining, regarding
each fraction, an intensity ratio between a peak derived from a
protein in the fraction obtained by means (a) and a peak derived
from a protein in the fraction obtained by means (b), and comparing
degrees of the binding ability of the plural kinds of proteins to
the compound. [0054] (9) A system for analyzing a binding ability
of protein to a compound, comprising: [0055] (a) means for
fractionating a first group of proteins into plural fractions using
a carrier having the compound immobilized thereon; [0056] (b) means
for fractionating a second group of proteins into one or plural
fractions using a carrier having the compound immobilized thereon;
[0057] (c) means for labeling the fractions obtained by means (a);
[0058] (d) means for adding a certain amount of the one fraction
obtained by means (b), or a certain amount of a mixture of all the
fractions or a mixture of plural contiguous fractions among the
fractions obtained by means (b), to each of the fractions labeled
by means (c); [0059] (e) means for analyzing the fractions obtained
by means (d) with mass spectrometry; and [0060] (f) means for,
based on the mass spectrometry information, obtaining, regarding
each fraction, an intensity ratio between a peak derived from a
protein in the fraction obtained by means (a) and a peak derived
from a protein in the fraction obtained by means (b), and comparing
degrees of the binding ability of the plural kinds of proteins to
the compound. [0061] (10) A system for analyzing a binding ability
of protein to a compound, comprising: [0062] (a) means for
fractionating a first group of proteins into plural fractions using
a carrier having the compound immobilized thereon; [0063] (b) means
for fractionating a second group of proteins into one or plural
fractions using a carrier having the compound immobilized thereon;
[0064] (c) means for labeling the one fraction obtained by means
(b), or a mixture of all the fractions or a mixture of plural
contiguous fractions among the fractions obtained by means (b);
[0065] (d) means for adding a certain amount of the fraction or the
mixture labeled by means (c) to each of the fractions obtained by
means (a); [0066] (e) means for analyzing the fractions obtained by
means (d) with mass spectrometry; and [0067] (f) means for, based
on the mass spectrometry information, obtaining, regarding each
fraction, an intensity ratio between a peak derived from a protein
in the fraction obtained by means (a) and a peak derived from a
protein in the fraction obtained by means (b), and comparing
degrees of the binding ability of the plural kinds of proteins to
the compound. [0068] (11) The system according to any one of (7)
through (10), wherein means (a) for fractioning and/or means (b)
for fractioning is means for performing the fractioning by changing
the strength of an eluting solvent. [0069] (12) The system
according to any one of (7) through (11), further comprising means
for identifying each protein contained in each fraction based on
the mass spectrometry information.
[0070] In (7) through (12) above, the second group of proteins may
be added in a certain amount to each of the fractions derived from
the first group of proteins without being fractionated into one or
plural fractions using the carrier having the compound immobilized
thereon.
[0071] In (7) through (12) above, the binding ability of protein to
the compound may be analyzed by using protein quantitation means or
by using an EMPAI of the protein as an index, instead of using
protein labeling means.
[0072] The present invention makes it possible to create rankings
of the binding ability of plural kinds of substances (proteins)
bindable to a compound. One embodiment of the present invention
makes it possible to analyze a binding ability of plural kinds of
unknown substances to a compound. One embodiment of the present
invention is useful in being applicable even to the case where the
target substance is unknown and the substances are not fully
separated in a mixed sample.
BRIEF DESCRIPTION OF THE DRAWINGS
[0073] FIG. 1 shows an exemplary protein elution profile provided
by affinity purification.
[0074] FIG. 2 shows an overview of a method of the present
invention.
[0075] FIG. 3 is a block diagram showing an exemplary structure of
a system of the present invention.
[0076] FIG. 4 is a schematic view showing an example of each unit
of the system of the present invention.
[0077] FIG. 5 shows an exemplary structure of a control unit in
detail.
[0078] FIG. 6 is a flowchart showing an exemplary operation of the
control unit.
DESCRIPTION OF THE REFERENCE NUMERALS
[0079] 1a: tube; 1b: tube; 2a: stirring blade; 2b: stirring blade;
11a: culture device; 11b: culture device; 12a: culture liquid
bottle; 12b: culture liquid bottle; 13a: cell crushing device; 13b:
cell crushing device; 14: labeling device; 15a: carrier having a
compound immobilized thereon; 15b: carrier having a compound
immobilized thereon; 16a: protein fractionation control device;
16b: protein fractionation control device; 17a: purified protein
separator; 17b: purified protein separator; 17c: mixing device;
18-1: tube; 18-2: tube; 18-3: tube; 18-4: tube; 18-5: tube; 19:
plate; 20: mass spectrometry device; 21: computer; 30: central
computer; 100: LAN; 301: control unit; 302: protein fractionation
unit; 303: protein mixing unit; 304: mass spectrometry unit; 501:
CPU; 502: transmission/receiving section; 503: input section; 504:
output section; 505: ROM; 506: RAM; 507: hard disc drive (HDD);
508: CD-ROM drive; 509: protein database (DB); 510: CD-ROM; 511:
Internet
BEST MODE FOR CARRYING OUT THE INVENTION
[0080] Hereinafter, embodiments of the present invention will be
described. The following embodiments are given in order to
illustrate the present invention and are not intended to limit the
present invention in any way. The present invention can be carried
out in various embodiments without departing from the gist
thereof.
[0081] The documents, laid-open publications, patents and other
patent documents cited in this specification are incorporated
herein by reference. The claims and the disclosure of the
specification, drawings and abstract of Japanese Application
JP2005-222097 filed on Jul. 29, 2005, based upon which the present
application claims the benefit of priority, are entirely
incorporated herein by reference.
[0082] As used herein, the term "protein" encompasses a peptide
comprising two or more amino acids bound together by peptide
binding. The "protein" also encompasses physiologically modified
proteins (e.g., phosphorylated protein, glycoprotein, etc.). As
used herein, the term "group of proteins" refers to an assembly
comprising two or more kinds of proteins.
[0083] As used herein, the term "labeled protein" refers to a
protein in which a part of molecules forming the protein is
labeled. Specifically, a protein labeled with an isotope is
referred to as an "isotope-labeled protein". As used herein, the
term "group of isotope-labeled proteins" refers to an assembly
comprising two or more kinds of isotope-labeled proteins.
[0084] As used herein, the term "metabolically isotope-labeled
protein" refers to a protein in which a part of molecules forming
the protein is metabolically labeled with an isotope as a result of
an isotope-labeled precursor of the protein (e.g., amino acid)
being added. As used herein, the term "group of metabolically
isotope-labeled proteins" refers to an assembly comprising two or
more kinds of metabolically isotope-labeled proteins. The term
"metabolically" refers to a physiological condition obtained via
enzyme reaction or the like, and preferably refers to a metabolic
reaction in a cultured cell.
1. Overview of the Present Invention
[0085] The present invention relates to a method for analyzing the
degree of the binding ability of a group of known or unknown
substances (proteins) bindable to a compound using mass
spectrometry and creating rankings of the substances in accordance
with the binding ability.
[0086] In general, for eluting a group of substances bound to a
compound immobilized on carriers in a column which is filled with
such carriers having the compound immobilized thereon (affinity
chromatography column), the eluate is fractionated while the
eluting power of the eluting solvent is gradually increased.
Therefore, the last substance eluted from the affinity
chromatography column has the highest binding ability to the
compound immobilized on the carriers. For example, when proteins
are eluted from the affinity chromatography column as shown in FIG.
1, the proteins contained in fraction 5 have the highest binding
ability. As shown in FIGS. 1; 2, a1; & 2, a2', for example,
protein A (which is a non-target protein) is included in fractions
1 and 2, and protein B (which is also a non-target protein) is
included in fractions 1, 2, and 3. Fractions 1-5 in FIG. 2, a2',
whether as one of said fraction, or as a mixture of all said
fractions, or a mixture of plural contiguous fractions, is referred
to as the internal standard fraction. As shown in the protein
elution profile of FIG. 2, a2', fractions 1-5 in FIG. 2, a2'
contain non-isotope-labeled proteins A, B, C, D and E in differing
amounts. It is assumed that the proteins contained in fraction 5
are identified to be three kinds of proteins C, D and E. In order
to compare the degrees of the binding ability of the proteins C, D
and E, the elution profile of each protein is checked using a
standard product of thereof, or using a different fluorescent color
tag or a different epitope tag. As a result, it is found that the
protein F is eluted at the latest, namely, has the highest binding
ability.
[0087] However, the protein eluted from the affinity chromatography
column may be entirely eluted in one fraction or may be eluted over
a wide range from the first fraction to the last fraction.
Moreover, one fraction contains plural kinds of proteins in a mixed
state. For these reasons, it is not easy to find the elution
pattern of each protein. Preparation of a standard product or
introduction of a tag is not easy and cannot be done routinely.
Introduction of a tag also causes an artificial influence and
prevents a true binding ability from being found. In addition, when
these methods are used, it is necessary to identify the bound
proteins in advance.
[0088] In the present invention, a group of proteins are
fractionated into plural fractions using a carrier having a
compound immobilized thereon. Separately, another group of proteins
are fractionated into one or plural fractions using a carrier
having the compound immobilized thereon, and a mixture of all the
obtained fractions or a mixture of plural contiguous fractions is
prepared as an internal standard fraction. Among the groups of
proteins to be loaded to a column filled with carries having the
compound immobilized thereon (affinity chromatography column), one
group of proteins are isotope-labeled (or are isotope-labeled after
being fractionated). Next, a certain amount of the mixture of all
the fractions (or of plural contiguous fractions) as the internal
standard fraction is added to each test sample separately
fractionated therefrom. Optionally, the fractions may be separated
by SDS-PAGE or the like so that the proteins are digested with
trypsin or the like. Then, each fraction is measured by a mass
spectrometry device.
[0089] Either the fractionated test samples or the internal
standard fraction sample is isotope-labeled. FIG. 2 shows an
embodiment in which the test samples are isotope-labeled before
affinity purification (FIG. 2, a.sub.1). The fractions obtained by
affinity purification of labeled samples (FIG. 2, a.sub.1) and the
fractions obtained by affinity purification of unlabeled samples
(FIG. 2, a.sub.2) are mixed together (FIG. 2, b), and the mixed
samples are analyzed with mass spectrometry (FIG. 2, c). The mass
spectrum shows the peaks of the proteins derived from the
isotope-labeled fractions (FIG. 2, c, peaks represented with dashed
lines) and the peaks of the proteins derived from the unlabeled
fractions (FIG. 2, c, peaks represented with solid lines) in pairs.
The intensity ratios of the peaks are obtained. In the case where a
protein is eluted in plural fractions, that protein is eluted while
being most concentrated in the fraction having the highest peak
intensity ratio. In the case where plural kinds of proteins are
contained in one fraction, the protein having the highest peak
intensity ratio is eluted while being most concentrated in that
fraction. For example, referring to FIG. 2, proteins C and D are
contained in a larger amount in fraction 4 than in fraction 5,
whereas the protein E is contained in a larger amount in fraction 5
than in fraction 4 (FIG. 2, c). In fraction 4, protein D has the
highest peak intensity ratio; whereas in fraction 5, protein E has
the highest peak intensity ratio. By comparing protein D and
protein E based on these, it is found that the proteins are
fractionated in the order of protein D and then protein E, and that
protein E is eluted at the latest.
[0090] In the step shown in FIG. 2, b, it is not necessary to mix
all the fractions as the internal standard fraction, but only the
continuous fractions to be compared may be mixed. For example, when
fractions 3, 4 and 5, or proteins C, D and E are the test target,
the continuous fractions, i.e., only fractions 3, 4 and 5 may be
mixed to obtain the internal standard fraction. This can prevent
the situation where the internal standard fraction is entirely
diluted and the target substance cannot be detected. All the amount
of each fraction may be mixed to obtain the internal standard
fraction, or a certain amount of each fraction may be mixed to
obtain the internal standard fraction. Regarding the step of
fractionating the unlabeled samples into one or plural fractions
(FIG. 2, a.sub.2), in the case where the samples are fractionated
into one fraction, that one fraction may be used as the internal
standard fraction (FIG. 2, a.sub.2').
[0091] It is found in which fraction each protein is most
concentrated when being eluted, and a protein concentrated in a
fraction which is eluted later can be determined to have a higher
binding ability to the compound immobilized on the carrier. It is
not absolutely necessary to fractionate the samples for the
internal standard fraction using a carrier having the compound
immobilized thereon. However, many of the proteins detected by a
mass spectrometry device from a sample which is not concentrated
are expressed in a very large amount. In addition, a protein which
is not concentrated and a protein concentrated with a carrier
having the compound immobilized thereon have different
concentrations. In this case, considering the narrowness of the
dynamic range of the mass spectrometry, it is difficult to adjust
the amount of the internal standard fraction. For these reasons, it
is desirable to concentrate the samples for the internal standard
fraction also with a carrier having the compound immobilized
thereon.
