Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Status of Claims
Claims 1-3, 7, 24, 27-29, 35-46 and 91-92 are pending and under examination.
Withdrawn Objections
In light of the amendments, the objections are hereby withdrawn.
Maintained Rejections
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-3, 7, 24, 27-29, 35-38, 44-46 and 91 are rejected under 35 U.S.C. 103 as being unpatentable over West et al. (US2012/0015371A1, published 01/19/2012) in view of Schmitt et al. (US2016/0138066A1, published 05/19/2016).
With respect to claims 1, 46 and 91, West teaches methods for measuring the absolute concentration of a biomolecule of interest in a subject wherein such biomolecules may be implicated in one or more neurological and neurodegenerative diseases or disorders (see abstract). West teaches the method includes contacting a sample from the subject with a Quantitation Standard, where the Quantitation standard is a known concentration of a labeled biomolecule of interest and isolating the biomolecule of interest from the sample and determining a ratio of labeled to unlabeled biomolecule in the sample, which is thereby used to calculate the concentration of the unlabeled biomolecule in the sample (see para. [0007]). Additionally, West teaches the method includes administering one or more labeled amino acids to the subject, where the labeled amino acids incorporate into the biomolecule of interest in the subject and the sample is then contacted with a Quantitation Standard and the ratio of the unlabeled biomolecule to the Quantitation Standard can then be used to calculate the concentrations of both labeled and unlabeled biomolecules (see paras. [0008] and [0088]). West teaches the biomolecule may be a peptide that is a synthesized in the central nervous system (CNS) such as amyloid-beta (Aβ) and Aβ may be Aβ1-40 or Aβ1-42 (see para. [0013] and Fig. 1). West further teaches Aβ1-40 or Aβ1-42 contains SEQ ID NO:4 and SEQ ID NO:5, respectively (e.g., see Table 1), which reads on the claimed Aβ40 having the amino acid sequence comprising SEQ ID NO:5 or Aβ42 having the amino acid sequence comprising SEQ ID NO:7. West teaches by way of example and not limitation, it is noted that several C-terminally unique isoforms of Aβ exist in CSF and trypsin digestion is used for these peptide yield a 29-x peptide which is unique to each isoform and thus, quantitation of the 29-x isoform allows for calculation of the concentration of these isoforms in the original biological fluid (see para. [0028]). West teaches the methods provide the ability to measure concentrations of fragments of various isoforms of Aβ, such as fragments produced after digestion with an endoprotease (e.g., trypsin or V8 protease) (see para. 0029]). West teaches several different moieties may be used to label the biomolecule of interest and the preferred stable isotopes such as 15N (see para. [0032]). West teaches 15N labeled amino acid (see para. [0034]). West teaches after the administration of the labeled moiety (e.g., labeled amino acid), one or more samples are obtained from the subject (see para. [0045]).
Furthermore, West teaches maintaining the 29-x peptides in the reduced state but these peptides contain one methionine residue which can be oxidized and found that 10% of the methionine is oxidized in CSF and media (see paras. [0081]-[0083]). West teaches demonstrating use of the Quantitation Standard wherein a sample containing Aβ40 and Aβ42, in both unlabeled and labeled forms, is spiked with Quantitation Standard (see paras. [0087]-[0088]). West further teaches the sample is digested with trypsin or another endoprotease and after digestion, mercaptoethanol is added to reduce oxidation of the methionine residue (see para. [0089]). West teaches for analysis, the sample is injected into a column and the separation of the peptides before injection into the mass spectrometer and the m/z ratio of each C-terminus tryptic peptide corresponding to, but not limited to isoforms 17-28, 29-37, 29-38, 29-39, 29-40, and 29-42 are then scanned for the selected for CID (done for all unlabeled, +6D labeled and +12D labeled (Quantitation Standard)) (see paras. [0090]-[0092]). West teaches the standard curve contains the Quantitation Standard – for Aβ 1-40, a peptide containing two 13C6 phenylalanines in positions 19 and 20 (part of the 17-28 peptides) and two 13C6 isoleucines in position 31 and 32 (part of the 29-x peptide) was used; in addition a 15N peptide could be used or a combination of other amino acids that will give a m/z signature that is distinct from the unlabeled and the metabolically labeled peptides (see para. [0092], right col.). Table 2 shows the location of the labeled amino acids in the Aβ 40 peptide and similar peptides can be created for Aβ1-42.
