DETAILED ACTION
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 .
Claim Status
Claims 1-23 are pending and under examination.
Claims 1-23 are rejected.
Claims 1, 3, 12, and 14 are objected to.
No claims are allowed, amended, canceled, new, or withdrawn.
Claims 1 and 12 are independent.
Office Action Outline
Rejections applied
Abbreviations
x
112/b Indefiniteness
PHOSITA
"a Person Having Ordinary Skill In The Art before the effective filing date of the claimed invention"
112/b "Means for"
BRI
Broadest Reasonable Interpretation
112/a Enablement,
Written description
CRM
"Computer-Readable Media" and equivalent language
112 Other
IDS
Information Disclosure Statement
x
102, 103
JE
Judicial Exception
x
101 JE(s)
112/a
35 USC 112(a) and similarly for 112/b, etc.
101 Other
N:N
page:line
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed in the 10/03/2022 filing receipt, this application claims priority to U.S. Provisional Application 63/408,987, filed 09/22/2022.
Specification
The disclosure is objected to because Specification paragraphs [0087], [0088], and [0089] contain embedded hyperlinks and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlinks and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Drawings
The 09/21/2023 drawings are objected to as failing to comply with 37 CFR 1.84(u) as follows: The drawings on pages 6/9, 7/9, 8/9, and 9/9 respectively recite "FIG. 4," "FIG. 4 (continued)," "FIG. 5," and "FIG. 5 (continued)." Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter (see MPEP 608.02(V) and 37 C.F.R. 1.84(u)).
It is suggested to amend pages 6/9, 7/9, 8/9, and 9/9 to respectively recite "FIG. 4A," "FIG. 4B," "FIG. 5A," and "FIG. 5B."
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 1, 3, 12, and 14 are objected to because of the following informalities:
Claims 1 and 12 recite a mass spectrometer ("MS")/liquid chromatography-mass spectrometer ("LC-MS"), in which the quotes around the abbreviations for MS and LC-MS are unnecessary, and should be deleted.
Similarly, claims 3 and 14 recite Markov Chain Monte Carlo ("MCMC") method, in which the quotes around the abbreviations for MCMC are unnecessary, and should be deleted.
Appropriate correction is required.
Claim Interpretation
Claims 1, 6, 12, and 18 recite the terms "quantification consistency parameters" and/or "quantified consistency parameters." These terms are being interpreted as including retention time (tR), profile (peak shape), relative abundance, etc., as discussed in Specification paragraph [0060].
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-23 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. Claims depending from rejected claims are rejected similarly, unless otherwise noted, and any amendments in response to the following rejections should be applied throughout the claims, as appropriate.
Claims 1 and 12 recite "a mass spectrometer ("MS")/liquid chromatography-mass spectrometer ("LC-MS") instrument" in which the order of the terms makes it unclear as to if the claim should be interpreted as an "MS/LC-MS instrument," or interpreted as an "MS or LC-MS instrument", or should be interpreted as an "LC-MS/MS instrument." For examination purposes, the claim will be interpreted as an MS or LC-MS instrument as in Specification paragraphs [0007, 0027, 0035, 0036].
The following bolded terms in the recitations below require but lack clear antecedent. If the bolded recitations refer to previously instantiated instances, then it is not clear which instances those are. If the bolded recitations instantiate the claim elements, this is not clear. (Bold emphasis added by the examiner.)
• "the presence, absence, or modulation of one or more factors of the one or more samples against a decision criterion" (claims 1 and 12)
• "applying the learning model to an unknown sample to detect the presence, absence, or modulation of the one or more factors in the unknown sample" (claims 1 and 12)
• "the presence, absence, or modulation of a disease state or multiple disease states" (claims 2 and 13)
• "the degree of misfit" (claims 8 and 20)
• "the group consisting of consistency" (claims 8 and 20)
These rejections might be overcome by for example amending "the" to "a" or by simply deleting "the" from the limitation lacking clear antecedent.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-23 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
MPEP 2106 details the following framework to analyze Subject Matter Eligibility:
• Step 1: Are the claims directed to a category of statutory subject matter (a process, machine, manufacture, or composition of matter)? (see MPEP § 2106.03)
• Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. an abstract idea, a law of nature, or a natural phenomenon? (see MPEP §§ 2106.04(a), 2106.04(a)(2), and 2106.04(b)).
• Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application? (see MPEP § 2106.04(d))
• Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept? (see MPEP § 2106.05)
Step 1:
Claims 1-11 are directed to a 101 machine or manufacture, here a MS/LC-MS instrument. Claims 12-23 are directed to a 101 process, here a method. As such, claims 1-23 are directed to a related instrument and method, which fall under categories of statutory subject matter. (See MPEP § 2106.03). (Step 1: Yes.)
