KR20160033987A - A quantitative method for protein in biological sample using mass spectrometry and a composition therefor - Google Patents

Abstract

The present invention relates to a method for quantitatively analyzing protein in a biological sample of a protein medicine product and a composition thereof wherein protein-specific fragment peptide by enzyme treatment, fragment peptide including glycan, medicine synthetic peptide of protein including stable isotope for quantification, labeling for quantification similar to the same, the fragments, and the total protein are quantified by using direct mass spectrometry.

Description

TECHNICAL FIELD The present invention relates to a protein quantitative analysis method and a composition thereof in a biological sample using mass spectrometry,

TECHNICAL FIELD The present invention relates to a quantitative analysis method and a composition thereof in a biological sample of a protein drug, and relates to a protein-specific fragment peptide, a glycan-containing fragment peptide by enzyme treatment, a protein synthesis peptide containing a stable- A similar quantitative target labeling method, and a mass spectrometry method and a composition thereof which are intended to quantify the whole fragment and the entire protein directly using mass spectrometry.

Recently, the development of new drugs and the development of biosimilar have led to an increasing demand for quantitative analysis of protein drugs present in biological samples such as plasma. In particular, protein drugs are different from chemicals and have difficulties in production process and have many technical limitations in the characterization and quantitative analysis of protein drugs. Recent developments in mass spectrometry have developed methods for characterizing protein drugs such as peptide mapping, Glycan identification and relative quantification, and disulfide bond site determination, and are essential for the development of biosimilars. In vivo metabolism of protein drugs and the amount of residual blood in the blood are of great interest. The ELISA method is the main method used for this. Antibody-based ELISA is easy to use if appropriate antibodies are developed for protein drugs, but other methods are required because of the time required for antibody development and the time for development of the assay. In addition, the use of glycan-containing protein drugs and monoclonal antibody protein drugs is relatively limited to quantitative methods using ELISA. In particular, it is not suitable as a method of monitoring protein drugs that are modified by other enzymes or other factors in the blood. However, with the recent use of mass spectrometry capable of multiplexing, there is a potential for quantitative analysis of protein drugs in the original form as well as other modified protein drugs in biological samples such as blood. It is also advantageous that quantitative analysis of a plurality of protein drugs simultaneously with various antibodies in the blood can be performed simultaneously.

[Prior Patent Literature]

Patent Publication No. 2003-0031911

The present invention has been devised in view of the above-mentioned needs, and an object of the present invention is to provide an effective sample pretreatment method and a new protein drug quantitative analysis method.

Another object of the present invention is to provide a fraction derived from a protein drug, that is, a composition for quantifying an enzyme cutting peptide.

In order to accomplish the above object, the present invention provides a method for detecting a protein, comprising: a) separating a protein from a plasma sample; b) treating the protein with a protease to form a peptide, c) adding a standard peptide, if necessary, having the same sequence as the peptide and containing a stable isotope, and d) Or a peptide sample is separated by a liquid chromatography method, and mass spectrometry is used.

In one embodiment of the present invention, the mass spectrometry continuously obtains a tandem spectrum during the LC-MS / MS run for a specific m / z section of the target protein and peptide and determines the intensity of a particular fragment ion, And the optimal combination of the target protein and the peptide-derived specific fragments in the full-range mass spectrum obtained at this time is found and utilized for quantitation, and the isolation width of the target ion It is desirable, but not limited, to widen or adjust the accumulation time.

In another embodiment of the present invention, the method comprises quantitatively measuring interceptions observed only in plasma samples containing target proteins and peptides, as compared to the target protein and peptide tandem spectra obtained from background plasma samples without target molecules Wherein the subject is a specific b- or y-ion of the target protein and peptide, or a combination thereof or another internal fragment, but is not limited thereto.

In another embodiment of the present invention, it is preferable that a specific fragment obtained after labeling a protein using a cysteine-specific or lysine-specific reactive chemical is used for quantitation, Or more.