However, West does not teach digesting the 15N labeled and unlabeled Aβ40 and Aβ42 peptides with cyanogen bromide to obtain the claimed labeled and unlabeled Aβ peptide fragments.
Schmitt teaches molecular biology, peptide, and protein expression (see abstract). Schmitt teaches chemical cleavage of peptide bonds is well known in the literature and the chemical compound such as cyanogen bromide (CNBr) cleaves C-terminal to methionine residues (see paras. [0077] and [0179]). Schmitt also teaches protease cleavage site such as trypsin (see para. [0076]). Schmitt further teaches that the peptide was separated from HlyA1 M88A-Met by CNBr and the identity of peptide was confirmed by mass spectrometry (see para. [0179]).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have used or incorporated the process of measuring distinct segments of the Aβ1-40 and Aβ1-42 peptides through peptide cleavage as taught by West with cyanogen bromide as taught by Schmitt because Schmitt teaches that peptide cleavage is well recognized in the literature and chemical compound such as CNBr cleaves C-terminal to methionine residues and West teaches the claimed peptide sequences (i.e., instant SEQ ID NOs: 5 and 7) contain a single methionine residue and once the peptides are cleaved, it has to be maintained in the reduced state due to the single methionine residue, which is prone to oxidative damage. Because West teaches producing distinct peptide segments through peptide cleavage for mass spectrometry measurements and the single methionine residue is known to be damaged, it would have been obvious to the person to have used CNBr to produce a distinctive peptide segment by cleaving the only methionine residue of said sequences which eliminates the need to maintain the peptide segments (e.g., 29-x peptides) in the reduced state.
The person would have a reasonable expectation of success in using CNBr to cleave the peptide sequences of West because it has been well recognized in the art to use CNBr to cleave methionine residues of peptides for mass spectrometry and West’s said sequences contain a single methionine residue.
With respect to claim 2, West teaches calculating the concentration of the labeled biomolecule comprises multiplying the concentration of the Quantitation Standard with the determined ratio of labeled biomolecule to the Quantitation Standard (see bottom of paras. [0008] and [0054]-[0055]).
With respect to claim 3, West teaches the methods further include the step of normalizing the calculated concentration to a standard curve based on the curve fitting equation generated by the standard curve and the standard curve used herein is generated by determining two or more ratios of unlabeled biomolecules to their respective Quantitation Standards, where the concentration of the unlabeled biomolecule of interest is known (see para. [0056]).
With respect to claim 7, West teaches in Fig. 5 a graphical diagram showing the absolute concentration of Aβ (Abeta) as measured in media samples from cells secreting Aβ (also see para. [0018]).
With respect to claim 24, West teaches the methods further include the step of normalizing the calculated concentration to a standard curve based on the curve fitting equation generated by the standard curve and the standard curve used herein is generated by determining two or more ratios of unlabeled biomolecules to their respective Quantitation Standards, where the concentration of the unlabeled biomolecule of interest is known (see para. [0056]).
With respect to claim 27, West teaches Aβ1-40 or Aβ1-42 contains SEQ ID NO:4 and SEQ ID NO:5, respectively (e.g., see Table 1), which reads on the claimed Aβ40 having the amino acid sequence comprising SEQ ID NO:5 or Aβ42 having the amino acid sequence comprising SEQ ID NO:7. Thus, West’s peptides would read on Aβ peptide fragments are post-translationally modified Aβ peptide fragments.
With respect to claim 28, West teaches the biological sample of the present invention is a sample of bodily fluid such as cerebral spinal fluid (CSF), blood, plasma, urine, saliva, and tears (see bottom of para. [0024]).
With respect to claim 29, West teaches isoforms of Aβ exist cerebral spinal fluid (CSF) (see para. [0028]).
With respect to claims 35-36, West teaches isolate the C-terminal isoforms of Aβ from a biological sample and liquid chromatography mass spectrometry (see paras. [0048] and [0060]), which would read on the Aβ peptide fragments specific C-terminal fragments are separated by chromatographic separation before the concentration is determined.
