DETAILED ACTION
The amendment and RCE filed on 12/10/2025 has been entered and fully considered. Claims 1-14, 16-18 and 20-22 are pending, of which claims 1, 9 and 20 are amended.
Response to Amendment
In response to amendment, the examiner maintains rejections under 101, 112b, and 103 established in the previous Office 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 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.
Claim 1-14 and 16 are rejected under 35 U.S.C. 101 the claimed invention is directed to abstract idea without significantly more.
Claim 1 is drawn to a method for estimating the molecular complexity of a sample.
The preamble and limitation “(c) calculating the molecular assembly index of the sample by scaling the number of unique peaks in the resulting MS2, NMR or IR spectrum by a magnitude (m)” of the claim 1 are focused on mental calculation without a practical application. As such, the claimed invention recites estimating the molecular complexity, which is an abstract idea. The claim remains directed to collecting data, analyzing the data, and reporting a numerical result, with the added limitation of a linear scaling factor. Such an amendment does not integrate the abstract idea into a practical application or add significantly more.
Limitation “(a) performing one of MS/MS, NMR or IR on a sample; (b) determining the unique peaks in the resulting MS2 spectrum for a parent ion in the MS1 spectrum, NMR spectrum, or IR spectrum” is routine data gathering steps.
This judicial exception is not integrated into a practical application. Considering claim 1 as a whole, none of the additional elements applies or uses the abstract idea in a meaningful way such that the claim as a whole is more than a drafting effort designed to monopolize the exception.
The additional elements recited in claim 1 do not "contain an 'inventive concept' sufficient to 'transform' the claimed abstract idea into a patent-eligible application." Alice, 573 U.S. at 221 (internal quotation marks omitted), or "include 'additional features' to ensure 'that the [claim] is more than a drafting effort designed to monopolize the [abstract idea]."' Id. (alterations in original) (quoting Mayo, 566 U.S. at 77). Instead, claim 1 merely recites well-understood, routine, or conventional activity in the field previously known to the industry, specified at a high level of generality, to the abstract idea.
The claim recites steps of:
collecting data (performing MS/MS, NMR, or IR on a sample);
analyzing data (determining unique peaks in the resulting spectrum); and
mathematically processing the data (scaling the number of peaks by a magnitude (m) to calculate an index).
The focus of the claim is on analyzing data from a measurement and performing a mathematical calculation (the molecular assembly index). Such concepts fall within the category of mathematical concepts and mental processes, which are judicial exceptions to § 101.
The additional elements (performing MS/MS, NMR, or IR on a sample) are recited at a high level of generality and are well-understood, routine, and conventional activities in the field of analytical chemistry. Merely applying a mathematical concept to the results of routine measurement techniques does not integrate the judicial exception into a practical application.
Functional language disclaiming “external input” does not convert an abstract data analysis into a patent-eligible application.
The claim does not improve the functioning of a computer, spectrometer, or other technology. Nor does it effect a transformation of matter beyond obtaining and analyzing data. Instead, the claim is directed to using known instruments to generate data and then applying a mathematical calculation to that data, which is insufficient to qualify as a practical application.
Accordingly, claim 1 is directed to an abstract idea without significantly more and is therefore ineligible subject matter under 35 U.S.C. § 101.
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.
Claim 1-10, 12-14 and 16 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.
1. Indefiniteness of “molecular assembly index”
Claim 1 recites:
“calculating the molecular assembly index of the sample by scaling the number of unique peaks … by a magnitude (m)”
The term “molecular assembly index” is indefinite because the claim fails to provide objective boundaries for determining what constitutes the index.
Although the claim states that the index is obtained by “scaling” the number of unique peaks, the claim does not specify:
whether the scaling is linear or non-linear;
whether the magnitude (m) is fixed, variable, empirically determined, or arbitrarily selected;
whether different values of (m) result in different molecular assembly indices for the same sample; or
whether two different practitioners using different values of (m) would arrive at the same or different claimed “molecular assembly index.”
As a result, multiple materially different calculations fall within the scope of the claim, and one of ordinary skill in the art cannot determine, with reasonable certainty, when a calculated value qualifies as the claimed molecular assembly index and when it does not.
See Nautilus, Inc. v. Biosig Instruments, Inc., 572 U.S. 898, 910 (2014).
2. Indefiniteness of the magnitude “(m)”
Claim 1 recites scaling by a magnitude “(m)” but provides no constraints on the magnitude.
The claim does not specify:
a numerical range for (m);
whether (m) must be constant across measurements;
whether (m) is selected based on instrument type, sample type, or user preference; or
whether (m) is determined experimentally, theoretically, or arbitrarily.