[0092] The present invention makes it possible to calculate the
binding ability degree ratio of plural kinds of proteins to a
compound. Therefore, the analysis of the present invention may be
conducted on plural kinds of compounds so as to calculate the
correlation of the binding ability between compounds and proteins.
Thus, the characteristics of these compounds to living organisms,
cells or the like can be analyzed.
2. Embodiments of the Present Invention
(1) First Embodiment
[0093] A first embodiment of the present invention comprises the
following steps for analyzing a binding ability of protein to a
compound, wherein the group of proteins as the target of analysis
are isotope-labeled before fractionation: [0094] (a) step of
fractionating a first group of isotope-labeled proteins into plural
fractions using a carrier having the compound immobilized thereon;
[0095] (b) step of fractionating a second group of proteins into
one or plural fractions using a carrier having the compound
immobilized thereon; [0096] (c) step of adding a certain amount of
the one fraction obtained in step (b), or a certain amount of a
mixture of all the fractions or a mixture of plural contiguous
fractions among the fractions obtained in step (b), to each of the
fractions obtained in step (a); [0097] (d) step of analyzing the
fractions obtained in step (c) with mass spectrometry; and [0098]
(e) step of, based on the mass spectrometry information, obtaining,
regarding each fraction, an intensity ratio between a peak derived
from a protein in the fraction obtained in step (a) and a peak
derived from a protein in the fraction obtained in step (b), and
comparing degrees of the binding ability of the plural kinds of
proteins to the compound. [0099] (a) The step of fractionating a
first group of isotope-labeled proteins into plural fractions using
a carrier having the compound immobilized thereon
[0100] In the present invention, the first group of proteins are
protein samples as the target of analysis, for which samples
obtained from, for example, tissues, bodily fluids from living
organisms, cells, cell organella, protein composites and the like
are usable.
[0101] For the group of isotope-labeled proteins, any protein in
which a part of molecules (amino acids) forming the protein is
labeled with an isotope may be used. There is no specific
limitation on the method for preparation or the labeling site.
[0102] Hereinafter, a specific method for preparation will be
described.
[0103] The group of isotope-labeled proteins may be prepared by
metabolic isotope labeling. For example, a protein in a cell may be
metabolically isotope-labeled by culturing a culturable cell in a
medium containing an isotope-labeled precursor of the protein
(e.g., amino acid). Any culturing condition is usable. A condition
preferable to culture the cell in a liquid medium or a solid medium
may be selected. For example, when an animal cell is selected, a
medium such as DMEM, MEM, RPMI1640, IMDM or the like may be used.
When necessary, serum such as fetal calf serum (FCS) or the like,
amino acid, glucose, penicillin, streptomycin or the like may be
added. Culturing may be performed at a pH value of about 6 to 8 and
30 to 40.degree. C. for 15 to 200 hours. When necessary, the medium
may be changed, or ventilation or stirring may be performed.
[0104] A cell containing the group of proteins metabolically
isotope-labeled thus obtained is crushed, and thus a group of
isotope-labeled proteins can be prepared. Usable methods for
crushing include methods using a Dounce-type Teflon.TM.
homogenizer, a polytron, a Waring blender, a Potter-type glass
homogenizer, an ultrasonic crushing device, a cell-dissolved
solution (e.g., M-PER: Cat. No. 78501; T-PER: Cat. No. 78510; both
by PIERCE, etc.) and the like, and a freezing and thawing method. A
method using a cell-dissolved solution is preferable. The crushed
cell is preferably deprived of insoluble substances by
centrifugation. In this way, the group of isotope-labeled proteins
can be prepared.
[0105] An isotope used in the present invention may be a
radioactive isotope, but a stable isotope with no radioactivity is
easy to handle and especially preferable. Usable stable isotopes
include, for example, .sup.2H, .sup.13C, .sup.15N, .sup.17,
.sup.18O, .sup.31P, .sup.34S or a combination thereof. .sup.2H,
.sup.13C, .sup.15N, .sup.18O or a combination thereof is
preferable; .sup.13C, .sup.15N, .sup.18O or a combination thereof
is more preferable; and .sup.13C is still more preferable.
According to the present invention, any type of isotope which can
label a protein is usable with no specific limitation.
Specifically, .sup.13C label (.sup.13C.times.6) leucine (produced
by Cambridge Isotope Labs (CIL), L-Leucine U-.sup.13C6, CLM-2262)
is usable as a precursor of an isotope-labeled protein. The
above-mentioned isotopes are applicable to all the embodiments of
the present invention.
[0106] The group of isotope-labeled proteins may also be prepared
in vitro. For example, the proteins may be isotope-labeled by
alkylating cysteine residue in the proteins using an
isotope-labeled alkylating reagent (see Rapid Communications in
Mass Spectroscopy, Vol. 16, No. 15 (2002), pp. 1416-1424).
Alternatively, the proteins may be isotope-labeled by biotinylating
cysteine residue in the proteins using an isotope-labeled
biotinylating reagent. After the labeling, only the labeled
proteins may be purified using an avidin column (Nature
Biotechnology, Vol. 17, No. 10, October 1999, pp. 994-999).
[0107] Alternatively, the group of isotope-labeled proteins may be
prepared by chemical synthesis.
[0108] The group of isotope-labeled proteins may be preliminary
fractionated. Usable preliminary fractionation methods include, for
example, differential centrifugation, sucrose density gradient
centrifugation, and the like. Sucrose density gradient
centrifugation is preferable.
[0109] Optionally, the group of isotope-labeled proteins may be
separated. Usable separation methods include, for example,
electrophoresis (e.g., two-dimensional electrophoresis, SDS-PAGE,
etc.), methods using group-specific affinity chromatography, cation
exchange chromatography, anion exchange chromatography and reverse
phase chromatography, immunoprecipitation, ammonium sulfate
precipitation, precipitation by an organic solvent,
ultrafiltration, gel filtration, dialysis, and the like. A method
using reverse phase chromatography is preferable.
[0110] The group of isotope-labeled proteins may be stored under an
appropriate condition, preferably at -20.degree. C. or lower,
especially preferably at -80.degree. C. or lower.
[0111] In the present invention, the expression "carrier having a
compound immobilized thereon" refers to a carrier having a compound
covalently or noncovalently bound thereto via a functional
group.
[0112] A carrier having the compound immobilized thereon is
obtained, for example, as follows. First, N-hydroxy-succinimide or
hydrazide as a functional group is covalently bound to the carrier;
simply an amino group is formed to the carrier; or Protein A,
heparin, Cibacron Blue F3GA or the like is immobilized on the
carrier. Then, a compound is covalently or noncovalently bound to
such a carrier, with or without the structure of the compound being
partially changed.
[0113] There is no specific limitation on the compound to be
immobilized on the carrier. Usable compounds include, for example,
synthesized compounds having a low molecular weight, proteins,
synthesized peptides, purified or partially purified polypeptides,
antibodies, cell released substances (encompassing cell metabolic
products), intra-biological cellular nucleic acid substances (e.g.,
ATP, GTP, NAD/NADH, NADP/NADPH, etc.), and lipid. Such a compound
may be a novel compound or a known compound.
[0114] Usable carriers include, for example, agarose gel,
acrylamide, magnetic bead, cellulose, silica gel, and the like.
Agarose gel is preferable. Such a carrier is available from, for
example, BioRad (Affi-gel, produced by BioRad, Cat. No.
153-6099).
[0115] A carrier having a compound immobilized thereon may be
produced by binding a desired compound to the carrier. A carrier
having, for example, a compound containing an amino group
immobilized thereon may be produced as follows. First, a compound
solution containing an amino group is added to a carrier having
N-hydroxy-succinimide binding thereto (e.g., Affi-gel 10). Next,
triethylamine is added thereto and incubated. Then, 2-aminoethanol
is added thereto and further incubated. Thus, a carrier having a
compound containing an amino group immobilized thereon is produced.
It is preferable to perform a washing operation when necessary.
[0116] A carrier having a compound containing, for example,
carboxylic acid immobilized thereon may be produced as follows.
First, carbodiamide is added to a compound solution containing
carboxylic acid, and incubated. The resultant substance is added to
a carrier having an amino acid binding thereto. Next, acetic acid
(or lactic acid) is added and further incubated. Thus, a carrier
having a compound containing carboxylic acid immobilized thereon is
produced. It is preferable to perform a washing operation when
necessary. A carrier having an NADP analog immobilized thereon is
available from, for example, Amersham Biosciences (2'5'ADP
Sepharose 4B (code number: 17-0700-01)).
[0117] A carrier having a compound containing a thiol group
immobilized thereon may be produced using, for example, SulfoLink
(PIERCE, Cat. No. 44895). A carrier having a compound containing an
aldehyde group immobilized thereon may be produced using, for
example, CarboLink (PIERCE, Cat. No. 44900).
[0118] A carrier having a compound containing a hydroxyl group such
as sugar immobilized thereon may be produced using CarboLink
(PIERCE, Cat. No. 44900) or the like, because an aldehyde group can
be generated from the hydroxyl group of the compound by, for
example, oxidation performed with 10 mM periodic acid at room
temperature. A compound having an active hydrogen atom
(exchangeable hydrogen atom) (an example of such a compound is
estradiol 17.beta. having a cholesterol backbone) can be
immobilized on a carrier by causing concentration by Mannich
reaction among three substances of the compound, formaldehyde, and
the amino group immobilized on the carrier.
[0119] There is no specific limitation on the amount of the
compound to be immobilized on the carrier. A preferable amount is
0.1 mg to several milligrams with respect to 1 ml of the
carrier.
[0120] A carrier having a compound immobilized thereon is usable
for affinity chromatography. When an appropriate column (e.g.,
Polyprep empty column (produced by BioRad, Cat. No. 731-1550),
etc.) is filled with such a carrier, the carrier is usable as an
affinity chromatography column having a compound immobilized
thereon. Such a carrier having a compound immobilized thereon is
also usable when being put into an appropriate tube (e.g.,
Eppendorf tube (produced by Eppendorf), etc.).
[0121] The group of isotope-labeled proteins are fractionated into
plural fractions using a carrier having a compound immobilized
thereon. By this, plural kinds of proteins bound to the compound
immobilized on the carrier can be fractionated to obtain fractions.
As used herein, the expression "using a carrier" refers to using a
carrier having a compound immobilized thereon when fractionating
the group of proteins as a population.
[0122] Hereinafter, this will be described in detail.
[0123] First, a carrier having a compound immobilized thereon is
equilibrated with an appropriate solution. There is no specific
limitation on the solution for equilibration, but a solution which
can dissolve proteins and does not denature the proteins is
preferable. For example, a phosphoric acid buffer solution, a Hepes
buffer solution, or Tris buffer solution, each prepared to have a
physiological pH value, is usable. When necessary, sodium chloride
and/or a surfactant (e.g., n-octylglucoside) may be added thereto
in an appropriate amount.
[0124] In the case where an appropriate column is filled with the
carrier having the compound immobilized thereon, the step of
equilibration may be performed by applying an appropriate solution
to the column. In the case where the carrier having the compound
immobilized thereon is put to an appropriate tube, the step of
equilibration may be performed by applying an appropriate solution
to the tube.
[0125] Next, the group of isotope-labeled proteins, and the carrier
having the compound immobilized thereon, are put into contact with
each other. In the case where an appropriate column is filled with
the carrier having the compound immobilized thereon, the step of
putting the group of isotope-labeled proteins, and the carrier
having the compound immobilized thereon, into contact with each
other may be performed by loading the group of isotope-labeled
proteins to the column. In the case where the carrier having the
compound immobilized thereon is put to an appropriate tube, the
above-mentioned step may be performed by adding the group of
isotope-labeled proteins to the tube.
[0126] Then, desirably, the carrier having a compound immobilized
thereon is washed with an appropriate solution. In the case where
an appropriate column is filled with the carrier having the
compound immobilized thereon, the washing operation may be
performed by adding an appropriate solution to the column. In the
case where the carrier having the compound immobilized thereon is
put to an appropriate tube, the washing operation may be performed
by adding an appropriate solution to the tube and conducting a
centrifugal operation.
[0127] Then, the group of isotope-labeled proteins are eluted with
an appropriate solution.
[0128] The samples may be eluted while changing the strength of the
eluting solvent. The "strength" is also referred to as the "eluting
power", and means a chemical strength for eluting a sample bound to
a column. The strength is influenced by the concentration of the
eluting solvent or the like. Accordingly, "changing the strength of
the eluting solvent" means, for example, applying a concentration
gradient of the solvent continuously or incontinuously. Elution may
be performed by a method of denaturing the samples bound to the
column with guadinine hydrochloride, urea or the like, a method of
changing the salt concentration with KCl, NaCl or the like, a
method of changing the pH value, or the like.