With respect to claim 37, West teaches Aβ is isolated from the biologic samples by immunoprecipitation using an antibody that recognizes either the central domain of or the N-terminal domain of Aβ and peptides are eluted from the antibody by formic acid and then digestion (see para. [0060]). West does not explicit teach the fragments are separated from matrix by precipitation. However, West does teach using formic acid to separate the targeted peptides. Therefore, it would have been obvious to have used formic acid to extract and separate the fragments for detection, as West teaches the claimed peptide sequences.
With respect to claim 38, as stated above, West teaches formic acid (see para. [0060]).
With respect to claim 44, West teaches the calculated concentration of one or more biomolecules of interest may be compared to the concentration of the same biomolecules in a corresponding normal sample, to the concentration of the same biomolecules in a subject of known neurological or neurodegenerative disease state, to the concentration of the same biomolecules from the same subject determined at an earlier time (see last sentence of para. [0065]).
With respect to claim 45, West teaches the neurological or neurodegenerative disease is Alzheimer’s Disease (see para. [0069]).
Claims 39-43 and 92 are rejected under 35 U.S.C. 103 as being unpatentable over West et al. in view of Schmitt et al., as applied to claim 1 above, and further in view of Kjellstrom et al. (“In Situ Liquid-Liquid Extraction as a Sample Preparation Method for Matrix-Assisted Laser Desorption/Ionization MS Analysis of Polypeptide Mixtures”, Anal. Chem., vol. 75, 2362-2369, published 2003).
With regard to claims 39-43 and 92, West and Schmitt have been discussed in the above rejection. However, the references do not teach the fragments are further extracted by liquid-liquid extraction with an organic solvent (claim 39), wherein the organic solvent is ethyl acetate or a combination of the claimed solvents (claims 40 and 41) and further extracted using a liquid-liquid aqueous two-phase system (ATPS) (claims 42-43 and 92).
Kjellstrom teaches liquid-liquid extraction (LLE) procedure was investigated for preparation of peptide and protein samples for mass spectrometry and using ethyl acetate as the water-immiscible organic solvent enabled segregation of hydrophobic and hydrophilic polypeptides in mixtures, thereby reducing the complexity of mass spectra obtained (see abstract). Kjellstrom teaches to investigate sample preparation methods that have the potential to improve the detection efficiency for specific classes of peptides and proteins based on their inherent physicochemical properties and liquid-liquid extraction takes advantage of the hydrophobic character of the molecules to segregate them into a two-phase system consisting of an aqueous phase water and an organic phase immiscible with water (see pg. 2363, right col., middle of para). Kjellstrom teaches LLE is a separation method that uses water-immiscible organic solvents for selective extraction and can be used in sample preparation methods for extracting peptides from biological samples to a hydrophobic phase (see right col., para. 1 of pg. 2364). Kjellstrom teaches ethyl acetate as the organic solvent (see pg. 2365, left col., para. 2). Kjellstrom also teaches performing the methods for analysis of peptide mixtures generated by proteolytic cleavage of proteins (see pg. 2366, left col., para. 3). Kjellstrom teaches the performance of the approach was demonstrated using a tryptic digest of β=casein that was extracted according to LLE (see pg. 2366, left col., last para and Table 1). Kjellstrom teaches that LLE is a fast and efficient sample preparation method when proteins and peptides are available in soluble form (see pg. 2368, right col., last para.). Kjellstrom teaches a number of different water-immiscible organic solvents can be used in liquid-liquid extraction such as chloroform, diethyl ether, and hexane (see pg. 2365, left col., para. 2). Kjellstrom also teaches a three-phase extraction (see pg. 2367, left col., last para.).
It would have been obvious to the person to have incorporated isolating peptide fragments of interest as taught by West and Schmitt with liquid-liquid extraction as taught by Kjellstrom because Kjellstrom teaches that liquid-liquid extraction is a separation method to selectively extract peptides from sample preparation methods, which reduces the complexity of mass spectra obtained. In particular, Kjellstrom teaches to improve the detection efficiency for specific classes of peptides based on their inherent physicochemical properties and liquid-liquid extraction takes advantage of characteristics of the molecules to segregate them into a two-phase system consisting of an aqueous phase water and an organic phase immiscible wherein the organic phase includes ethyl acetate. Therefore, it would have been obvious to have used the two-phase system extraction of Kjellstrom to separate the targeted peptides which reduces the complexity of mass spectra readouts.