In another embodiment of the present invention, it is preferable, but not limited, to add the known peptide to the mass spectrometry.

The present invention also provides a method for detecting a target protein in a biological sample, the method comprising the steps of: (a) detecting a target protein in a biological sample, which is the same as a peptide of the target protein separated and contains a stable isotope, The present invention provides a composition for quantitative analysis of a protein in a biological sample using mass spectrometry, which comprises the different stable isotopes.

In one embodiment of the present invention, when the target protein is avastin, the peptide is preferably derived from residues 210 to 250 of avastin, but is not limited thereto.

Hereinafter, the present invention will be described.

The present invention includes a method for efficiently separating and purifying a protein drug in a biological sample such as blood and quantitatively analyzing the protein drug using mass spectrometry.

In one embodiment, a mass spectrometer is used with the substrate of the present invention. A sample located on a terrain of the substrate according to the invention is introduced into the input system of the mass spectrometer. Thereafter, the sample is ionized with an ionization source. Typical ionization sources include lasers, fast atom bombardment, or plasma. The resulting ions are collected by an ion optical assembly and then analyzed for ions passing through a mass spectrometer. Ions exiting the mass spectrometer are detected by a detector. The detector then decodes the information of the detected ions in a mass-to-charge ratio. Detection of the detectable substance generally involves detection of the signal intensity, which reflects the content of the detectable substance bound to the substrate. Further information related to mass spectrometry can be found in Principles of Instrument Analysis, 3 rd ed., Skoog, Saunders College Publishing, Philadelphia, 1985 and Kirk-Othmer Encyclopedia of Chemical Technology, 4th ed. Vol. 15 (John Wiley & Sons, New York 1995), pp. 1071-1094.

Tandem mass spectrometry (eg, MS / MS, MS / MS / MS, and ESI-MS / MS) can be used to obtain sequence information for biological molecules such as proteins and peptides. Tandem mass spectrometry refers to mass spectrometry that generates a parent ion, wherein the parent ion is fragmented into daughter ions, which are then mass analyzed. Generally, a mass filter is used to select mother ions having a specific mass-to-charge ratio that are fragmented.

In certain embodiments, the fragmentation is a collision-induced dissociation (CID). The CID can be performed in a collision chamber located between the first mass analyzer and the second mass analyzer. The impingement chamber is filled with a buffer gas, particularly an inert gas such as helium. Alternatively, parent ions can be fragmented into surface-induced dissociation, optical dissociation (eg, with a laser), and electron-induced dissociation (eg, with an electron beam).

In mass spectrometers using time-of-flight spectroscopy, post-source decay (PSD) and in-source decay (ISD) are used to trigger fragmentation (Li et al. PSDs include the step of "filtering" precursor ions from a peptide ion composition using a timed-ion-selector. The selected mass ion spontaneously collapses into a fragment ion that separates from the reflectron. ISD uses a different condition than PSD, which includes rapid metastable collapse at the ion source.

In a preferred embodiment, the tandem mass spectrometry comprises all tandem mass spectrometry including a laser desorption / ionization mass spectrometer further coupled to a quadrupole time-of-flight mass spectrometer QqTOF MS (Krutchinsky et al., WO 99/38 185) . MALDI-QqTOF MS (Krutchinsky et al., WO 99/38185; Shevchenko et al. (2000) Anal. Chem. 72: 2132-2141), ESI-QqTOF MS (Fig. Mass Spec. 12: 1435-144), chip capillary electrophoresis (Chip-CE) -QqTOF MS (Li et al. (2000) Anal. Chem. 72: 599-609).