[0129] Chemically bound samples may be eluted by adding an
excessive amount of a compound having the same or a similar
backbone to that of the compound immobilized on the carrier.
[0130] In the case where an appropriate column is filled with the
carrier having the compound immobilized thereon, the step of
eluting the group of isotope-labeled proteins may be performed by
loading an appropriate solution to the column. In the case where
the carrier having the compound immobilized thereon is put to an
appropriate tube, the step of eluting the group of isotope-labeled
proteins may be performed by applying an appropriate solution to
the tube and performing centrifugation.
[0131] By these methods, the group of proteins bound to the carrier
having the compound immobilized thereon can be fractionated to
obtain fractions.
[0132] The temperature for the above-described operation is not
specifically limited, but is preferably 4.degree. C. to 37.degree.
C., and more preferably 4.degree. C. to 20.degree. C. [0133] (b)
The step of fractionating a second group of proteins into one or
plural fractions using a carrier having the compound immobilized
thereon
[0134] In this step, the second group of proteins are samples for
the internal standard fraction.
[0135] In this step, separately from step (a) above, the same
samples (second group of proteins) which are not isotope-labeled
are fractionated into one or plural fractions using the carrier
having the compound immobilized thereon. In the first embodiment of
the present invention, the fractions of the group of
isotope-labeled proteins are used as the test target (target of
analysis), and the fractions of the group of non-isotope-labeled
proteins are used as the internal standard fraction. The internal
standard fraction means a fraction acting as a standard in a
measurement system.
[0136] As used herein, the term "group of non-isotope-labeled
proteins" refers to an assembly comprising proteins on which the
act of isotope labeling is not conducted.
[0137] As the group of non-isotope-labeled proteins (the second
group of proteins in the first embodiment), samples obtained from,
for example, tissues, bodily fluids from living organisms, cells,
cell organella, protein composites and the like are usable.
[0138] Usable methods for crushing include be methods using a
Dounce-type Teflon.TM. homogenizer, a polytron, a Waring blender, a
Potter-type glass homogenizer, an ultrasonic crushing device, a
cell-dissolved solution (e.g., M-PER: Cat. No. 78501; T-PER: Cat.
No. 78510; both by PIERCE, etc.) and the like, and a freezing and
thawing method. A method using a cell-dissolved solution is
preferable. The crushed cell is preferably deprived of insoluble
substances by centrifugation. In this way, the group of
non-isotope-labeled proteins can be prepared.
[0139] Alternatively, the group of non-isotope-labeled proteins may
be prepared by chemical synthesis.
[0140] The group of non-isotope-labeled proteins may be stored
under an appropriate condition, preferably at -20.degree. C. or
lower, especially preferably at -80.degree. C. or lower.
[0141] In the present invention, the "group of non-isotope-labeled
proteins" are preferably prepared by the same method as the "group
of isotope-labeled proteins" using a naturally-occurring reagent
(non-isotope reagent).
[0142] According to the present invention, instead of the "group of
non-isotope-labeled proteins", a group of proteins labeled with an
isotope different from the isotope in the "group of isotope-labeled
proteins" (hereinafter, referred to also as a "group of
different-isotope-labeled proteins") are usable. The isotope in the
"group of different-isotope-labeled proteins" may be different from
the isotope in the "group of isotope-labeled proteins" or may
include the same isotope, as long as the proteins can be labeled
such that proteins derived from these groups of proteins and
corresponding to each other have different masses.
[0143] The group of non-isotope-labeled proteins may be preferably
fractionated using the same carrier as that used in step (a). By
this, plural kinds of proteins bound to the compound immobilized on
the carrier can be fractionated to obtain fractions.
[0144] The samples may be eluted while changing the strength of the
eluting solvent, or at a constant eluting power without changing
the strength of the eluting solvent. In step (b) of fractionating a
second group of proteins into one or plural fractions using a
carrier having the compound immobilized thereon, the same eluting
condition as that of step (a) is desirably selected. In this
specification, the number of fractions obtained by fractionating
the samples for the internal standard fraction may be one as
described in the example provided later. [0145] (c) The step of
adding a certain amount of the one fraction obtained in step (b),
or a certain amount of a mixture of all the fractions or a mixture
of plural contiguous fractions among the fractions obtained in step
(b), to each of the fractions obtained in step (a)
[0146] In this step, the internal standard fraction is added to
each of the fractions obtained by fractionating the group of
isotope-labeled proteins using the carrier having the compound
immobilized thereon. The term "addition" means mixing
fractions.
[0147] In this step, the internal standard fraction means the "one
fraction obtained in step (b)", or the "mixture of all the
fractions" or the "mixture of plural contiguous fractions" among
the fractions obtained in step (b). The "one fraction obtained in
step (b)" means the obtained fraction when one fraction is obtained
by the fractionation in step (b). The "mixture of all the
fractions" means a mixture of all the eluted fractions or a mixture
of a certain amount of each of all the eluted fractions. The
"mixture of plural contiguous fractions" means a mixture of a
series of plural contiguous fractions or a mixture of a certain
amount of each of such plural contiguous fractions.
[0148] According to the present invention, the protein samples for
the internal standard fraction may be fractionated in substantially
the same manner as the test protein samples (FIG. 2, a.sub.1) to
obtain five fractions (FIG. 2, a.sub.2) as follows, for example.
FIG. 2 shows an example of elution in affinity purification. The
fractions are respectively referred to as fractions 1 through 5.
The "plural contiguous fractions" means an assembly comprising a
series of contiguous fractions, for example, fractions 1 and 2,
fractions 2 and 3, fractions 3 through 5, or the like. The "certain
amount" may be arbitrarily set in accordance with the purpose, and
is preferably set such that the amounts to be added to the
fractions (for example, fractions 1 through 5 in FIG. 2, b) are
equal. In the case where the samples for the internal standard
fraction are fractionated to obtain one fraction (FIG. 2, a.sub.2)
also, it is preferable that the amounts to be added to the
fractions (for example, fractions 1 through 5 in FIG. 2, b) are
equal. [0149] (d) The step of analyzing the fractions obtained in
step (c) with mass spectrometry
[0150] In this step, the fractions obtained in step (c), namely,
the mixture samples obtained after the internal standard fraction
is added to the isotope-labeled fractions are analyzed with mass
spectrometry.
[0151] The mixture samples may be analyzed with mass spectrometry
as they are or may be pre-treated with concentration, separation or
the like. A usable method for concentration uses, for example,
Amicon Ultra-15 10,000MWCO or the like. Usable methods for
separation include, for example, electrophoresis (e.g.,
two-dimensional electrophoresis, SDS-PAGE, etc.), various types of
chromatography (e.g., affinity chromatography, reverse phase
chromatography, anion exchange chromatography, cation exchange
chromatography, etc.), and the like.
[0152] The mixture samples may also be digested. Usable methods for
digestion include enzymatic digestion, chemical decomposition and
the like. Enzymatic digestion is preferable. Enzymes usable for
enzymatic digestion include trypsin, chymotrypsin, Lys-C, Asp-N,
Glu-C and the like. Trypsin is preferable. For enzymatic digestion,
it is desirable to add a surfactant, preferably,
5-cyclohexyl-pentyl-beta-D-maltoside (U.S. Pat. No. 5,674,987 and
U.S. Pat. No. 5,763,586, Anatrace Inc., Maumee, Ohio, USA).
[0153] Usable spectrometry devices include general-purpose devices
such as a gas chromatography mass spectrometry (GC/MS) device,
which is a mass spectrometry device combined with a gas
chromatography device, a liquid chromatography mass spectrometry
(LC/MS) device, which is a mass spectrometry device combined with a
liquid chromatography device, and the like. Ionization methods
usable by a mass spectrometry device include, for example, MALDI
(matrix-assisted laser desorption/ionization), ESI (electrospray
ionization), EI (electron impact ionization), CI (chemical
ionization), APCI (atmospheric pressure chemical ionization), FAB
(fast atom bombardment), LD, FD, SIMS, TSP and the like. MALDI and
ESI are preferable. Usable analyzers include, for example, devices
of TOF (time of flight) type, ion trap type, double-focusing type,
quadruple pole type, Fourier transformation type and the like.
[0154] As the mass spectrometry device, a device having two mass
spectrometers connected in series (MS/MS) is preferable.
[0155] A mass spectrum is obtained by the measurement performed by
the mass spectrometry device. From the mass spectrum, information
on the peaks derived from proteins (or peptides) can be
obtained.
[0156] By checking the data obtained by the measurement performed
by the mass spectrometry device against protein database using
software, the proteins in the samples can be identified. Examples
of the software include SonarMSMS (produced by Genomic Solution),
MASCOT (produced by Matrix Science), The Global Proteome Machine
(GPM; The Global Proteome Machine Organization,
http://h451.thegpm.org/tandem/thegpm_tandem.html), and the like.
Usable databases include, for example, NCBInr
(http://www.ncbi.nlm.nih.gov/), IPI, Sprot and the like. By
checking the data obtained by the measurement performed by the mass
spectrometry device against protein database, the proteins can be
identified (Nat Genet. 1998: 20, 46-50; J Cell Biol. 1998: 141,
967-977; J Cell Biol. 2000: 148, 635-651; Nature. 2002: 415,
141-147; Nature. 2002: 415, 180-183; Curr Opin Cell Biol. 2003: 15,
199-205; Curr Opin Cell Biol. 2003: 7, 21-27). Based on the
information on the identified proteins, amino acid sequence
information can be obtained. [0157] (e) The step of, based on the
mass spectrometry information, obtaining, regarding each fraction,
an intensity ratio between a peak derived from a protein in the
fraction obtained in step (a) and a peak derived from a protein in
the fraction obtained in step (b), and comparing degrees of the
binding ability of the plural kinds of proteins to the compound
[0158] In the present invention, the "peak derived from a protein
in the fraction obtained in step (a)" refers to each of signal
strengths derived from the test protein sample or a total thereof
(usually represented with an area as understood by those skilled in
the art) in the mass spectrum obtained by the measurement performed
by the mass spectrometry device (hereinafter, such a peak may be
occasionally referred to simply as the "test fraction peak" for the
convenience of explanation).
[0159] The "peak derived from a protein in the fraction obtained in
step (b)" refers to each of signal strengths derived from the
internal standard fraction or a total thereof in the mass spectrum
obtained by the measurement performed by the mass spectrometry
device (hereinafter, such a peak may be occasionally referred to
simply as the "internal standard peak" for the convenience of
explanation).
[0160] Using the data obtained by the measurement performed by the
mass spectrometry, the intensity ratio between the test fraction
peak and the internal standard peak (="intensity of the test
fraction peak"/"intensity of the internal standard peak:
hereinafter, occasionally referred to simply as the "peak intensity
ratio") is found for each protein. By this, the degrees of the
binding ability of the plural kinds of proteins to the compound can
be compared. As used herein, the expression "compare the degrees of
the binding ability of the plural kinds of proteins to the
compound" means to find in which fraction each protein is most
concentrated, using the peak intensity ratios of the plural kinds
of proteins, and thus to compare the binding ability to the
compound among the proteins.
[0161] An isotope-labeled protein has a larger molecular weight
than a non-isotope-labeled protein by the difference of the
isotope-labeled molecules, and the isotope-labeled protein and the
non-isotope-labeled protein are observed as a pair of peaks on the
mass spectrum (FIG. 2, c). In the case where the mass spectrometry
is conducted on groups of proteins labeled with different isotopes,
these groups of proteins are observed as a pair of peaks. The
molecular weight of the isotope-labeled protein can be obtained by
calculation based on the identified protein and the amino acid
sequence thereof. In the case where a protein is eluted in plural
fractions, the protein is eluted while being most concentrated in
the fraction having the largest peak intensity ratio. Regarding
each fraction, the protein having the largest peak intensity ratio
can be determined to be most concentrated in that fraction. A
protein concentrated in a fraction eluted later (fraction eluted
with a stronger eluting solvent) can be determined to have a higher
binding ability to the compound immobilized to the carrier.
(2) Second Embodiment
[0162] A second embodiment of the present invention comprises the
following steps for analyzing a binding ability of protein to a
compound, wherein samples for the internal standard fraction are
isotope-labeled before fractionation: [0163] (a) step of
fractionating a first group of proteins into plural fractions using
a carrier having the compound immobilized thereon; [0164] (b) step
of fractionating a second group of isotope-labeled proteins into
one or plural fractions using a carrier having the compound
immobilized thereon; [0165] (c) step of adding a certain amount of
the one fraction obtained in step (b), or a certain amount of a
mixture of all the fractions or a mixture of plural contiguous
fractions among the fractions obtained in step (b), to each of the
fractions obtained in step (a); [0166] (d) step of analyzing the
fractions obtained in step (c) with mass spectrometry; and [0167]
(e) step of, based on the mass spectrometry information, obtaining,
regarding each fraction, an intensity ratio between a peak derived
from a protein in the fraction obtained in step (a) and a peak
derived from a protein in the fraction obtained in step (b), and
comparing degrees of the binding ability of the plural kinds of
proteins to the compound.