Because the claim places no objective limits on (m), the scope of the claim varies depending on the subjective choice of the practitioner. This renders the claim indefinite because the metes and bounds of the claimed invention cannot be determined.
See MPEP §2173.02 (“A claim is indefinite when it depends on a variable that is not clearly defined or bounded.”).
3. Indefiniteness of “unique peaks”
Claim 1 recites:
“determining the unique peaks in the resulting MS2 spectrum … NMR spectrum, or IR spectrum”
The term “unique peaks” is indefinite because the claim does not clearly define what makes a peak “unique.”
In particular, the claim does not specify whether a “unique peak” is:
a peak distinct from noise;
a peak distinct from other peaks within a single spectrum;
a peak distinct relative to other components in a mixture;
a peak distinct relative to a reference spectrum or database; or
a peak distinct based on intensity, mass resolution, chemical shift tolerance, or frequency bandwidth.
Absent such definition, different practitioners may identify different sets of “unique peaks” from the same spectrum, leading to different molecular assembly indices for the same sample. This lack of objective criteria renders the claim indefinite.
4. Functional Language: “without external input”
Claim 1 further recites:
“wherein the method enables an estimation of the molecular complexity of the sample based on the intrinsic properties of the sample and without external input.”
This limitation is indefinite and non-limiting because it recites a result or intended advantage, rather than a clear structural or procedural limitation.
The claim does not specify what constitutes “external input,” nor does it exclude:
user-defined peak thresholds;
instrument calibration parameters;
selection of parent ions;
selection of spectral acquisition conditions; or
selection of the magnitude (m).
As such, it is unclear what steps or conditions are excluded by the phrase “without external input,” rendering the scope of the claim uncertain.
See Halliburton Energy Servs. v. M-I LLC, 514 F.3d 1244, 1255 (Fed. Cir. 2008) (functional language that fails to provide objective boundaries renders a claim indefinite).
5. Indefiniteness Due to Multiple Analytical Modalities
Claim 1 recites performing “one of MS/MS, NMR or IR,” yet applies the same definitions of “unique peaks” and “molecular assembly index” across fundamentally different analytical techniques.
The claim fails to specify:
how peaks from MS2, NMR, and IR—each governed by different physical principles—are normalized or treated equivalently;
whether the same magnitude (m) applies across all modalities; or
whether modality-specific criteria apply.
As a result, the claim encompasses multiple materially different methods without clearly defining how the claimed index is consistently determined across them.
Conclusion
For the foregoing reasons, claim 1 fails to inform those skilled in the art, with reasonable certainty, of the scope of the invention. Accordingly, the rejection of claim 1 under 35 U.S.C. § 112(b) is maintained.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim(s) 1-10, 12-14, 16-18 and 20-22 is/are rejected under 35 U.S.C. 103 as being unpatentable over Marshall et al. (ARXIV, 2017, IDS) (Marshell) in view of Merwin et al. (US 2018/0373833, IDS) (Merwin).
Regarding claim 1, Marshell teaches a method for estimating the molecular complexity of a sample (pathway complexity) (abstract), the method comprising:
(a) performing one of detection on a sample (Fig. 2, page 4-5);
(b) determining the unique peaks (unique substructures) (Fig. 2, page 4-5); and
(c) calculating the molecular assembly index of the sample based on the number of unique peaks (unique substructures) (Fig. 2, page 4-5),
wherein the method enables an estimation of the molecular complexity of the sample based on the intrinsic properties of the sample and without external input (Fig. 2, page 4-5).
Marshall discloses the core concept of quantifying the complexity of an object based on objective criteria. Specifically, Marshall teaches that complexity can be reduced to a quantifiable metric (pathway complexity) derived from features of the object itself, without requiring knowledge of the object’s function or external context (page 2, 6, 10-15). This directly corresponds to the applicant’s claimed concept of generating a molecular assembly index from features (unique peaks) of an analytical spectrum.
While Marshall does not explicitly disclose spectral peaks, Marshall’s framework teaches the general concept of deriving a complexity index from constituent features of an object.
Scaling or weighting features to generate a numerical index is a routine mathematical operation and would have been an obvious implementation choice to a person of ordinary skill in the art when applying Marshall’s complexity framework to experimentally obtained features, such as spectral peaks. For example, Merwin teaches scaling the number of unique peaks in the resulting MS2, NMR or IR spectrum by a magnitude (m) (par [0155]).
Thus, Marshall teaches the concept of calculating a complexity index from object features, and the scaling of feature counts by a magnitude represents an obvious mathematical modification.