The mass spectral data obtained by the mass spectrometry of the present invention can be utilized to obtain information on the content and uniqueness of the product by applying an analysis algorithm such as a function. Data generated by polypeptide desorption and detection can be analyzed by any suitable means (e.g., time, computer, etc.). In one embodiment, the data is analyzed using a programmable digital computer. A computer program includes a readable medium storing code. Certain codes can be faithfully delivered to the memory including the location of each feature in the substrate, the identity of the absorbent in each feature, and the elution conditions used to clean the absorbent. The program can then use this information to identify a set of characteristics on the substrate that define the characteristic selectivity (eg, the type of absorbent and eluent used). The computer also has a code that accepts as input data about the strength of the signal at various molecular masses received from a particular addressable location in the substrate. This data suggests the total number of products, including the signal intensity of the peak value and the molecular mass measured at each detected product.

Data analysis involves measuring the signal strength (eg, the height of the peak) of the detected peak value (eg, a specific mass-to-charge value or range of values) and measuring the "extreme value" (data outside the pre-measured statistical distribution) And a step of removing the data. The observed peaks can be normalized, where the height of each peak relative to some reference group is calculated. For example, the reference group may be a reference noise generated by a device and a chemical (e.g., energy absorbing molecules) set to zero on the scale. Subsequently, the signal intensity detected in each polypeptide or other material can be presented in relative intensity form with a desired scale (e.g., 100). Alternatively, standards may be introduced into the sample, and peaks from these standards may be used as a reference for measuring the relative intensities of the signals observed in the detected products. Software programs such as the Biomarker Wizard program (Ciphergen Biosystems, Inc., Fremont, Calif.) Can be used to assist in the analysis of mass spectra.

As can be seen from the present invention, the present invention is also advantageous in that quantitative analysis of a plurality of protein drugs can be selectively performed simultaneously on various antibodies in blood. The present invention can effectively separate and purify a protein drug from a biological sample such as blood and quantitatively analyze a protein drug using mass spectrometry.

Figure 1 is a sequence comparison of Avastin and Herceptin,
FIG. 2 is a chromatogram (trypsinization) for quantifying N-terminal and C-terminal peptides of avastin using an extracted ion chromatogram method.

The present invention will now be described in more detail by way of non-limiting examples. The following examples are intended to illustrate the invention and the scope of the invention is not to be construed as being limited by the following examples.

A method for separating an antibody drug from a blood sample and quantifying using the mass spectrometry is as follows.

A. Detection of antibody from blood sample The composition of the purified solution is shown in Table 1 below.

Tablet solution composition Ammonium Biocarbonate buffer (Ambic) 100 mM (pH 8.0) Acetic acid 50 mM (pH 3.0)

B. Sample Preparation

1. Mix 50 μL of plasma sample with purified solution at 1: 1 (v / v) and centrifuge at 18,000 x g for 20 min at 4 ° C to remove remaining cells and debris from the sample.

2. Capture the antibody protein using a column made of Protein G fragments, wash it three times with purified solution, add DW, and wash once with 50 mM acetic acid (pH 3), while taking care not to mix the centrifuged debris. Partially purified by dissolving the antibody drug.

3. Wash the solution using speed-vac, add 50 uL of 5 mM TCEP / 5 mM Iodoacetamide / 50 mM Ambic buffer (pH 8.0) and incubate at 37 ° C for 30 minutes.

4. Add 300 μL of acetone acetone and incubate at 4 ° C for 10 minutes to precipitate. Discard the supernatant. After incubation, the reaction mixture was diluted with 15 uL of 8M Urea solution, followed by addition of 500 uL of Ambic buffer and protease (eg, trypsin) for 3 h, followed by addition of an appropriate amount of heavy synthetic peptides if necessary, followed by SEP-PAK (C18) Keep together by desalting and dry. Prepare the analytical sample by resuspension in 50uL of 0.1% formic acid just before mass spectrometry. When performing direct mass spectrometry of the antibody protein, prepare the sample preparation 2, dry the solution using speed-vac, Resuspension with 50 uL of 1% formic acid.