[0168] In the second embodiment of the method of the present
invention, the group of proteins are isotope-labeled before being
fractionated like in the first embodiment. In the first embodiment,
the first group of proteins as the test samples are
isotope-labeled; whereas in the second embodiment, the second group
of proteins for the internal standard fraction are isotope-labeled.
In the second embodiment, the other steps are the same as in the
first embodiment. It should be noted that the first group of
proteins may be labeled with an isotope different from the isotope
used for labeling the second group of proteins.
(3) Third Embodiment
[0169] A third embodiment of the present invention is directed to a
method for analyzing a binding ability of protein to a compound,
comprising the following steps, wherein test protein samples are
labeled after fractionation: [0170] (a) step of fractionating a
first group of proteins into plural fractions using a carrier
having the compound immobilized thereon; [0171] (b) step of
fractionating a second group of proteins into one or plural
fractions using a carrier having the compound immobilized thereon;
[0172] (c) step of labeling the fractions obtained in step (a);
[0173] (d) step of adding a certain amount of the one fraction
obtained in step (b), or a certain amount of a mixture of all the
fractions or a mixture of plural contiguous fractions among the
fractions obtained in step (b), to each of the fractions labeled in
step (c); [0174] (e) step of analyzing the fractions obtained in
step (d) with mass spectrometry; and [0175] (f) step of, based on
the mass spectrometry information, obtaining, regarding each
fraction, an intensity ratio between a peak derived from a protein
in the fraction obtained in step (a) and a peak derived from a
protein in the fraction obtained in step (b), and comparing degrees
of the binding ability of the plural kinds of proteins to the
compound.
[0176] In the third embodiment, after the first group of proteins
as the target of analysis are fractionated, the post-fractionation
fractions (test fractions) are labeled. Namely, the fractions after
being fractionated in FIG. 2, a.sub.1 (fractions 1 through 5 in
FIG. 2, a.sub.1) are labeled. Except for this, the third embodiment
is substantially the same as the first embodiment.
[0177] Any labeling is usable as long as a protein derived from the
first group of proteins and the same type of protein derived from
the second group of proteins are distinguishable in mass
spectrometry. Usable methods for labeling include, for example,
methylation. ethylation, biotinylation and a combination thereof in
addition to isotope labeling in the above-described embodiments.
Those skilled in the art would carry out such labeling of proteins
using known methods.
[0178] The first group of proteins and the second group of proteins
may be labeled with different isotopes, or labeled with different
labeling substances.
(4) Fourth Embodiment
[0179] A fourth embodiment of the present invention is directed to
a method for analyzing a binding ability of protein to a compound,
comprising the following steps, wherein the samples for the
internal standard fraction are fractionated and the
post-fractionation fractions for the internal standard fraction are
labeled: [0180] (a) step of fractionating a first group of proteins
into plural fractions using a carrier having the compound
immobilized thereon; [0181] (b) step of fractionating a second
group of proteins into one or plural fractions using a carrier
having the compound immobilized thereon; [0182] (c) step of
labeling the one fraction obtained in step (b), or a mixture of all
the fractions or a mixture of plural contiguous fractions among the
fractions obtained in step (b); [0183] (d) step of adding a certain
amount of the fraction or the mixture labeled in step (c) to each
of the fractions obtained in step (a); [0184] (e) step of analyzing
the fractions obtained in step (d) with mass spectrometry; and
[0185] (f) step of, based on the mass spectrometry information,
obtaining, regarding each fraction, an intensity ratio between a
peak derived from a protein in the fraction obtained in step (a)
and a peak derived from a protein in the fraction obtained in step
(b), and comparing degrees of the binding ability of the plural
kinds of proteins to the compound.
[0186] In the fourth embodiment, the protein samples for the
internal standard fraction are fractionated and then a mixture of
all the fractions eluted or a mixture of plural contiguous
fractions eluted is entirely labeled. The mixture of fractions is
as described above in the section of "1. Overview of the present
invention" or "First embodiment". It should be noted that in step
(c), it is not necessary to label all the fractions (for example,
fractions 1 through 5 in FIG. 2), and a certain amount of each
fraction may be sampled and the sampled fractions may be labeled.
Alternatively, the elution may be performed such that one fraction
would be obtained by fractionation and the entire amount or a
certain amount of that fraction may be labeled. A mixture of the
fractions may be labeled, or each of the fractions may be labeled
before being mixed.
[0187] Any labeling is usable as long as a protein derived from the
first group of proteins and the same type of protein derived from
the second group of proteins are distinguishable in mass
spectrometry. Usable methods for labeling include, for example,
methylation, ethylation, biotinylation and a combination thereof in
addition to isotope labeling in the above-described embodiments.
Those skilled in the art would carry out such labeling of proteins
using known methods. In this embodiment also, the first group of
proteins and the second group of proteins may be labeled with
different isotopes, or labeled with different labeling
substances.
(5) Fifth Embodiment
[0188] A fifth embodiment of the present invention is directed to a
method for analyzing a binding ability of protein to a compound,
comprising the following steps, wherein the test protein samples
and the samples for the internal standard fraction are fractionated
and then quantitated: [0189] (a1) step of fractionating a first
group of proteins into plural fractions using a carrier having the
compound immobilized thereon; [0190] (a2) step of analyzing the
fractions obtained in step (a1) with mass spectrometry; [0191] (a3)
step of identifying each of the proteins in the fractions obtained
in step (a1) based on the mass spectrometry information obtained in
step (a2); [0192] (a4) step of quantitating each of the proteins in
the fractions obtained in step (a1); [0193] (b1) step of
fractionating a second group of proteins into one or plural
fractions using a carrier having the compound immobilized thereon;
[0194] (b2) step of analyzing the one fraction obtained in step
(b1), or a mixture of all the fractions or a mixture of plural
contiguous fractions among the fractions obtained in step (b1),
with mass spectrometry; [0195] (b3) step of identifying each of the
proteins in the one fraction or the mixture recited in step (b2)
based on the mass spectrometry information obtained in step (b2);
[0196] (b4) step of quantitating each of the proteins in the one
fraction or the mixture recited in step (b2); and [0197] (c) step
of obtaining, regarding each fraction obtained in step (a1), a
ratio between the protein quantity obtained in step (a4) and the
protein quantity obtained in step (b4), and comparing degrees of
the binding ability of the plural kinds of proteins to the
compound.
[0198] In the fifth embodiment, the first group of proteins as the
target of analysis are fractionated, and then the
post-fractionation fractions (test fractions) are quantitated. The
protein samples for the internal standard fraction are
fractionated, and then a mixture of all the fractions eluted or a
mixture of plural contiguous fractions eluted is formed and the
mixture is entirely quantitated.
[0199] Hereinafter, the fifth embodiment will be described in
detail. [0200] (a1) The step of fractionating a first group of
proteins into plural fractions using a carrier having the compound
immobilized thereon
[0201] This step can be performed by substantially the same manner
as "(a) the step of fractionating a first group of isotope-labeled
proteins into plural fractions using a carrier having the compound
immobilized thereon" in the first embodiment. It should be noted
that the first group of proteins do not need to be isotope-labeled.
[0202] (a2) The step of analyzing the fractions obtained in step
(a1) with mass spectrometry
[0203] This step can be performed by substantially the same manner
as "(d) the step of analyzing the fractions obtained in step (c)
with mass spectrometry" in the first embodiment. [0204] (a3) The
step of identifying each of the proteins in the fractions obtained
in step (a1) based on the mass spectrometry information obtained in
step (a2)
[0205] This step can be performed by the manner described regarding
"(d) the step of analyzing the fractions obtained in step (c) with
mass spectrometry" in the first embodiment. [0206] (a4) The step of
quantitating each of the proteins in the fractions obtained in step
(a1)
[0207] In this step, there is no specific limitation on the method
for quantitating each protein. For example, the proteins can be
quantitated as follows.
[0208] Regarding the proteins identified in step (a3), the number
of detected peptides (N.sub.obsd) and the number of detectable
peptides (N.sub.obsbl) are calculated.
[0209] The "number of detected peptides (N.sub.obsd)" refers to the
number of peptides actually detected in "(a2) the step of analyzing
the fractions obtained in step (a1) with mass spectrometry". The
number of detected peptides (N.sub.obsd) may be calculated based on
the mass spectrometry data and sequence information of the
identified proteins. When calculated based on the mass spectrometry
data, the number of detected peptides (N.sub.obsd) matches the
number of peaks detected in mass spectrometry for each protein.
[0210] The "number of detectable peptides (N.sub.obsbl)" refers to
the number of peptides which can be theoretically detected in "(a2)
the step of analyzing the fractions obtained in step (a1) with mass
spectrometry". The number of detectable peptides (N.sub.obsbl) may
be calculated based on the sequence information of the identified
proteins. Regarding each protein, the number of peptides
theoretically generated by the concentration, separation (e.g.,
HPLC separation), digestion or other operations in the
above-described steps is calculated based on the sequence
information, and thus the number of peptides detectable by mass
spectrometry (N.sub.obsbl) can be obtained. For example, when mass
spectrometry is performed on the samples treated with digestion
with trypsin, the peptide chains are cut by trypsin on the carboxyl
side of lysine and arginine. Therefore, the number of peptides
generated by the cutting can be predicted based on the sequence
information of each protein. In some cases, the number of
detectable peptides (N.sub.obsbl) may be obtained in consideration
of the measurement range of the mass spectrometer.
[0211] Next, in order to quantitate each protein using the number
of detectable peptides (N.sub.obsbl) and the number of detected
peptides (N.sub.obsd), EMPAI (exponentially modified protein
abundance index) is set in accordance with expression (I).
EMPAI=10.sup.Nobsd/Nobsbl-1 Expression (I):
[0212] EMPAI is an index in proportion to the protein content in a
protein mixture.
[0213] Then, the protein content (mol %) may be calculated in
accordance with expression (II).
Protein content ( mol % ) = EMPAI ( EMPAI ) .times. 100 Expression
( II ) ##EQU00001##
[0214] In the expression, .SIGMA.(EMPAI) represents a sum of EMPAIs
of all the identified proteins.
[0215] The protein content (wt. %) may be calculated in accordance
with expression (III).
Protein content ( wt . % ) = EMPAI .times. MW ( EMPAI .times. MW )
.times. 100 Expression ( III ) ##EQU00002##
[0216] In the expression, MW represents the molecular weight of
each identified protein. .SIGMA.(EMPAI.times.MW) represents the sum
of the EMPAI.times.MW values of all the identified proteins.
[0217] The molecular weight of each protein may be calculated from
the amino acid sequence. The total weight of the proteins in the
fractions obtained in step (a1) may be easily measured by a known
method, for example, the Lowry method, the Bradford method,
absorbance measurement at 280 nm or the like. Based on the total
weight of the proteins in the fractions obtained in step (a1) and
the above-obtained protein content, each protein can be
quantitated.
[0218] Thus, each protein can be quantitated by the above-described
method.
[0219] The step of quantitating each protein may be performed using
a computer. [0220] (b1) The step of fractionating a second group of
proteins into one or plural fractions using a carrier having the
compound immobilized thereon
[0221] This step can be performed by substantially the same manner
as "(b) fractionating a second group of proteins into one or plural
fractions using a carrier having the compound immobilized thereon"
in the first embodiment. [0222] (b2) The step of analyzing the one
fraction obtained in step (b1), or a mixture of all the fractions
or a mixture of plural contiguous fractions among the fractions
obtained in step (b1), with mass spectrometry
[0223] In this step, the "one fraction obtained in step (b1)", the
"mixture of all the fractions", and the "mixture of plural
contiguous fractions" are as described regarding the "one fraction
obtained in step (b)", the "mixture of all the fractions", and the
"mixture of plural contiguous fractions" in the section of the
"First embodiment". This step can be performed by substantially the
same manner as "(d) analyzing the fractions obtained in step (c)
with mass spectrometry" in the first embodiment. [0224] (b3) The
step of identifying each of the proteins in the one fraction or the
mixture recited in step (b1) based on the mass spectrometry
information obtained in step (b2)
[0225] This step can be performed by the manner described regarding
"(d) analyzing the fractions obtained in step (c) with mass
spectrometry" in the first embodiment. [0226] (b4) The step of
quantitating each of the proteins in the one fraction or the
mixture recited in step (b2)
[0227] This step can be performed by substantially the same manner
as "(a4) quantitating each of the proteins in the fractions
obtained in step (a1)" above. [0228] (c) The step of obtaining,
regarding each fraction obtained in step (a1), a ratio between the
protein quantity obtained in step (a4) and the protein quantity
obtained in step (b4), and comparing degrees of the binding ability
of the plural kinds of proteins to the compound
[0229] In this step, regarding each of the proteins identified in
step (a3) and each of the proteins identified in step (b3), the
ratio between the protein quantity in each fraction obtained in
step (a1) and the protein quantity in the one fraction or the
mixture recited in step (b2) (="protein quantity obtained in step
(a4)"/"protein quantity obtained in step (b4)" is found. By this,
the degrees of the binding ability of the plural kinds of proteins
to the compound can be compared.