Step 2A, Prong One:
The claims are found to recite a judicial exception (JE) of abstract ideas in the form of mental processes and mathematical concepts as follows:
Independent claims 1 and 12 recite mental processes and mathematical concepts of:
• quantifying consistency parameters
• assigning criteria
• determining probability ratios
• constructing a learning model quantitation step
• weighing the presence, absence, or modulation of one or more factors of the one or more samples against a decision criterion for positivity
• applying the learning model to an unknown sample
Claims 3 and 14 recite mental processes and mathematical concepts of nested sampling and/or a Markov Chain Monte Carlo method.
Claims 5 and 17 recite mental processes and mathematical concepts of leave-one-out cross-validation.
Claims 6 and 18 recite mental processes and mathematical concepts of quantifying peak detection results.
Claims 7 and 19 recite mental processes and mathematical concepts of the peak detection results are determined from a ranking scheme of chromatographic peaks..
Claims 8 and 20 recite mental processes and mathematical concepts of selecting components of distance, reflecting the degree of misfit of various aspects of the chromatographic peaks, from the group consisting of consistency of retention time placement, peak width, and peak area.
Claims 9 and 21 further limit the raw chromatographic data.
Claims 10 and 22 further limit the samples.
Claims 11 and 23 recite mental processes and mathematical concepts of determining one or multiple disease states based on the presence or absence of the one or more factors in the unknown sample.
Claims 2 and 13 further limit the one or more factors respectively of claims 1 and 12.
Step 2A Prong One Summary: The claims recite mental processes and mathematical concepts. When considering the broadest reasonable interpretation (BRI) of the claims, the mental processes recited in the claims (e.g., "quantifying consistency parameters," "assigning criteria," "determining probability ratios," etc.) are directed to processes that may be performed in the human mind, or with pen and paper, as there are no particular limitations recited in the claims which would prevent the mental processes from being performed in the human mind or with pen and paper. The claims recite inherent mathematical processes in e.g., determining probability ratios, using nested sampling or MCMC model, performing leave-one-out cross-validation, etc) these concepts are discussed throughout the Specification, e.g., at paragraphs [0011, 0012, 0041, 0043-0049, 0066, 0067, 0071, etc.]. Although claims 1-11 recite a processing device for executing computer readable instructions, a claim that requires a computer may still recite a mental process [see MPEP 2106.04(a)(2)(III)(C)]. Further, although a general-purpose computer can perform the analysis at a rate and accuracy that can far exceed the mental performance of a skilled artisan, the nature of the activity is essentially the same, and therefore constitutes an abstract idea. Therefore, the claims recite elements that constitute a judicial exception in the form of abstract ideas (Step 2A, Prong One: Yes.)
Step 2A, Prong Two:
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs). Here at Step 2A, Prong Two, any remaining steps and/or elements not identified as JEs are therefore in addition to the identified JE(s), and are considered additional elements. Because the claims have been interpreted as being directed to judicial exceptions (abstract ideas in this instance) then Step 2A, Prong Two provides that the claims be examined further to determine whether the judicial exception is integrated into a practical application [see MPEP § 2106.04(d)]. A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception.
MPEP § 2106.04(d)(I) lists the following five example considerations for evaluating whether a judicial exception is integrated into a practical application:
(1) An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a).
(2) Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2).
(3) Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b).
(4) Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c).
(5) Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
The claims recite additional elements as follows:
Additional elements of data gathering, inputting, and outputting steps: Collecting raw chromatographic data from samples (claims 1, 4, 10-12, 15, and 22-23). Data gathering steps are additional elements which perform functions of inputting, collecting, and outputting the data needed to carry out the abstract idea. These steps are considered insignificant extra-solution activity, and are not sufficient to integrate an abstract idea into a practical application as they do not impose any meaningful limitation on the abstract idea or how it is performed, nor do they provide an improvement to technology (see MPEP § 2106.04(d)(I)).
Additional elements of an MS or LC-MS instrument and computer components: An MS or LC-MS instrument, a processing device, and computer readable instructions (claim 1). The claims require only generic analytical instruments and computer components, which do not improve analytical or computer technology, and do not integrate the recited judicial exception into a practical application (see MPEP § 2106.04(d)(1) and MPEP § 2106.05(f)).
Step 2A Prong Two summary: The claims have been further analyzed with respect to Step 2A, Prong Two, and no additional elements have been found, alone or in combination, that would integrate the judicial exception into a practical application. At this point in examination, it is not yet the case that any of the Step 2A Prong Two considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of: (1) an improvement, (2) a treatment, (3) a particular machine, or (4) a transformation is clear in the record. For example, regarding the first consideration for improvement at MPEP 2106.04(d)(1), the record, including the Specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field, and the claims do not yet clearly result in such an improvement. (Step 2A, Prong Two: No).