C. Liquid Chromatography

1. Analyze the protein / peptide samples prepared above using Waters UPLC and Triple-Tof 5600 mass spectrometry.

2. Examples of liquid chromatography are shown in Table 2.

D. Antibody Drug-Specific Peptide Selection and Peptide Synthesis

1. In the case of Avastin's anti-VEGF antibody protein, the present invention can generate a peptide fragment with trypsin. In this case, an antibody fragment (peptide fragment) that selectively or commonly shares the antibody amount with other antibody drugs such as Herceptin is selected . A quantitative target of a peptide containing an optional sequence (eg, a sequence-containing peptide that can be distinguished from other antibody drugs, such as Avastin or Herceptin, as a specific tryptic fragment of the variable region) or a commonly identifiable enzyme by-product peptide Can be selected. It is also possible to synthesize heavy standard peptides containing the stable isotope sequence, and to use them for absolute quantitative analysis.

In the case of avastin, from 210 to about 250, this partial peptide contains a preferential Avastin or Herceptin specific sequence (Fig. 1). Quantitative analysis can be carried out using the enzyme fragments corresponding to the region or region showing the difference in sequence.

E. New Mass Spectrometry

1. A method for quantitatively analyzing an antibody drug using the new mass spectrometry method by separating the previously prepared protein / peptide solution sample using the liquid chromatography method.

2. Provide a method for continuously obtaining the tandem spectrum during LC-MS / MS performance for specific m / z intervals (eg, 0.7 to 20 Da) of the target protein and peptide and considering only the intensity of a specific fragment ion. In this case, the optimal combination of specific fragments derived from the target protein / peptide in the full range mass spectrum can be found and used for quantification, a method of widening the isolation width of the target ion for increasing the sensitivity and controlling the accumulation time to provide.

3. Provides a method for quantifying target fragment / peptide tandem spectra obtained from a background plasma sample without a target molecule against fragment ions observed only in a plasma sample containing a target protein / peptide. These may be combinations of specific b-ions or / and y-ions of the target protein / peptide (or other internal fragments).

4. Provide methods for quantitation of specific fragments obtained after labeling antibody proteins using cysteine-specific or lysine-specific reactive chemicals (eg, iTRAQ) (eg, reporter ions of iTRAQ, immonium ion).

5. Identification and Identification of Peptides by Extracted Ion Chromatogram (XIC) Method: The data obtained through mass spectrometry were analyzed using the ProteinPilot program using the avastin database. Detected Protein Threshold [Unused ProtScore (Conf)]> 0.05 (10% ). Peptides of N-term and C-term are confirmed by comparison with the searched results (Fig. 2). When obtaining the peak by XIC, RT width and mass width are set to 1 and gaussian smoothed is set to 2 point to get the graph. We provide a baseline evaluation method (confirm peak intensity and retention time) by confirming the presence of Avastin mAb and confirming the basic quantitative results through XIC, which is a method of identifying the parent molecular value of the identified peptides.