Marshall teaches a framework for estimating the complexity of an object by analyzing features inherent to the object itself, rather than relying on external reference databases, prior classifications, or knowledge of origin or function.
1. Complexity in Marshall Is Derived from Intrinsic Structure
Marshall’s pathway complexity is determined by examining the internal composition and structure of the object—specifically, how the object can be decomposed into fundamental units and reassembled through a minimal sequence of operations.
Although Marshall uses illustrative examples (letters, shapes, graphs), the key teaching is not tied to the illustrative domain, but rather to the general principle that:
complexity is a function of the object’s intrinsic structural organization.
In Marshall, the complexity value is derived solely from the object’s internal features, not from:
reference libraries,
known identities,
biological function,
origin (natural vs synthetic), or
prior labeling.
Thus, Marshall teaches estimating complexity based on intrinsic properties of the object itself.
2. “Without External Input” Does Not Mean “Without Any Parameters”
Under patent law, selection of analytical parameters does not constitute disqualifying external input.
In Marshall:
The choice of basic units (e.g., nodes, components, primitives) is analogous to:
selecting m/z resolution,
selecting peak thresholds,
selecting fragmentation rules.
These are routine analytical design choices, not external informational inputs about the object.
Critically, Marshall does not require:
prior knowledge of the object’s identity,
external training data,
comparison to known objects, or
reference libraries.
Once the rules are set, the complexity is computed solely from the object itself, satisfying the “without external input” limitation as properly construed.
3. Marshall’s Framework Is Object-Agnostic
Marshall expressly emphasizes that its framework applies to unknown objects, not just known or classified ones. Complexity is computed without regard to:
chemical name,
biological role,
synthetic pathway,
empirical labels.
This directly aligns with Applicant’s claimed advantage of being agnostic to molecular origin and structure.
Thus, Marshall teaches that:
complexity can be estimated for previously unknown entities, based only on their internal composition.
Thus, Marshall teaches estimating the complexity of an object by deriving a numerical complexity measure from features inherent to the object itself, without reliance on external reference information, object identity, or prior classification. Although Marshall illustrates this concept using abstract examples, the underlying teaching is general and would have motivated a person of ordinary skill in the art to apply the same intrinsic-feature-based complexity estimation to molecular samples using experimentally obtained structural features, such as spectral peaks.
Marshall explicitly teaches that its probabilistic framework is intended to be generalized to biological and molecular systems (page 18). The absence of worked chemical examples does not negate the teaching that complexity may be quantified from measurable system characteristics. A person of ordinary skill in the art would have been motivated to apply Marshall’s framework to molecular data, including spectroscopic features, in order to obtain a quantitative index of complexity.
Marshell does not specifically teach using which experiment to determine the unique peaks (unique substructures). However, in the analogous art of natural product data analysis, Merwin teaches (a) performing one of MS/MS, NMR or IR on a sample; and (b) determining the unique peaks in the resulting MS2 spectrum for a parent ion in the MS1 spectrum, NMR spectrum, or IR spectrum (Fig. 40, par [0145][0150] [0161] [0163]), scaling the number of unique peaks in the resulting MS2, NMR or IR spectrum by a magnitude (m) (par [0155]).
Thus, it would have been obvious to one of ordinary skill in the art to a) performing one of MS/MS, NMR or IR on a sample; and (b) determining the unique peaks in the resulting MS2 spectrum for a parent ion in the MS1 spectrum, NMR spectrum, or IR spectrum, and c) calculating the molecular assembly index of the sample based on the number of unique peaks in the resulting MS2, NMR or IR spectrum, because Merwin teaches that MS2 peaks is the real detected data relating to the substructures.
While Merwin is directed to natural product discovery, it explicitly discloses the use of MS/MS, NMR, and IR spectral analysis to characterize chemical structures (par [0018][0145][0150][0161][0163]). Merwin teaches the importance of spectral data, including the identification of unique peaks, in distinguishing and characterizing chemical compounds (Fig. 40, par [0163]). Marshall, in turn, teaches a framework for quantifying the complexity of an object by reference to features that define its structure.
A person of ordinary skill in the art, seeking to quantify molecular complexity, would have been motivated to apply Marshall’s framework of complexity quantification to the spectral features disclosed in Merwin, since both references are directed to extracting structural information from objects (molecules or otherwise) and reducing that information to a quantifiable measure.
Regarding claim 2, Merwin teaches that wherein the method comprises:
(a) performing MS/MS on the sample (Fig. 40, par [0145][0150] [0161] [0163]);
(b) determining the unique peaks in an MS2 spectrum for a parent ion in the MS 1 spectrum (Fig. 40, par [0145][0150] [0161] [0163]).