[0230] Namely, in the fifth embodiment of finding the protein
quantity ratio, in the case where a protein is eluted in plural
fractions obtained in step (a1), the protein is eluted while being
most concentrated in the fraction having the largest protein
quantity ratio. Regarding each fraction, the protein having the
largest protein quantity ratio can be determined to be most
concentrated in that fraction. A protein concentrated in a fraction
eluted later (fraction eluted with a stronger eluting solvent) can
be determined to have a higher binding ability to the compound
immobilized to the carrier.
[0231] The method in the fifth embodiment is characterized in that
it is not necessary to label each protein with an isotope.
(6) Sixth Embodiment
[0232] A sixth embodiment of the present invention is directed to a
method for analyzing a binding ability of protein to a compound,
comprising the following steps, wherein the test protein samples
and the samples for the internal standard fraction are fractionated
and then the EMPAI of each protein is calculated: [0233] (a1) step
of fractionating a first group of proteins into plural fractions
using a carrier having the compound immobilized thereon; [0234]
(a2) step of analyzing the fractions obtained in step (a1) with
mass spectrometry; [0235] (a3) step of identifying each of the
proteins in the fractions obtained in step (a1) based on the mass
spectrometry information obtained in step (a2); [0236] (a4) step of
calculating an EMPAI of each of the proteins in the fractions
obtained in step (a1); [0237] (b1) step of fractionating a second
group of proteins into one or plural fractions using a carrier
having the compound immobilized thereon; [0238] (b2) step of
analyzing the one fraction obtained in step (b1), or a mixture of
all the fractions or a mixture of plural contiguous fractions among
the fractions obtained in step (b1), with mass spectrometry; [0239]
(b3) step of identifying each of the proteins in the one fraction
or the mixture recited in step (b2) based on the mass spectrometry
information obtained in step (b2); [0240] (b4) step of calculating
an EMPAI of each of the proteins in the one fraction or the mixture
recited in step (b2); and [0241] (c) step of obtaining, regarding
each fraction obtained in step (a1), a ratio between the EMPAI
obtained in step (a4) and the EMPAI obtained in step (b4), and
comparing degrees of the binding ability of the plural kinds of
proteins to the compound.
[0242] As described above, EMPAI is an index in proportion to the
protein content in a protein mixture. Therefore, by finding,
regarding each of the proteins identified in step (a3) and step
(b3), the ratio between the EMPAI of a protein in each fraction
obtained in step (a1) and the EMPAI of a protein in the one
fraction or the mixture recited in step (b2) (="EMPAI obtained in
step (a4)"/"EMPAI obtained in step (b4)", the degrees of the
binding ability of the plural kinds of proteins to the compound can
be compared.
[0243] Namely, in the sixth embodiment of finding the EMPAI ratio,
in the case where a protein is eluted in plural fractions, the
protein is eluted while being most concentrated in the fraction
having the largest EMPAI ratio. Regarding each fraction, the
protein having the largest EMPAI ratio can be determined to be most
concentrated in that fraction. A protein concentrated in a fraction
eluted later can be determined to have a higher binding ability to
the compound immobilized to the carrier.
[0244] As described above, in the first through sixth embodiments
of the method for analysis of the present invention, the samples
for the internal standard fraction are fractionated using a carrier
having a compound immobilized thereon. Embodiments in which the
samples for the internal standard fraction are used without being
fractionated using a carrier having a compound immobilized thereon
are also encompassed in the present invention.
(7) Seventh Embodiment
[0245] A seventh embodiment of the present invention comprises the
following steps for analyzing a binding ability of protein to a
compound: [0246] (a) step of fractionating a first group of
isotope-labeled proteins into plural fractions using a carrier
having the compound immobilized thereon; [0247] (b) step of adding
a certain amount of a second group of proteins to each of the
fractions obtained in step (a); [0248] (c) step of analyzing the
fractions obtained in step (b) with mass spectrometry; and [0249]
(d) step of, based on the mass spectrometry information, obtaining,
regarding each fraction, an intensity ratio between a peak derived
from a protein in the fraction obtained in step (a) and a peak
derived from a protein in the second group of proteins, and
comparing degrees of the binding ability of the plural kinds of
proteins to the compound.
[0250] In the seventh embodiment, unlike in the first embodiment,
the second group of proteins for the internal standard fraction are
added in a certain amount to each of the fractions obtained in step
(a) without being fractionated into one or plural fractions using
the carrier having the compound immobilized thereon. Except for
this, the seventh embodiment is substantially the same as the first
embodiment.
(8) Eighth Embodiment
[0251] An eighth embodiment of the present invention comprises the
following steps for analyzing a binding ability of protein to a
compound: [0252] (a) step of fractionating a first group of
proteins into plural fractions using a carrier having the compound
immobilized thereon; [0253] (b) step of adding a certain amount of
a second group of isotope-labeled proteins to each of the fractions
obtained in step (a); [0254] (c) step of analyzing the fractions
obtained in step (b) with mass spectrometry; and [0255] (d) step
of, based on the mass spectrometry information, obtaining,
regarding each fraction, an intensity ratio between a peak derived
from a protein in the fraction obtained in step (a) and a peak
derived from a protein in the second group of proteins, and
comparing degrees of the binding ability of the plural kinds of
proteins to the compound.
[0256] In the eighth embodiment, unlike in the second embodiment,
the second group of isotope-labeled proteins for the internal
standard fraction are added in a certain amount to each of the
fractions obtained in step (a) without being fractionated into one
or plural fractions using the carrier having the compound
immobilized thereon. Except for this, the eighth embodiment is
substantially the same as the second embodiment.
(9) Ninth Embodiment
[0257] A ninth embodiment of the present invention comprises the
following steps for analyzing a binding ability of protein to a
compound: [0258] (a) step of fractionating a first group of
proteins into plural fractions using a carrier having the compound
immobilized thereon; [0259] (b) step of labeling the fractions
obtained in step (a); [0260] (c) step of adding a certain amount of
a second group of proteins to each of the fractions labeled in step
(b); [0261] (d) step of analyzing the fractions obtained in step
(c) with mass spectrometry; and [0262] (e) step of, based on the
mass spectrometry information, obtaining, regarding each fraction,
an intensity ratio between a peak derived from a protein in the
fraction obtained in step (a) and a peak derived from a protein in
the second group of proteins, and comparing degrees of the binding
ability of the plural kinds of proteins to the compound.
[0263] In the ninth embodiment, unlike in the third embodiment, the
second group of proteins for the internal standard fraction are
added in a certain amount to each of the fractions obtained in step
(b) without being fractionated into one or plural fractions using
the carrier having the compound immobilized thereon. Except for
this, the ninth embodiment is substantially the same as the third
embodiment.
(10) Tenth Embodiment
[0264] A tenth embodiment of the present invention comprises the
following steps for analyzing a binding ability of protein to a
compound: [0265] (a1) step of fractionating a first group of
proteins into plural fractions using a carrier having the compound
immobilized thereon; [0266] (a2) step of analyzing the fractions
obtained in step (a1) with mass spectrometry; [0267] (a3) step of
identifying each of the proteins in the fractions obtained in step
(a1) based on the mass spectrometry information obtained in step
(a2); [0268] (a4) step of quantitating each of the proteins in the
fractions obtained in step (a1); [0269] (b1) step of analyzing a
second group of proteins with mass spectrometry; [0270] (b2) step
of identifying each protein in the second group of proteins based
on the mass spectrometry information obtained in step (b1); [0271]
(b3) step of quantitating each protein in the second group of
proteins; and [0272] (c) step of obtaining, regarding each fraction
obtained in step (a1), a ratio between the protein quantity
obtained in step (a4) and the protein quantity obtained in step
(b3), and comparing degrees of the binding ability of the plural
kinds of proteins to the compound.
[0273] In the tenth embodiment, unlike in the fifth embodiment,
each protein in the second group of proteins is quantitated without
being fractionated into one or plural fractions using the carrier
having the compound immobilized thereon. Except for this, the tenth
embodiment is substantially the same as the fifth embodiment.
(11) Eleventh Embodiment
[0274] An eleventh embodiment of the present invention comprises
the following steps for analyzing a binding ability of protein to a
compound: [0275] (a1) step of fractionating a first group of
proteins into plural fractions using a carrier having the compound
immobilized thereon; [0276] (a2) step of analyzing the fractions
obtained in step (a1) with mass spectrometry; [0277] (a3) step of
identifying each of the proteins in the fractions obtained in step
(a1) based on the mass spectrometry information obtained in step
(a2); [0278] (a4) step of calculating an EMPAI of each of the
proteins in the fractions obtained in step (a1); [0279] (b1) step
of analyzing a second group of proteins with mass spectrometry;
[0280] (b2) step of identifying each protein in the second group of
proteins based on the mass spectrometry information obtained in
step (b1); [0281] (b3) step of calculating an EMPAI of each protein
in the second group of proteins; and [0282] (c) step of obtaining,
regarding each fraction obtained in step (a1), a ratio between the
EMPAI obtained in step (a4) and the EMPAI obtained in step (b3),
and comparing degrees of the binding ability of the plural kinds of
proteins to the compound.
[0283] In the eleventh embodiment, unlike in the sixth embodiment,
the EMPAI of each protein in the second group of proteins is
calculated without the second group of proteins being fractionated
into one or plural fractions using the carrier having the compound
immobilized thereon. Except for this, the eleventh embodiment is
substantially the same as the sixth embodiment.
3. Analysis System
[0284] An analysis system of the present invention is for carrying
out a method for analyzing a binding ability of protein to a
compound, comprising the following means: [0285] (1) Embodiment in
which the samples are isotope-labeled before fractionation [0286]
(a) means for fractionating a first group of isotope-labeled
proteins into plural fractions using a carrier having the compound
immobilized thereon; [0287] (b) means for fractionating a second
group of proteins into one or plural fractions using a carrier
having the compound immobilized thereon; [0288] (c) means for
adding a certain amount of the one fraction obtained by means (b),
or a certain amount of a mixture of all the fractions or a mixture
of plural contiguous fractions among the fractions obtained by
means (b), to each of the fractions obtained by means (a); [0289]
(d) means for analyzing the fractions obtained by means (c) with
mass spectrometry; and [0290] (e) means for, based on the mass
spectrometry information, obtaining, regarding each fraction, an
intensity ratio between a peak derived from a protein in the
fraction obtained by means (a) and a peak derived from a protein in
the fraction obtained by means (b), and comparing degrees of the
binding ability of the plural kinds of proteins to the compound.
[0291] (2) Embodiment in which the samples for the internal
standard fraction are isotope-labeled before fractionation [0292]
(a) means for fractionating a first group of proteins into plural
fractions using a carrier having the compound immobilized thereon;
[0293] (b) means for fractionating a second group of
isotope-labeled proteins into one or plural fractions using a
carrier having the compound immobilized thereon; [0294] (c) means
for adding a certain amount of the one fraction obtained by means
(b), or a certain amount of a mixture of all the fractions or a
mixture of plural contiguous fractions among the fractions obtained
by means (b), to each of the fractions obtained by means (a);
[0295] (d) means for analyzing the fractions obtained by means (c)
with mass spectrometry; and [0296] (e) means for, based on the mass
spectrometry information, obtaining, regarding each fraction, an
intensity ratio between a peak derived from a protein in the
fraction obtained by means (a) and a peak derived from a protein in
the fraction obtained by means (b), and comparing degrees of the
binding ability of the plural kinds of proteins to the compound.
[0297] (3) Embodiment in which the samples are labeled after
fractionation [0298] (a) means for fractionating a first group of
proteins into plural fractions using a carrier having the compound
immobilized thereon; [0299] (b) means for fractionating a second
group of proteins into one or plural fractions using a carrier
having the compound immobilized thereon; [0300] (c) means for
labeling the fractions obtained by means (a); [0301] (d) means for
adding a certain amount of the one fraction obtained by means (b),
or a certain amount of a mixture of all the fractions or a mixture
of plural contiguous fractions among the fractions obtained by
means (b), to each of the fractions labeled by means (c); [0302]
(e) means for analyzing the fractions obtained by means (d) with
mass spectrometry; and [0303] (f) means for, based on the mass
spectrometry information, obtaining, regarding each fraction, an
intensity ratio between a peak derived from a protein in the
fraction obtained by means (a) and a peak derived from a protein in
the fraction obtained by means (b), and comparing degrees of the
binding ability of the plural kinds of proteins to the compound.