Pept. # Location Mass [M] Sequence ΔMass Modification m / z z RT T1 1 to 18 1877.8789 DIQMTQSPSSLSASVGDR -0.0007 None 939.9467 2 33.69 T1-T2 1 to 42 4660.2173 DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGK 0.0120 C # @ 23 1166.0616 4 62.77 T1-T3 1 to 45 4956.4023 DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPK -0.0010 C # @ 23 1240.1078 4 60.94 T2 19 - 42 2800.3491 VTITCSASQDISNYLNWYQQKPGK -0.0010 C # @ 5 934.4570 3 54.98 T2-T3 19 - 45 3096.5339 VTITCSASQDISNYLNWYQQKPGKAPK -0.0011 C # @ 5 775.1407 4 52.56 T4 46 - 61 1761.9414 VLIYFTSSLHSGVPSR 0.0005 None 588.3210 3 43.40 T5 62 - 103 4659.1064 FSGSGSGTDFTLTISSLQPEDFATYYCQQYSTVPWTFGQGTK 0.0038 C # @ 27 1165.7839 4 75.97 T7-T8 108 - 126 2101.1208 RTVAAPSVFIFPPSDEQLK -0.0015 None 701.3809 3 50.76 T8 109 - 126 1945.0197 TVAAPSVFIFPPSDEQLK -0.0004 None 973.5171 2 55.40 T9 127 - 142 1796.8879 SGTASVVCLLNNFYPR 0.0026 C # @ 8 899.4512 2 61.63 T11-T13 146 - 183 4160.0034 VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSK -0.0003 None 1041.0081 4 48.26 T12 150 - 169 2134.9614 VDNALQSGNSQESVTEQDSK -0.0101 None 712.6611 3 17.54 T12-T13 150 - 183 3618.7021 VDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSK 0.0031 None 1207.2413 3 42.32 T13 170 - 183 1501.7512 DSTYSLSSTLTLSK -0.0010 None 751.8829 2 39.24 T15-T16 189 - 207 2140.0735 HKVYACEVTHQGLSSPVTK 0.0005 C # @ 6 536.0256 4 21.70 T16 191 - 207 1874.9197 VYACEVTHQGLSSPVTK 0.0013 C # @ 4 625.9805 3 26.79 T17-T18 208 - 214 868.3497 SFNRGEC -0.0001 C # @ 7 435.1822 2 2.69

Table 3 shows the tryptic mapping of the peptides identified in the light chain of Avastin.

Pept. # Location Mass [M] Sequence ΔMass Modification m / z z RT T1 1 to 19 1880.9956 EVQLVESGGGLVQPGGSLR 0.0026 None 941.5051 2 40.76 T2 20 - 38 2196.9722 LSCAASGYTFTNYGMNWVR 0.0030 C # @ 3 1099.4933 2 51.48 T4 44 - 65 2517.1853 GLEWVGWINTYTGEPTYAADFK -0.0025 None 840.0690 3 66.38 T4-T5 44 - 66 2673.2864 GLEWVGWINTYTGEPTYAADFKR 0.0045 None 892.1027 3 62.10 T6-T7 67 - 76 1200.6139 RFTFSLDTSK -0.0023 None 601.3142 2 31.99 T7 68 - 76 1044.5128 FTFSLDTSK 0.0004 None 523.2637 2 36.21 T8 77 - 87 1282.6339 STAYLQMNSLR -0.0014 None 642.3243 2 31.64 T9 88 - 98 1289.5598 AEDTAVYYCAK 0.0005 C # @ 9 645.7872 2 16.94 T10 99 - 127 3322.5359 YPHYYGSSHWYFDVWGQGTLVTVSSASTK 0.0050 None 1108.5193 3 58.94 T11 128 - 139 1185.6394 GPSVFPLAPSSK 0.0002 None 593.8270 2 34.88 T11-T12 128 - 153 2488.2996 GPSVFPLAPSSKSTSGGTAALGCLVK -0.0001 C # 23 830.4405 3 51.30 T12 140 - 153 1320.6708 STSGGTAALGCLVK -0.0010 C # @ 11 661.3427 2 30.37 T13 154 - 216 6712.3071 DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTK 0.0123 C # @ 53 1119.7251 6 78.09 T14-T16 217 - 224 941.5546 VDKKVEPK -0.0014 None 471.7846 2 0.79 T17-T18 225 - 254 3333.6348 SCDKTHTCPPCPAPELLGGPSVFLFPPKPK -0.0007 C # @ 2; C # @ 8; C # @ 11 834.4160 4 55.70 T18 229 - 254 2843.4502 THTCPPCPAPELLGGPSVFLFPPKPK 0.0005 C # @ 4; C # @ 7 948.8240 3 57.93 T19 255 - 261 834.4269 DTLMISR 0.0016 None 418.2207 2 19.43 T20 262 - 280 2138.0203 TPEVTCVVVDVSHEDPEVK -0.0005 C # @ 6 713.6807 3 41.37 T21 281 - 294 1676.7947 FNWYVDGVEVHNAK 0.0002 None 559.9388 3 38.91 T22-T23 295 - 307 1671.7853 TKPREEQYNSTYR -0.0009 Deamidated (N) @ 9 558.2690 3 8.62 T23 299 - 307 1189.4888 EEQYNSTYR -0.0019 Deamidated (N) @ 5 595.7516 2 9.25 T24 308 - 323 1806.9993 VVSVLTVLHQDWLNGK 0.0024 None 603.3403 3 60.27 T24-T25 308 - 326 2227.2002 VVSVLTVLHQDWLNGKEYK 0.0008 None 743.4073 3 57.25 T28 333 - 340 837.4960 ALPAPIEK 0.0003 None 419.7553 2 20.40 T31-T33 347 - 366 2342.1689 GQPREPQVYTLPPSREEMTK -0.0018 None 586.5495 4 28.56 T32 351 - 361 1285.6666 EPQVYTLPPSR -0.0020 None 643.8406 2 26.80 T32-T33 351 - 366 1903.9349 EPQVYTLPPSREEMTK -0.0009 None 635.6523 3 30.30 T34 367 - 376 1160.6223 NQVSLTCLVK -0.0018 C # @ 7 581.3184 2 34.47 T35 377 - 398 2543.1240 GFYPSDIAVEWESNGQPENNYK -0.0067 None 848.7153 3 50.35 T36 399 - 415 1872.9146 TTPPVLDSDGSFFLYSK -0.0007 None 937.4645 2 52.70 T37-T38 416 - 422 817.4658 LTVDKSR -0.0009 None 409.7402 2 2.80 T39 423 - 445 2800.2598 WQQGNVFSCSVMHEALHNHYTQK -0.0011 C # @ 9 934.4272 3 40.24 T40 446 - 453 787.4440 SLSLSPGK 0.0012 None 394.7292 2 16.48