The person would have reasonably expected success in using liquid-liquid extraction with the peptides because it has been well understood in the art to selectively extract peptides with recognized organic solvents, as taught by Kjellstrom.
With regard to claim 41, although Kjellstrom teaches chloroform, diethyl ether, hexane, and ethyl acetate (see pg. 2365, left col., para. 2), the reference does not teach the organic solvent is a combination of two or more organic solvents. However, it would have been obvious to the person to use different organic solvents for liquid-liquid extraction because Kjellstrom teaches a possible three-phase extraction are used with the recognized solvents.
With regard to claims 43 and 92, the claims recite “may be extracted using an ATPS consisting of…” would be interpreted as optional and thus the limitations are not required.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 1-3, 7, 24, 27-29, 35-38, 44-46 and 91 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. US10481167B2 (‘167) in view of West et al. (US2012/0015371A1, published 01/19/2012) and Schmitt et al. (US2016/0138066A1, published 05/19/2016).
With respect to instant claims 1, 46, and 91, Claim 1 of Patent ‘167 recites a method of determining the absolute concentration of an amyloid-beta protein (Aβ), or digestion product thereof in a subject, comprising: (a) metabolically labeling the endogenous Aβ protein isoform or digestion product thereof by administering at least one labeled moiety to the subject, wherein the at least one labeled moiety metabolically incorporates into the endogenous Aβ protein isoform or digestion product thereof; (b) contacting a biological sample obtained from the subject with a Quantitation Standard (QS) comprising a known concentration of a biomolecule labeled with two labeled moieties such that the labeled QS has a molecular weight that differs from the metabolically labeled endogenous Aβ protein isoform or digestion product thereof, wherein the QS is an Aβ peptide, wherein the biological sample comprises a metabolically labeled fraction of the endogenous Aβ protein isoform, variant or digestion product thereof and an unlabeled fraction of the Aβ protein, isoform or digestion product thereof; (c) isolating the metabolically labeled, the unlabeled and the labeled QS forms of Aβ protein isoform or digestion product thereof from the biological sample using a detergent to increase the labeled Aβ, unlabeled Aβ peptides and QS solubility; (d) maintaining the labeled Aβ, unlabeled Aβ peptides and QS in a reduced state to increase said peptides detection; (e) subjecting the labeled Aβ, unlabeled Aβ peptides and QS to mass spectroscopy analysis; and (f) calculating the absolute concentration of the endogenous, metabolically labeled and unlabeled, Aβ protein isoform, variant or digestion product thereof using the known concentration of Aβ protein isoform or digestion product in the labeled QS. Claim 3 Patent recites the labels moieties are selected from 15N. Claim 4 Patent recites isoform or digestion product thereof is labeled with a labeled amino acid. Claim 15 recites the biomolecule is Aβ1-40 or Aβ1-42.
Patent ‘167 does not recite the instant claimed SEQ ID NO:5 or SEQ ID NO: 7 and digesting the labeled and unlabeled Aβ40 and Aβ42 peptides with cyanogen bromide, thereby obtaining labeled and unlabeled Aβ peptide fragments.
West and Schmitt have been discussed in the above rejection. It would have been obvious to the person at the time of filing the claimed invention to have determined the concentration of Aβ isoform or digestion product as recited in the Patent with the sequences of West because West exemplifies the claimed Aβ1-40 and Aβ1-42 sequences (i.e., as instant claims) that are digested and quantified through mass spectrometry with the Quantitation Standard containing labeled isoform peptides. Additionally, West’s sequences contain a single methionine residue. Therefore, it would have been obvious to have incorporated the process of determining the concentration of the Aβ digestion product as recited in the Patent with cyanogen bromide as taught by Schmitt because Schmitt teaches that peptide cleavage such as CNBr cleaving C-terminal to methionine residues is well recognized in the art. Because the Patent recites digestion of Aβ isoform (i.e., cleaved) for mass spectrometry measurements while maintaining in the reduced state to increase said peptide detection, it would have been obvious to the person to have used CNBr to produce a distinctive peptide segment by cleaving the only methionine residue of said sequences and maintaining in the peptides in a reduced state.
The person would have reasonably expected success in using the process of determining Aβ isoforms or digestion with Quantitation Standard of the Patent with West’s sequences because it has been well understood that Quantitation Standard is used to measure Aβ peptides.