Step 2B analysis:
Because the additional claim elements do not integrate the abstract idea into a practical application, the claims are further examined under Step 2B, which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept. An inventive concept is furnished by an element or combination of elements that is recited in the claim in addition to the judicial exception, and is sufficient to ensure that the claim, as a whole, amounts to significantly more than the judicial exception itself (see MPEP § 2106.05).
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are well-understood, routine, and conventional. Those additional elements are as follows:
Additional elements of data gathering, inputting, and outputting steps: The additional elements of collecting raw chromatographic data from samples (claims 1, 4, 10-12, 15, and 22-23). does not cause the claims to rise to the level of significantly more than the judicial exception. The courts have recognized receiving or transmitting data over a network; storing and retrieving information in memory; determining the level of a biomarker in blood by any means; [see MPEP§2106.05(d)(II)], as well-understood, routine, conventional activity when they are claimed in a merely generic manner (e.g., at a high level of generality) or as extra-solution activity.
Additionally, the collecting raw chromatographic data from samples is shown to be conventional by the following reference:
Campanale (TrAC Trends in Analytical Chemistry, vol. 144 (2021):116423, pages 1-16; cited on the 09/22/2023 IDS) shows LC-MS/MS of samples (p.10-11).
Additional elements of an MS or LC-MS instrument and computer components: The additional elements of an MS or LC-MS instrument, a processing device, and computer readable instructions in claim 1 do not cause the claims to rise to the level of significantly more than the judicial exception, and as such do not provide an inventive concept; these are conventional MS or LC-MS instruments and computer components.
Additionally, Campanale (cited above) shows LC-MS/MS (p.10-11).
All limitations of claims 1-23 have been analyzed with respect to Step 2B, and none provides a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception, and thus do not transform the judicial exception into a patent eligible application of the exceptions. Step2B: NO.
Therefore, the claims, when the limitations are considered individually and as a whole, are rejected under 35 U.S.C. § 101 as being directed to non patent-eligible subject matter.
Claim Rejections - 35 USC § 103
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.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-23 are rejected under 35 U.S.C. 103 as being unpatentable over Tuli (Journal of proteomics & bioinformatics, vol.2, p.416-438 (2009); cited on the attached form PTO-892), in view of Martínez-Bartolomé (Mol Cell Proteomics, vol. 7(6), pp.1135-1145 (2008); cited on the attached form PTO-892), in view of Banerjee (Cancer Informatics, vol. 14: CIN-S30798, pages 175-182 (2015); cited on the attached form PTO-892).
Regarding claim 1 and 12, the recited mass spectrometer (MS)/liquid chromatography-mass spectrometer (LC-MS) instrument for collecting raw chromatographic data of analytes from samples reads on the "Basic LC-MS system and different kinds of chromatography" (Tuli, p.420, fig.1).
Regarding claim 1 and 12, the recited quantifying consistency parameters from the raw data reads on "peak intensities or peak areas (are) used to relatively quantify protein samples." (Tuli, bridging p.426-427.
Regarding claim 1 and 12, the recited constructing a learning model based on the quantified consistency parameters comprising weighing factors for positivity reads on an "approach has been used in a supervised way (e.g., partial least squares, PLS), where the recited training examples with known disease status are used to calculate the factor...The weight plot obtained from this PLS analysis provides a tool to select useful peaks" (Tuli, p.433, col.1, ¶ 3).
Regarding claim 1 and 12, the recited applying the learning model to a sample to detect one or more factors in the sample reads on "an approach has been used in a supervised way (e.g., partial least squares, PLS), where the recited training examples with known disease status are used to calculate the factors... The weight plot obtained from this PLS analysis provides a tool to select useful peaks." (Tuli, p.433, col.1, ¶ 3.)
Regarding claim 2 and 13, the recited factors describe the presence, absence, or modulation of a disease state reads on an "approach has been used in a supervised way (e.g., partial least squares, PLS), where the recited training examples with known disease status are used to calculate the factor." (Tuli, p.433, col.1, ¶ 3.)
Regarding claim 4 and 15, the recited analytes run simultaneously or sequentially reads on "When coupled to LC, peptides separated continuously can be examined sequentially." (Tuli, p.422, col.2, ¶ 2.)
Regarding claim 5 and 16-17, the recited eave-one-out cross-validation (cross-validation in claim 16) reads on "In k-fold cross-validation, ...if k equals the sample size, this is called “leave-one-out” cross-validation. In the leave-one-out method, one sample is selected as a validation sample and feature selection and classifier building are performed using the remaining data set." (Tuli, p.434, col.1, ¶ 2.)