[0304] (4) Embodiment in which the samples for the internal
standard fraction are fractionated and then labeled [0305] (a)
means for fractionating a first group of proteins into plural
fractions using a carrier having the compound immobilized thereon;
[0306] (b) means for fractionating a second group of proteins into
one or plural fractions using a carrier having the compound
immobilized thereon; [0307] (c) means for labeling the one fraction
obtained by means (b), or a mixture of all the fractions or a
mixture of plural contiguous fractions among the fractions obtained
by means (b); [0308] (d) means for adding a certain amount of the
fraction or the mixture labeled by means (c) to each of the
fractions obtained by means (a); [0309] (e) means for analyzing the
fractions obtained by means (d) with mass spectrometry; and [0310]
(f) means for, based on the mass spectrometry information,
obtaining, regarding each fraction, an intensity ratio between a
peak derived from a protein in the fraction obtained by means (a)
and a peak derived from a protein in the fraction obtained by means
(b), and comparing degrees of the binding ability of the plural
kinds of proteins to the compound. [0311] (5) Embodiment in which
the test protein samples and the samples for the internal standard
fraction are fractionated and then quantitated [0312] (a1) means
for fractionating a first group of proteins into plural fractions
using a carrier having the compound immobilized thereon; [0313]
(a2) means for analyzing the fractions obtained by means (a1) with
mass spectrometry; [0314] (a3) means for identifying each of the
proteins in the fractions obtained by means (a1) based on the mass
spectrometry information obtained by means (a2); [0315] (a4) means
for quantitating each of the proteins in the fractions obtained by
means (a1); [0316] (b1) means for fractionating a second group of
proteins into one or plural fractions using a carrier having the
compound immobilized thereon; [0317] (b2) means for analyzing the
one fraction obtained by means (b1), or a mixture of all the
fractions or a mixture of plural contiguous fractions among the
fractions obtained by means (b1), with mass spectrometry; [0318]
(b3) means for identifying each of the proteins in the one fraction
or the mixture recited by means (b2) based on the mass spectrometry
information obtained by means (b2); [0319] (b4) means for
quantitating each of the proteins in the one fraction or the
mixture recited by means (b2); and [0320] (c) means for obtaining,
regarding each fraction obtained by means (a1), a ratio between the
protein quantity obtained by means (a4) and the protein quantity
obtained by means (b4), and comparing degrees of the binding
ability of the plural kinds of proteins to the compound. [0321] (6)
Embodiment in which the test protein samples and the samples for
the internal standard fraction are fractionated and then the EMPAI
of each protein is calculated [0322] (a1) means for fractionating a
first group of proteins into plural fractions using a carrier
having the compound immobilized thereon; [0323] (a2) means for
analyzing the fractions obtained by means (a1) with mass
spectrometry; [0324] (a3) means for identifying each of the
proteins in the fractions obtained by means (a 1) based on the mass
spectrometry information obtained by means (a2); [0325] (a4) means
for calculating an EMPAI of each of the proteins in the fractions
obtained by means (a1); [0326] (b1) means for fractionating a
second group of proteins into one or plural fractions using a
carrier having the compound immobilized thereon; [0327] (b2) means
for analyzing the one fraction obtained by means (b1), or a mixture
of all the fractions or a mixture of plural contiguous fractions
among the fractions obtained by means (b1), with mass spectrometry;
[0328] (b3) means for identifying each of the proteins in the one
fraction or the mixture recited by means (b2) based on the mass
spectrometry information obtained by means (b2); [0329] (b4) means
for calculating an EMPAI of each of the proteins in the one
fraction or the mixture recited by means (b2); and [0330] (c) means
for obtaining, regarding each fraction obtained by means (a1), a
ratio between the EMPAI obtained by means (a4) and the EMPAI
obtained by means (b4), and comparing degrees of the binding
ability of the plural kinds of proteins to the compound.
[0331] In the above embodiments of the system of the present
invention, the samples for the internal standard fraction are
fractionated using a carrier having a compound immobilized thereon.
Embodiments in which the samples for the internal standard fraction
are used without being fractionated using a carrier having a
compound immobilized thereon as follows are also encompassed in the
present invention. [0332] (7) Embodiment in which the second group
of proteins for the internal standard fraction in the embodiment
(1) of the system are added in a certain amount to each of the
fractions obtained by means (a) without being fractionated into one
or plural fractions using a carrier having the compound immobilized
thereon [0333] (a) means for fractionating a first group of
isotope-labeled proteins into plural fractions using a carrier
having the compound immobilized thereon; [0334] (b) means for
adding a certain amount of a second group of proteins to each of
the fractions obtained by means (a); [0335] (c) means for analyzing
the fractions obtained by means (b) with mass spectrometry; and
[0336] (d) means for, based on the mass spectrometry information,
obtaining, regarding each fraction, an intensity ratio between a
peak derived from a protein in the fraction obtained by means (a)
and a peak derived from a protein in the second group of proteins,
and comparing degrees of the binding ability of the plural kinds of
proteins to the compound. [0337] (8) Embodiment in which the second
group of isotope-labeled proteins for the internal standard
fraction in the embodiment (2) of the system are added in a certain
amount to each of the fractions obtained by means (a) without being
fractionated into one or plural fractions using a carrier having
the compound immobilized thereon [0338] (a) means for fractionating
a first group of proteins into plural fractions using a carrier
having the compound immobilized thereon; [0339] (b) means for
adding a certain amount of a second group of isotope-labeled
proteins to each of the fractions obtained by means (a); [0340] (c)
means for analyzing the fractions obtained by means (b) with mass
spectrometry; and [0341] (d) means for, based on the mass
spectrometry information, obtaining, regarding each fraction, an
intensity ratio between a peak derived from a protein in the
fraction obtained by means (a) and a peak derived from a protein in
the second group of proteins, and comparing degrees of the binding
ability of the plural kinds of proteins to the compound. [0342] (9)
Embodiment in which the second group of proteins for the internal
standard fraction in the embodiment (3) of the system are added in
a certain amount to each of the fractions obtained by means (b)
without being fractionated into one or plural fractions using a
carrier having the compound immobilized thereon [0343] (a) means
for fractionating a first group of proteins into plural fractions
using a carrier having the compound immobilized thereon; [0344] (b)
means for labeling the fractions obtained by means (a); [0345] (c)
means for adding a certain amount of a second group of proteins to
each of the fractions labeled by means (b); [0346] (d) means for
analyzing the fractions obtained by means (c) with mass
spectrometry; and [0347] (e) means for, based on the mass
spectrometry information, obtaining, regarding each fraction, an
intensity ratio between a peak derived from a protein in the
fraction obtained by means (a) and a peak derived from a protein in
the second group of proteins, and comparing degrees of the binding
ability of the plural kinds of proteins to the compound. [0348]
(10) Embodiment in which each protein in the second group of
proteins in the embodiment (5) of the system is quantitated without
being fractionated into one or plural fractions using a carrier
having the compound immobilized thereon [0349] (a1) means for
fractionating a first group of proteins into plural fractions using
a carrier having the compound immobilized thereon; [0350] (a2)
means for analyzing the fractions obtained by means (a1) with mass
spectrometry; [0351] (a3) means for identifying each of the
proteins in the fractions obtained by means (a1) based on the mass
spectrometry information obtained by means (a2); [0352] (a4) means
for quantitating each of the proteins in the fractions obtained by
means (a1); [0353] (b1) means for analyzing a second group of
proteins with mass spectrometry; [0354] (b2) means for identifying
each protein in the second group of proteins based on the mass
spectrometry information obtained by means (b1); [0355] (b3) means
for quantitating each protein in the second group of proteins; and
[0356] (c) means for obtaining, regarding each fraction obtained by
means (a1), a ratio between the protein quantity obtained by means
(a4) and the protein quantity obtained by means (b3), and comparing
degrees of the binding ability of the plural kinds of proteins to
the compound. [0357] (11) Embodiment in which the EMPAI of each
protein in the second group of proteins in the embodiment (6) of
the system is calculated without the second group of proteins being
fractionated into one or plural fractions using a carrier having
the compound immobilized thereon [0358] (a1) means for
fractionating a first group of proteins into plural fractions using
a carrier having the compound immobilized thereon; [0359] (a2)
means for analyzing the fractions obtained by means (a1) with mass
spectrometry; [0360] (a3) means for identifying each of the
proteins in the fractions obtained by means (a1) based on the mass
spectrometry information obtained by means (a2); [0361] (a4) means
for calculating an EMPAI of each of the proteins in the fractions
obtained by means (a1); [0362] (b1) means for analyzing a second
group of proteins with mass spectrometry; [0363] (b2) means for
identifying each protein in the second group of proteins based on
the mass spectrometry information obtained by means (b1); [0364]
(b3) means for calculating an EMPAI of each protein in the second
group of proteins; and [0365] (c) means for obtaining, regarding
each fraction obtained by means (a1), a ratio between the EMPAI
obtained by means (a4) and the EMPAI obtained by means (b3), and
comparing degrees of the binding ability of the plural kinds of
proteins to the compound. [0366] (12) Details of the system of the
present invention
[0367] FIG. 3 is a block diagram showing an exemplary structure of
a system according to the present invention. In the example shown
in FIG. 3, the system according to the present invention includes a
control unit 301, a protein fractionation unit 302, a protein
mixing unit 303, and a mass spectrometry unit 304.
[0368] The control unit 301 controls the entire operation of each
unit necessary for carrying out the method according to the present
invention. The protein fractionation unit 302, the protein mixing
unit 303 and the mass spectrometry unit 304 are each connected to
the control unit 301, and are each controlled by the control unit
301 so as to operate independently or in association with one
another. For example, for carrying out the method according to the
present invention mainly in a batch system, the units (the protein
fractionation unit 302, the protein mixing unit 303 and the mass
spectrometry unit 304) are each controlled independently, and the
control unit 301 instructs each unit to perform a respective
operation. For carrying out the method according to the present
invention mainly in a continuous flow system, the control unit 301
monitors the operation of each unit, for example, how each unit
proceeds with the operation, and the units are controlled in
association with one another.
[0369] The protein fractionation unit 302 is a unit for eluting
proteins bound to the compound immobilized on carriers in the
column, and includes a carrier for fractionating the first group of
proteins into plural fractions, a carrier for fractionating the
second group of proteins into one or plural fractions, a cell
culture device, a cell crushing device, an eluting device for the
compound bound to the carrier, a recovery device for the eluted
proteins (fractionated proteins), and the like. The elements
included in the fractionation unit are controlled independently or
in association with one another by an instruction from the control
unit 301.
[0370] The protein mixing unit 303 is a unit for mixing the
proteins fractionated by the protein fractionation unit 302. For
example, in the first embodiment described above, the protein
mixing unit 303 controls the step of adding a certain amount of one
fraction, or a certain amount of a mixture of all the fractions or
a mixture of plural contiguous fractions, derived from the second
group of protein samples to the fractions derived from the first
group of isotope-labeled protein samples. The protein mixing unit
303 is connected to the control unit 301, and performs mixing upon
receiving an instruction on the amount to be added and the like
from the control unit 301.
[0371] The mass spectrometry unit 304 is a unit for analyzing the
mixed proteins with mass spectrometry, and includes a spotter for
spotting the mixed proteins on a measurement plate, a tray for
putting the measurement plate on a mass spectrometry device and the
like. The elements in the mass spectrometry unit 304 are connected
to the control unit 301, and executes mass spectrometry in
accordance with an instruction from the control unit 301.
[0372] FIG. 4 is a schematic view showing an embodiment of the
units.
[0373] As shown in FIG. 4, the protein fractionation unit 302
includes, for example, culture devices 11a and 11b, culture liquid
bottles 12a and 12b, cell crushing devices 13a and 13b, a labeling
device 14, carriers 15a and 15b having a compound immobilized
thereon, protein fractionation control devices (hereinafter, also
referred to as "control devices") 16a and 16b, purified protein
separators 17a and 17b, a mixing device 17c and the like.
[0374] The culture devices 11a and 11b are devices for culturing
cells, and culture cells for a predetermined time period while
adjusting the temperature, CO.sub.2 concentration and the like. The
culture devices 11a and 11b are respectively connected to the
culture liquid bottles 12a and 12b. The culture liquid bottles 12a
and 12b may supply a culture liquid to the culture devices via
tubes 1a and 1b, respectively. The culture devices 11a and 11b may
respectively include stirring blades 2a and 2b. The culture devices
11a and 11b are shown here as vessels for culturing floating cells,
but this is merely one embodiment for illustrating the system
according to the present invention. The present invention is not
limited to this. For culturing cells adhering to the culture
plates, those skilled in the art could select culture devices in
accordance with the purpose. The culture devices 11a and 11b are
connected to the control unit 301 via a LAN 100.