With respect to instant claim 2, the claim 8 Patent recites wherein calculating the concentration of the unlabeled endogenous biomolecule comprises multiplying the concentration of the Quantitation Standard with the determined ratio of unlabeled endogenous biomolecule to the Quantitation Standard.
With respect to instant claim 3, the Patent does not explicit recite further comprising normalizing the calculated concentration to a standard curve, wherein the standard curve is generated by determining two or more ratios of unlabeled Aβ peptide fragments to the Quantitation Standard, wherein the concentration of the unlabeled Aβ peptide fragments is known. West teaches normalizing the calculated concentration to a standard curve, wherein the standard curve is generated by determining two or more ratios of unlabeled Aβ peptide fragments to the Quantitation Standard, wherein the concentration of the unlabeled Aβ peptide fragments is known (see para. [0056]). It would have been obvious to have normalized the process with the standard curve for adjustment is values.
With respect to instant claim 7, claim 5 Patent recites the biomolecule is in a subject of known neurological or neurodegenerative disease state.
With respect to instant claim 24, the Patent does not explicit recite the sample is contacted with two or more Quantitation Standards and the concentrations of two or more unlabeled Aβ peptide fragments are calculated. West teaches the methods further include the step of normalizing the calculated concentration to a standard curve based on the curve fitting equation generated by the standard curve and the standard curve used herein is generated by determining two or more ratios of unlabeled biomolecules to their respective Quantitation Standards, where the concentration of the unlabeled biomolecule of interest is known (see para. [0056]). It would have been obvious to have calculated with multiple values for a more accurate result.
With respect to instant claim 27, claim 15 Patent recites Aβ1-40 and Aβ1-42 peptides. However, the Patent does not recite the Aβ peptide fragments are post-translationally modified Aβ peptide fragments. West teaches the claimed sequences (see above). As stated above, it would have been obvious to have used West’s peptide sequences because the reference exemplifies the claimed sequences with Quantitation Standard.
With respect to instant claim 28, claim 12 Patent recites cerebral spinal fluid (CSF).
With respect to instant claim 29, claim 4 Patent recites amyloid-beta protein (Aβ).
With respect to instant claims 35 and 36, the Patent does not recite the fragments specific C-terminal fragments are separated by liquid or gas chromatography before concentration is determined. West teaches isolate the C-terminal isoforms of Aβ from a biological sample and liquid chromatography mass spectrometry (see paras. [0048] and [0060]). It would have been to have separated the fragments through liquid chromatography before mass spectrometry because it has been recognized in the art to isolate the peptides before mass spectrometry.
With respect to instant claims 37 and 38, the Patent does not explicit recite separated by precipitation with the claimed chemical reagent. West teaches formic acid (see above). It would have been obvious to have used formic acid because the Patent recites digestion product, which requires extract and West teaches formic acid will extract and preserve the peptide for detection.
With respect to instant claim 44, claim 5 Patent recites further comprising comparing the concentration of the unlabeled endogenous amyloid-beta protein (Aβ), isoform, variant or digestion product thereof to the concentration of the same biomolecule in a corresponding normal sample, to the concentration of the same biomolecule in a subject of known neurological or neurodegenerative disease state, to the concentration of the same biomolecule from the same subject determined at an earlier time, or any combination thereof.
With respect to instant claim 45, claim 6 Patent recites wherein the neurological or neurodegenerative disease is selected from the group consisting of Alzheimer's Disease, Parkinson's Disease, stroke, frontal temporal dementias (FTDs), Huntington's Disease, progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), aging-related disorders and dementias, Multiple Sclerosis, Prion Diseases, Lewy Body Disease, Pick's Disease, motor neuron diseases, restless leg syndrome, seizure disorders, tremors, depression, mania, anxiety disorders, brain trauma or injury, narcolepsy, sleep disorders, autism, normal pressure hydrocephalus, pain disorders or syndromes, migraines, headaches, spinocerebellar disorders, muscular dystrophies, myasthenia gravis, retinal degeneration, and Amyotrophic Lateral Sclerosis.
Claims 39-43 and 92 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. US10481167B2 (‘167) in view of West et al. and Schmitt et al., as applied to claim 1 above, and further in view of Kjellstrom et al. (“In Situ Liquid-Liquid Extraction as a Sample Preparation Method for Matrix-Assisted Laser Desorption/Ionization MS Analysis of Polypeptide Mixtures”, Anal. Chem., vol. 75, 2362-2369, published 2003).