Regarding claim 6 and 18, the recited quantifying peak detection results reads on "Comparison based on peak intensities or peak areas is used to relatively quantify protein samples." (Tuli, bridging p.426-427.)
Regarding claim 7 and 19, the recited ranking scheme of chromatographic peaks; and regarding claim 8 and 20, the recited ranking scheme comprises components of distance reflecting the degree of misfit of various aspects of consistency of retention time placement, peak width, and peak area reads on "The peaks are then ranked by their shrinkage t-statistic for the permutation. This process is repeated for a large number of permutations. Consequently, for any threshold, we compute the distribution of the number of peptides/glycans that would have t-statistic better than that threshold for permutations." (Tuli (p.433, col.1, ¶ 4.)
Regarding claim 9 and 21, the recited raw chromatographic data includes retention times and relative abundances reads on "Peptide ion intensity method measures peptide ion intensity by integrating area under the curve and comparing them for their relative abundance" and "Comparison of ion intensities, is a method where LC-MS runs are compared to identify differentially abundant ions at specific m/z and retention time (RT) points." (Tuli (p.428, col.2,
¶ 1.)
Regarding claim 10 and 22, the recited samples comprise of endogenous or isotopically labeled analytes reads on "Based on the introduction of stable isotope labels into analytes, isotope labeling is categorized as metabolic (in vivo or culture) and chemical (in vitro)." (Tuli, p.426, col.2.)
Regarding claim 11 and 23, the recited determining a disease state based on presence or absence of a factor in the sample reads on "an approach has been used in a supervised way (e.g., partial least squares, PLS), where the recited training examples with known disease status are used to calculate the factors... The weight plot obtained from this PLS analysis provides a tool to select useful peaks." (Tuli, p.433, col.1, ¶ 3.)
While Tuli shows quantifying consistency parameters from the raw data of claims 1 and 12, Tuli does not show assigning criteria and determining probability ratios f claims 1 and 12 (shown by Martínez-Bartolomé).
While Tuli shows the learning model, Tuli does not specifically shows the unknown sample of claims 1, 11-12, and 23 (shown by Banerjee).
Tuli does not show the Markov Chain Monte Carlo (MCMC) method of claims 3 and 14 (shown by Banerjee).
Regarding claim 1 and 12, the recited quantifying consistency parameters from the raw data by assigning criteria and determining probability ratios reads on "a mathematical analysis of SEQUEST average score distributions (was performed) and the behavior and properties of these distributions (was analyzed)....Using this mathematical framework we make inferences about the dependence of these distributions on database size and use the concept of probability ratio as a statistical indicator to take into account the information provided by the best and second best scores." (Martínez-Bartolomé, p.1136, col.2, ¶ 2), and "Filtering of SEQUEST outputs has traditionally been done using the parameters Xcorr and ΔCn by establishing empirically a set of criteria. Because it has been described that these criteria do not usually provide enough discriminative power to be used universally on any data set, alternative filtering criteria have been developed based on the distribution of SEQUEST scores and/or machine learning algorithms to achieve better separation between correct and incorrect assignments (Martínez-Bartolomé, p.1135, col.2, ¶ 2).
Regarding claim 1, 11-12, and 23, the recited unknown sample reads on "a large synthetic test set containing 1000 sample points." (Banerjee, p.180, col.2, ¶ 3.)
Regarding claim 3 and 14, the recited nested sampling and/or a Markov Chain Monte Carlo (MCMC) method reads on "the ABC method (was) implemented via an MCMC procedure to obtain samples from the posterior distribution of the protein concentrations in order to derive the ABC-MCMC classifier for LC-MS data." (Banerjee, p.177, col.2, ¶ 2.)
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the methods and instruments for LC-MS based data analysis of Tuli with the SEQUEST method for probability ratio and assigning criteria of Martínez-Bartolomé, and with the MCMC classifier of Banerjee. This is because the method of Martínez-Bartolomé for MS spectra analysis leads to a novel, robust indicator, the probability ratio, which takes optimally into account the statistical information provided by the first and second best scores. The MCMC classification rule of Banerjee outperforms classical methods.
One of ordinary skill in the art would have understood how to and been motivated to modify Tuli with Martínez-Bartolomé and Banerjee, to result in a robust method and system for classifying LC-MS data. One would have had a reasonable expectation of success in doing so because Tuli, Martínez-Bartolomé, and Banerjee are generally drawn to related teaching of analysis and classification of LC-MS data, and as such, the combination would have been obvious.
Conclusion
No claims are allowed.
This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Meredith A Vassell whose telephone number is (571)272-1771. The examiner can normally be reached 8:30 - 4:30.
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/M.A.V./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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