[0375] The culture liquid bottles 12a and 12b are vessels for
storing a culture liquid for culturing cells. In the first
embodiment and the seventh embodiment of the present invention, the
culture liquid bottle 12a contains amino acids for isotope-labeling
the first group of proteins and the like in a mixed state. As shown
in FIG. 4, the labeling device 14 may be connected to the culture
liquid bottle 12a. The culture liquid bottles 12a and 12b may be
connected to the control unit 301 via the LAN 100.
[0376] The cell crushing devices 13a and 13b are devices for
crushing cultured cells to obtain proteins. The cell crushing
devices 13a and 13b perform the step of collecting the cells from
the culture devices 11a and 11b and crushing the cells, thereby
obtaining a suspension of proteins. The cell crushing devices 13a
and 13b may be connected to the control unit 301 via the LAN
100.
[0377] The labeling device 14 is a device for labeling (for
example, isotope-labeling) protein samples or protein fractions
obtained by fractionation. FIG. 4 shows an embodiment in which the
labeling device 14 for labeling protein samples before
fractionation is connected to the culture liquid bottle 12a. In the
second embodiment of the present invention, the samples for the
internal standard fraction are isotope-labeled before
fractionation. In this case, the labeling device 14 may be
connected to a culture liquid for culturing the samples for the
internal standard fraction (the culture liquid bottle 12b).
[0378] In the eighth embodiment of the present invention, the
samples for the internal standard fraction are isotope-labeled
before being added to the fractions derived from the first group of
proteins. In this case, the labeling device 14 may be connected to
a culture liquid for culturing the samples for the internal
standard fraction (the culture liquid bottle 12b).
[0379] In the third and fourth embodiments of the present
invention, the test samples or the samples for the internal
standard fraction are labeled after fractionation. For labeling the
test samples, the labeling device 14 may be connected between the
carrier 15a and the control device 16a, between the control device
16a and the purified protein separator 17a, or after the purified
protein separator 17a. For labeling the samples for the internal
standard fraction, the labeling device 14 may be connected between
the carrier 15b and the control device 16b, between the control
device 16b and the purified protein separator 17b, after the
purified protein separator 17b, or after the mixing device 17c.
[0380] In the ninth embodiment of the present invention, the test
samples are labeled after fractionation. In this case, the labeling
device 14 may be connected between the carrier 15a and the control
device 16a, between the control device 16a and the purified protein
separator 17a, or after the purified protein separator 17a.
[0381] According to the present invention, the labeling device 14
is not limited to the above-described embodiments and may be in
other embodiments for achieving the object of the present invention
as easily understood by those skilled in the art. The labeling
device 14 may be connected to the control unit 301 via the LAN
100.
[0382] In the fifth, sixth, tenth and eleventh embodiments of the
present invention, the proteins do not need to be labeled. In this
case, the protein fractionation unit 302 does not need to include
the labeling device 14.
[0383] The carriers 15a and 15b are columns for purifying the
proteins, and have a substance having a binding ability to protein
immobilized thereon.
[0384] In accordance with an instruction from the control unit 301,
the control devices 16a and 16b perform the step of introducing the
proteins into the carriers 15a and 15b having a compound
immobilized thereon, and also passing the eluting solvent to send
the eluted protein fractions to the purified protein separators 17a
and 17b. The eluting solvent may be flown to the carriers such that
the concentration of the solvent has a gradient, or solvents having
concentrations different in a step-by-step manner may be flown to
the carriers. The control devices 16a and 16b may be connected to
the control unit 301 via the LAN 100.
[0385] The purified protein separators 17a and 17b are devices for
separating proteins obtained in one fractionation step and proteins
obtained in the other fractionation step from each other and thus
obtaining fractions. In some cases, the purified protein separators
17a and 17b may temporarily store the fractions. For an internal
standard fraction, the mixing device 17c may be provided for mixing
all the fractions or plural contiguous fractions of the protein
fractions.
[0386] FIG. 4 shows one type of fractionation step. Alternatively,
plural systems may be provided in parallel so as to allow plural
kinds of fractionation steps to be performed. In this way, proteins
derived from plural different kinds of cells can be
fractionated.
[0387] In the embodiment shown in FIG. 4, the purified protein
separators 17a and 17b are controlled by the control devices 16a
and 16b, but the present invention is not limited to this. The
purified protein separators 17a and 17b may be connected to the
control unit 301 via the LAN 100 independently from the control
devices 16a and 16b.
[0388] In the seventh, eighth, ninth, tenth and eleventh
embodiments of the present invention, the samples for the internal
standard fraction are used without being fractionated by a carrier
having a compound immobilized thereon. In this case, the protein
fractionation unit 302 does not need to include none of the carrier
15b, the control unit 16b, the purified protein separator 17b and
the mixing device 17c.
[0389] In FIG. 4, the protein mixing unit 303 is a unit for adding
the fractions derived from the second group of proteins to the
fractions derived from the first group of proteins obtained as a
result of the fractionation by the protein fractionation unit 302.
In accordance with an instruction from the control unit 301, the
protein mixing unit 303 selects fractions arranged in the purified
protein separator 17a and adds a certain amount of the fractions
arranged in the purified protein separator 17b or the mixing device
17c. FIG. 4 shows an exemplary embodiment in which a mixture of
fractions 1 through fraction 3 arranged in the purified protein
separator 17b to tubes (tubes 18-1 through 18-5) respectively
containing the eluted fractions 1 through 5 (fractions from the
purified protein separator 17a) via the mixing device 17c.
[0390] In the fifth, sixth, tenth and eleventh embodiments of the
present invention, the fractions derived from the first group of
proteins, and the fractions derived from the second group of
proteins or the second group of proteins, are analyzed with mass
spectrometry without the first and second groups of proteins being
added together. In this case, the operation in the protein
fractionation unit 302 may be followed by the operation in the mass
spectrometry unit 304 with the operation in the protein mixing unit
303 being skipped. Therefore, in these embodiments, the system of
the present invention does not need to include the protein mixing
unit 303.
[0391] The mass spectrometry unit 304 is a unit for analyzing one
or plural kinds of proteins as a target of mass spectrometry. In
accordance with an instruction from the control unit 301, the mass
spectrometry unit 304 spots a sample mixed by the protein mixing
unit 303 on a plate 19 for mass spectrometry and executes mass
spectrometry using a mass spectrometry device 20. For transferring
the plate 19 to the mass spectrometry device 20, a
computer-controlled robot-type sample handling device is also
usable.
[0392] Mass spectrometry is executed in accordance with an
instruction from the control unit 301 via the LAN 100.
Alternatively, the mass spectrometry may be executed by a computer
21 provided as an accessory to the mass spectrometry device 20.
[0393] Mass spectrometry information is transmitted to the control
unit 301 via the LAN 100, and is processed to obtain an
identification profile, an intensity ratio profile, a binding
ability ratio profile, a mass ratio profile, and an EMPAI ratio
profile of proteins.
[0394] The control unit 301 is a central control unit for operating
the system according to the present invention, and includes a
central computer 30, an internet communication line and the
like.
[0395] The control unit 301 identifies the proteins, determines the
intensity ratio and the binding ability ratio between the
isotope-labeled peak and the non-isotope-labeled peak, and displays
the results in a display device in the control unit 301.
Alternatively, based on the information on the identified proteins,
the control unit 301 determines the protein quantity ratio or the
EMPAI ratio between each of the proteins in the test fractions and
each of the proteins in the internal standard fraction using the
index EMPAI, and displays the results in the display device in the
control unit 301. Each piece of data is automatically organized by
the control unit 301.
[0396] FIG. 5 is an exemplary detailed structural view of the
control unit 301. As shown in FIG. 5, the central computer 30
includes a CPU 501, a transmission/receiving section 502, an input
section 503, an output section 504, a ROM 505, a RAM 506, a hard
disc drive (HDD) 507, a CD-ROM drive 508, and a protein database
(hereinafter, referred to as "DB") 509.
[0397] The CPU 501 controls the entire operation of the system
according to the present invention, and also records data on the
mass spectrometry results, data on the identified protein,
intensity ratio data, binding ability data and the like on the DB
509. The CPU 501 may control the communication of the
transmission/receiving section 502 and check the data stored on the
DB 509 against data of other proteins via the Internet 511.
[0398] In accordance with an instruction from the CPU 501, the
transmission/receiving section 502 performs data transmission and
receiving between the protein fractionation unit 302, the protein
mixing unit 303, and the mass spectrometry unit 304.
[0399] The input section 503 includes a keyboard, a mouse, a touch
panel or the like, and is operated when the user inputs information
or updates the database. The output section 504 includes an LCD
(liquid crystal display) or the like. For updating various
databases, the output section 504 converts the code data from the
CPU 501 into display data each time the code data is received, and
displays the data. The ROM 505 stores a processing program of the
system according to the present invention. The RAM 506 temporarily
stores data necessary for processing executed by the system
according to the present invention. The HDD 507 is a drive for
storing mass spectrometry data and the like. In accordance with an
instruction from the CPU 501, the CD-ROM drive 508 reads a program
or the like necessary for executing the processing by the system
according to the present invention (for executing the processing in
various embodiments), which is stored on a CD-ROM 510, and writes
the program onto the RAM 506 or the like. Instead of the CD-ROM, a
rewritable medium such as a CD-R, CD-RW or the like may be used as
a storage medium. In that case, a drive for CD-R or CD-RW is
provided instead of the CD-ROM drive 508. Instead of the
above-mentioned mediums, a DVD, MO, flash memory stick or the like
may be used and a corresponding drive may be provided.
[0400] The central computer 30 communicates with the protein
fractionation unit 302, the protein mixing unit 303, and the mass
spectrometry unit 304, and transmits control information such that
these units function. The central computer 30 also receives the
protein identification results and the protein mass spectrometry
results, and displays the identification results including the
intensity ratio, the binding ability ratio, the protein quantity
ratio, the EMPAI ratio and the like.
[0401] Hereinafter, an operation of the control unit (first
embodiment) will be described with reference to the drawing (FIG.
6).
[0402] The central computer 30 of the control unit 301 instructs a
filling device to fill one culture device 11a with a culture
liquid, a protein sample (cell) and other reagents necessary to
carry out the present invention, and also instructs the labeling
device 14 to add an isotope-labeled substance (isotope-labeled
amino acid, etc.) necessary for labeling proteins. The labeling
device 14 performs the addition of the isotope-labeled substance
(S601a). In parallel, the central computer 30 instructs the sample
filling device (not shown) to fill the other culture device 11b
with a culture liquid, a sample (cell) and other reagents necessary
to carry out the present invention. The filling device (not shown)
performs the filling operation (S601b). When each of the culture
devices 11a and 11b is filled with the culture liquid and the like,
the central computer 30 instructs each culture device 11a, 11b to
culture under predetermined conditions. Each culture device 11a,
11b performs the culture operation (S602a, S602b).
[0403] The "predetermined conditions" include the culturing time,
the culturing temperature, the CO.sub.2 concentration, whether or
not to stir, and the like. When the culture operation under the
predetermined conditions is completed, the central computer 30
instructs the cell crushing devices 13a and 13b to perform the cell
crushing step. The cell crushing devices 13a and 13b perform the
cell crushing operation (S603a, S603b). After the cell sampled from
the medium containing the isotope-labeled substance is crushed in
S603a, the central computer 30 instructs the carrier 15a having a
predetermined substance (compound) immobilized thereon to perform
the protein fractionation step. The carrier fractionates the
proteins (first group of test proteins) (S604a). After the cell
sampled from the medium not containing the isotope-labeled
substance is crushed in S603b, the central computer 30 instructs
the carrier 15b having a predetermined compound immobilized thereon
to perform the protein fractionation step. The carrier fractionates
the proteins (the second group of proteins for the internal
standard fraction) (S604b). After the protein fractionation is
completed, the central computer 30 instructs the protein
fractionation control devices 16a and 16b to separate the protein
samples into the purified protein separators 17a and 17b and
temporarily store the protein samples in preparation of the
subsequent mixing (S606, S607). The control devices perform the
separation and temporary storage (S605a, S605b). Whether or not to
perform the temporary storage is optional. Next, the central
computer 30 instructs the mixing device 17c to mix all the
fractions derived from the second group of proteins for the
internal standard fraction or to mix plural contiguous fractions
derived therefrom, and the mixing device 17c mixes the protein
fractions (S606). When only one fraction is obtained as a result of
the fractionation, the mixing device 17c does not mix the fractions
derived from the second group of protein. Then, the central
computer 30 instructs the protein mixing unit 303 to add the
protein fractions for the internal standard fraction to each of the
test protein fractions, and the protein mixing unit 303 adds a
certain amount of the protein fractions for the internal standard
fraction to each of the test protein fractions and mixes the
fractions (S607).