Patent No. ‘167, West and Schmitt have been discussed in the above rejection but fail to recite or teach the fragments is further extracted by liquid-liquid extraction with the claimed organic solvents (see claims 39-43). Kjellstrom has also been discussed above.
It would have been obvious to the person to have incorporated determining and isolating peptide fragments of interest as recited in the Patent and taught by West and Schmitt with liquid-liquid extraction as taught by Kjellstrom because Kjellstrom teaches that liquid-liquid extraction is a separation method to selectively extract peptides from sample preparation methods, which reduces the complexity of mass spectra obtained. In particular, Kjellstrom teaches to improve the detection efficiency for specific classes of peptides based on their inherent physicochemical properties and liquid-liquid extraction takes advantage of characteristics of the molecules to segregate them into a two-phase system consisting of an aqueous phase water and an organic phase immiscible wherein the organic phase includes ethyl acetate. Therefore, it would have been obvious to have used the two-phase system extraction of Kjellstrom to separate the targeted peptides which reduces the complexity of mass spectra readouts.
The person would have reasonably expected success in separating the target peptides through a two-phase system because it has been well recognized to separate peptide sample through liquid-liquid extraction for mass spectrometry.
With respect to instant claim 41, it would have been obvious to the person to use different organic solvents for liquid-liquid extraction because Kjellstrom teaches a possible three-phase extraction are used with the recognized solvents.
With respect to instant claims 43 and 92, the claims recite “may be extracted using an ATPS consisting of…” would be interpreted as optional and thus the limitations are not required.
Response to Arguments
Applicant's arguments filed 11/11/2025 have been fully considered but they are not persuasive under the 35 U.S.C. 103 rejections and the nonstatutory double patenting rejections.
Applicant argues on pages 10-12 that Schmitt (secondary reference) not does cure the deficiencies of the primary reference (West). Applicant argues that Schmitt discusses the confirmation of the identify of the cleaved peptides using mass spectrometry, Schmitt does not disclose or suggest the use of CNBr as suitable for the preparation of a sample for quantitative mass spectrometry analysis. Schmitt describes a method in which, before the digestion of the fusion protein by CNBr. Schmitt is completely silent about the effects of those steps by quantitative mass spectrometry. There is no indication in Schmitt that the sample handling and preparation and notably use of CNBr yields a sample that is suitable for quantitative mass spectrometry analysis. Additionally with respect to Kjellstrom, Applicant argues on page 12 that Kjellstrom does not cure the deficiencies because Kjellstrom is silent about CNBr digestion of protein/peptide samples for quantitative mass spectrometry analysis.
The arguments are not found persuasive for the following reasons. As stated in the rejection above, that West teaches the claimed quantitative mass spectrometry analysis and the claimed sequences of SEQ ID NO: 5 and SEQ ID NO:7. As stated above, Schmitt teaches that cyanogen bromide has been well recognized in the literature to cleave methionine residues. It would have been obvious because West teaches the claimed peptide sequences (i.e., instant SEQ ID NOs: 5 and 7) contain a single methionine residue and once the peptides are cleaved, it has to be maintained in the reduced state due to the single methionine residue, which is prone to oxidative damage. Because West teaches producing distinct peptide segments through peptide cleavage for mass spectrometry measurements and the single methionine residue is known to be damaged, it would have been obvious to the person to have used CNBr to produce a distinctive peptide segment by cleaving the only methionine residue of said sequences which eliminates the need to maintain the peptide segments (e.g., 29-x peptides) in the reduced state. In other words, West provides a blueprint and motivation to cleave the methionine residue and CNBr has been well recognized in the literature for cleaving methionine from peptides. Therefore, the 103 rejections are maintained.
With respect to the nonstatutory double patenting rejections, Applicant argues that the rejections be held in abeyance until claims are determined allowable.
The argument is not found persuasive because without a terminal disclaimer or amendments to overcome the rejections, the nonstatutory double patenting rejections are maintained.
Conclusion
No claim is allowed.
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/N.P.N/Examiner, Art Unit 1678
/SHAFIQUL HAQ/Primary Examiner, Art Unit 1678