* C #: Carbamidomethyl (C)

Table 4 shows the tryptic mapping of the peptide identified in the heavy chain of Avastin.

Claims (7)

a) separating the protein from the plasma sample;
b) treating the protein with a proteolytic enzyme to form a peptide;
c) if necessary, adding a standard peptide comprising the same sequence as said peptide and comprising a stable isotope; and
d) separating the protein or peptide sample using a liquid chromatography method, and using mass spectrometry. The mass spectrometry of claim 1, wherein the mass spectrometry continuously obtains a tandem spectrum for a particular m / z interval of the target protein and peptide during LC-MS / MS and considers the intensity of a particular fragment ion The optimal combination of the target protein and peptide-specific fragments in the full-range mass spectrum obtained at this time is found out and used for quantitation, and the separation width of the target ion (for broadening the isolation width or directly And adjusting the accumulation time. The method according to claim 1, characterized in that the method comprises quantifying the fragment ions observed only in a target protein and a peptide-containing plasma sample as compared to a target protein and peptide tandem spectra obtained from a background plasma sample without a target molecule Wherein the subject is a specific b- or y- ion of the target protein and peptide, or a combination thereof, or another internal fragment. The method according to claim 1, wherein the specific label is obtained by labeling the protein using a cysteine-specific or lysine-specific reactive chemical substance. 2. The method of claim 1, wherein the method comprises adding a known concentration of a peptide to a mass spectrometry method. The peptide is the same as the peptide of the target protein separated in the biological sample and contains a stable isotope and the peptide is a peptide common to the target protein to be analyzed or a different protein, A composition for quantitative analysis of a protein in a biological sample using mass spectrometry. The composition for quantitative analysis of protein in a biological sample according to claim 6, wherein the peptide is derived from residue 210 to residue 250 of Avastin when the target protein is Avastin.

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