[0404] When the mixing in S607 is completed, the central computer
30 instructs to prepare a sample for mass spectrometry (S608).
Whether or not to perform the preparation is optional. Next, the
central computer 30 instructs the spotter (not shown) to spot the
prepared sample to a mass spectrometry plate (e.g., the plate 19 in
FIG. 4) and instructs the mass spectrometry device to start the
mass spectrometry of the sample. The spotter performs the spotting
operation, and the mass spectrometer starts the mass spectrometry
(S609).
[0405] The central computer 30 identifies the proteins (S610), and
finds the intensity ratio between the peak with labeling and the
peak without labeling of each protein and quantitates the binding
ability ratio of the compound to the proteins (S611). The data on
the protein identification results and the intensity ratio are
transmitted to the central computer 30, and the output device or
the computer display presents the identification results and the
intensity ratio (S612), and also creates rankings of the binding
ability of proteins bindable to a compound.
[0406] The central computer 30 checks the data on the intensity
ratio and the identification results against the existing
information, and accumulates the data on the hard disc for creating
a database (S613).
[0407] Hereinafter, the present invention will be described more
specifically by way of examples, but the present invention is not
limited to these examples.
EXAMPLES
(1) Production of a Affinity Chromatography Having a Compound
Immobilized Thereon
[0408] About 10 mg of the compound represented by formula (1):
##STR00001##
was dissolved in 4 mL of tetrahydrofuran (THF) and 4 mL of methanol
(MeOH), and 4 mL of water was added thereto.
[0409] 6 mL of the resultant solution was diluted with 18 mL of
THF/MeOH/Water=1/1/1 (v/v/v), and was added to 25 mL of Affi-gel 10
(produced by BioRad, Cat No. 153-6099), which had been washed with
THF/MeOH/Water=1/1/1 (v/v/v) beforehand.
[0410] To the resultant substance, 100 .mu.L of triethylamine
(produced by Tokyo Chemical Industry Co., Ltd., Cat No. T0424) was
added thereto and incubated at room temperature for 2 hours. Then,
500 .mu.L of 2-aminoethanol (produced by Tokyo Chemical Industry
Co., Ltd., Cat No. A0297) was added thereto and incubated at room
temperature for 2 hours. The resultant gel was fully washed with
THF/MeOH/Water=1/1/1 (v/v/v), and was stored at 4.degree. C. after
replacement with a methanol solution. The resultant gel was set to
be used as an affinity gel. By this reaction, the compound
represented by formula (1) was bound at a ratio of about 0.2 mg for
1 mL of gel. A column was filled with about 0.9 ml of the produced
affinity gel. Thus, an affinity chromatography column was
produced.
(2) Preparation of Cells
[0411] Human colon glandular cancer cell line HCT116 (ATCC) was
cultured. Used as a medium was RPMI-1640 (Sigma, R-7130) containing
10% fetal calf serum (MOREGATE, BATCH 32300102), 100 U/ml of
penicillin G, and 100 .mu.g/ml of streptomycin (Invitrogen,
15140-122). As for the RPMI-1640 medium, a powder medium which
contains none of L-glutamine, L-methionine, L-leucine, and sodium
hydrogen carbonate was selected. Then, components absent in the
medium were added. The absent components were added as follows.
L-glutamine (produced by Sigma, G-8540), L-lysine (produced by
Sigma, L-9037), L-methionine (produced by Sigma, M-5308), and
sodium hydrogen carbonate (Wako Pure Chemical Industries, Ltd.,
191-01305) were added in 0.3 g/L, 0.04 g/L, 0.015 g/L, and 2 g/L,
respectively; and then naturally-occurring L-leucine and L-leucine
labeled with a stable isotope .sup.13C (six) (Cambridge Isotope
Laboratories, CLM-2262) were separately added in 0.05 g/L. Each
medium thus prepared was used to culture cells in 5% CO.sub.2 at
37.degree. C. The cells obtained by such culturing were used in the
following tests as cells cultured in a naturally-occurring medium
and cells cultured in a stable isotope medium, respectively.
(3) Extraction of Proteins
[0412] Cells cultured in the naturally-occurring medium were
provided in an amount corresponding to ten 15-cm diameter plates.
Cells cultured in the stable isotope medium were provided in an
amount corresponding to ten 15-cm diameter plates. The cells were
collected. The cells were solubulized with about 2 ml of M-PER
(PIERCE, 78501) per 15-cm diameter plate. Insoluble fractions were
removed by centrifugation to prepare soluble fractions. The soluble
fractions thus obtained were set to be used as a protein extract
liquid metabolically labeled with a stable isotope and a protein
extract liquid not metabolically labeled with a stable isotope,
respectively. To these protein extract liquids (about 20 ml each),
a quadruple amount of PBS was added (final amount: about 100 ml
each).
(4) Affinity Column Operation
[0413] Next, about 0.9 ml of affinity gel was put into an open
column, and a diluted protein extract liquid metabolically labeled
with a stable isotope was added to the open column from above and
was naturally dropped. Then, 10 ml of PBS containing 1 M NaCl was
flown to this column. Next, 7 ml of PBS containing 1 M urea and
0.01% CHAPS, 7 ml of PBS containing 2 M urea and 0.01% CHAPS, 7 ml
of PBS containing 4 M urea and 0.01% CHAPS, and 7 ml of PBS
containing 8 M urea and 0.01% CHAPS were sequentially flown, and
the eluted fractions were collected (4 fractions in total).
[0414] In parallel with the above operation, a diluted protein
extract liquid not metabolically labeled with a stable isotope was
added to 0.9 ml of affinity gel from above and was naturally
dropped. Then, 10 ml of PBS containing 1 M NaCl was flown to this
column. Next, 12 ml of PBS containing 8 M urea and 0.01% CHAPS was
flown, and the eluted fractions were collected to be used as an
internal standard fraction.
(5) Treatment of Fractionated Samples
[0415] 3 ml of the internal standard fraction was added to each of
the four fractionated samples and mixed together. Each of the
mixture liquids was concentrated to about 0.5 ml with Amicon
Ultra-15 10,000MWCO (Millipore, Cat No. UFC901096), and then
concentrated to about 25 .mu.l with 0.5 ml of BIOMAX-10 K NMWL
MEMBRANE (Millipore, Cat No. UFV5BGC00). The obtained substance was
mixed with an equal amount of SDS-PAGE sample buffer. Then, the
total amount thereof was separated with SDS-PAGE (DRC K.K., 5 to
20% T gel, 1 mm, 7 wells, 4 cm, 200 V), and digested with trypsin
in a gel in an electrophoresis lane equally divided into 12. The
resultant solution was set to be used as a digested protein
solution (H. Katayama, T. Tabata, Y. Ishihama, T. Sato, Y. Oda and
T. Nagasu, Rapid Commun. Mass Spectrom., 18, 2388-2394(2004)).
(6) Measurement with LC/MS
[0416] The digested protein solution was dissolved in 5%
acetonitrile containing 8 .mu.l of 0.1% trifluoroacetic acid, and
the resultant substance was set to be used as a protein solution,
which is a target of LC/MS measurement. MS of LC/MS was performed
using LCQ-Duo (produced by Thermo Electron). LC of LC/MS was
performed as follows. A Lab-made ODS column (Y. Ishihama, J.
Rappsilber, J. S. Andersen, M. Mann, J. Chromatogr A. 979, 233-239
(2002)) (inner diameter: 0.2 mm; length: about 15 cm) was used.
0.5% acetic acid was incorporated as a mobile phase. Over the first
1 minute, the acetonitrile concentration was reduced to 4%. Then,
over the subsequent 35 minutes, the acetonitrile concentration was
linearly increased to 20%. Then, within 0.1 minute, the
acetonitrile concentration was increased to 80%, which was kept for
5 minutes. Then, the acetonitrile concentration was reduced to 0%.
12 minutes later, the next sample was implanted.
[0417] As the pump, an LC-10A series device of Shimadzu Corporation
was used with the ROM being made compatible to the order of
micrometers. As the mixing chamber, T connector of Barco was used
instead of the Shimadzu chamber attached to the pump.
[0418] For the flow rate, the flow-splitting system was used. The
flow rate in the column was adjusted to be about 0.5 to 1 .mu.L per
minute. The protein solution as the target of measurement was
implanted in 3 .mu.L to the column by Autosampler PAL of CTC. Ions
obtained by directly spraying the eluted substance from the column
outlet were transferred to the LTQ to perform the measurement. As a
spray voltage, 2.4 kV was applied. The measurement was performed in
the data dependent mode, with the Repeat of Dynamic Exclusion being
set to 1. In order to maximize the number of times of scanning, the
so-called double play mode was used for the measurement, without
the zoom scan mode.
(7) Data Analysis
[0419] The proteins were automatically identified using X!Tandem
(http://thegpm.org/GPM/index.html) and the NCBInr database. The
program was partially modified such that the proteins could be
searched using the NCBInr even with leucine labeled with a stable
isotope (the molecular weight is increased by 6 per leucine).
[0420] Quantitation was to be performed at the peak of the peptides
containing leucine. Therefore, only the peptides containing leucine
were selected from the peptides identified by X!Tandem. In order to
specify the elution position at the peptide peak (retaining time
with HPLC=scanning number with MS), software for automatically
selecting scanning information was constructed using the function
of Mass Navigator co-developed with Mitsui Knowledge Industry Co.,
Ltd. Based on the scanning number information, the MS spectrum of
the scanning number was extracted. Regarding the peak of the
naturally-occurring leucine peptides and the peak of the isotope
peptides, the following was obtained from the search result by
X!Tandem: information on the parent ions (m(mass)/z(charge) value)
when the MS/MS was performed; how many leucines were contained in
the peptides; and how many charges were present, Peaks forming a
pair were found, and the peak intensity ratio thereof was
automatically calculated. In this manner, proteins were identified
and the peak intensity ratio was calculated using the constructed
software.
(8) Results
[0421] The results are shown in Table 1.
TABLE-US-00001 TABLE 1 locus_link.locus ID gene symbol product 1M
Urea 2M Urea 4M Urea 8M Urea 191 AHCY S-adenosylhomocysteine
hydrolase 0.63 0.99 1.88 3.27 4507 MTAP 5'-methylthioadenosine
phosphorylase 0.77 0.78 0.71 0.88 81848 SPRY4 sprouty homolog 4
3.70 1.17 0.83 0.67 10956 OS9 amplified in osteosarcoma isoform 2
precursor 1.24 3.57 1.62 0.73 amplified in osteosarcoma isoform 3
precursor amplified in osteosarcoma isoform 4 precursor amplified
in osteosarcoma isoform 1 precursor 5110 PCMT1
protein-L-isoaspartate (D-aspartate) 1.14 1.57 2.52 1.02
O-methyltransferase
[0422] In Table 1, the numerical figures provided in the "Urea"
sections of various concentrations each represent the peak
intensity ratio (peak area of the labeled protein/peak area of the
non-labeled protein). In Table 1, as the concentration of urea is
higher, the eluting power is stronger, and the numerical figure of
the intensity ratio is larger, a larger amount is eluted in the
corresponding fraction. In this example, elution was performed with
four different concentrations of urea, i.e., 1 M, 2 M, 4 M and 8 M.
Therefore, a protein having a higher peak in the fraction of 8 M
urea has a higher binding ability to the compound represented by
formula (1). Paying attention to the results of only the fraction
of 8 M urea, a protein having a larger numerical figure is more
concentrated in this fraction, namely, is bound more strongly.
[0423] In this example, AHCY has the highest peak in the 8 M urea
fraction, PCMT1 has the highest peak in the 4 M urea fraction, OS9
has the highest peak in the 2 M urea fraction, and SPRY4 has the
highest peak in the 1 M urea fraction (Table 1). Therefore, it is
analyzed that the binding ability of the proteins to the compound
represented by formula (1) is ordered, from highest to lowest, as
AHCY, PCMT1, OS9 and SPRY4. Comparing the peak intensity ratios of
the proteins in the 8 M urea fraction, the numerical figure is
largest with AHCY and is decreased in the order of PCMT1, OS9 and
SPRY4. Based on this also, it is analyzed that the binding ability
of the proteins to the compound represented with formula (1) is
ordered, from highest to lowest, as AHCY, PCMT1, OS9 and SPRY4.
MTAP shows the value of about 0.8 in all the four fractions. Since
the highest peak is not clear, the eluting fraction cannot be
clearly specified.
INDUSTRIAL APPLICABILITY
[0424] The present invention makes it possible to create rankings
of the binding ability of plural kinds of substances (proteins)
bindable to a compound. The method of the present invention makes
it possible to analyze a binding ability of plural kinds of unknown
substances to a compound. The method of the present invention is
useful in being applicable even to the case where the target
substance is unknown and the substances are not fully separated in
a mixed sample.
* * * * *
References