Marshall- Merwin fairly suggests (c) calculating the molecular assembly index of the sample based on the number of unique peaks in the MS2 spectrum (Marshall, Fig. 2, page 4-5).
Regarding claim 3, Merwin teaches that wherein step (a) comprises selecting a parent ion in the MS1 spectrum having a mass of 250 Da or more (Table 5).
Regarding claim 4, Merwin teaches that wherein step (a) comprises selecting a parent ion in the MS1 spectrum having a mass of 1000 Da or less (Fig. 40, Table 5).
Regarding claim 5, it is conventional to disregard weak peaks in the calculation, in order to reduce noise.
Regarding claim 6-7, it is conventional to merge close peaks in the MS2 spectrum, in order to reduce noise.
Regarding claim 8, it is conventional to recording multiple MS2 spectra for a parent chosen ion in the MS1 spectrum; and disregard all peaks not present in at least 25 % of the MS2 spectra from the chosen parent ion, in order to reduce noise.
Regarding claim 9, Merwin teaches scaling the number of unique peaks in the MS2 spectrum by a magnitude (m) (par [0155]). It would have been obvious to one of ordinary skill in the art to optimize the magnitude (m) by routine experimentation.
Regarding claim 10, offsetting a number is a conventional mathematical manipulation.
Regarding claim 12, Merwin teaches selecting most intense peaks in the MS1 spectrum and recording MS2 spectra for each peak (Fig. 42). It would have been obvious to one of ordinary skill in the art to optimize the number of peaks by routine experimentation.
Regarding claim 13, it is conventional to exclude parent ions appearing twice in a set time interval, for example using dynamic exclusion (Methods of temporarily excluding parent ions from analysis are known) (see instant spec, page 11, lines 3-4).
Regarding claim 14, it is conventional to disregard all peaks with a relative intensify below 10% of the highest recorded intensity in each MS2 spectrum, in order to reduce the noise.
Regarding claim 16, it is conventional to calculate the molecular assembly index of the sample from the parent ion having the largest number of unique peaks in the MS2 spectrum, because the largest number of unique peaks in the MS2 spectrum contains the most information.
Regarding claim 17, Marshall teaches a method for the detection of life (abstract), the method comprising:
(a) estimating the molecular complexity of a sample according to the method of claim 1 (see claim 1 above); and
(b) comparing the calculated molecular assembly index of the sample to a threshold value (page 5).
Regarding claim 18, Marshall fairly suggests that wherein the sample is a sample of extraterrestrial material or the sample is a sample of terrestrial material, such as terrestrial soil, water, ice or rock (page 2).
Regarding claim 20, Marshall-Merwin teaches a method for identifying a candidate pharmaceutical or agrochemical molecule, the method comprising:
(a) estimating the molecular complexity of a sample in a molecular library using the method of claim 1 (see claim 1 above); and
(b) selecting a sample having a molecular assembly index greater than a threshold value as a candidate agrochemical or pharmaceutical molecule (Merwin, par [0178]).
Regarding claim 21, Merwin teaches that wherein the method comprises:
(c) separating the sample constituents (par [0195]); and optionally
(d) screening the sample constituents for biological activity (par [0256]).
Regarding claim 22, Merwin teaches that wherein the sample is an extract from a biological source, such as an extract from a fermentation broth or a plant extract (par [0181]).
Allowable Subject Matter
Claim 11 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims and with additional elements applies or uses the abstract idea in a meaningful way such that the claim as a whole is more than a drafting effort designed to monopolize the exception
Response to Arguments
Applicant's arguments filed 12/10/2025 have been fully considered but they are not persuasive.
Regarding 101 rejection
Applicant’s arguments have been fully considered but are not persuasive.
Step 2A, Prong One: Judicial Exception
Claim 1 remains directed to a judicial exception, namely a mathematical concept and mental process, including:
collecting data (performing MS/MS, NMR, or IR),
analyzing data (determining unique peaks), and
mathematically processing the data (scaling the number of peaks by a magnitude (m) to calculate an index).
These steps collectively recite data acquisition and mathematical analysis, which fall within the abstract idea category under Alice Corp. v. CLS Bank Int’l, 573 U.S. 208 (2014), and Electric Power Group, LLC v. Alstom S.A., 830 F.3d 1350 (Fed. Cir. 2016).
Step 2A, Prong Two: Integration Into a Practical Application
Applicant argues that the claimed method is integrated into a practical application because molecular complexity is a useful analytical measurement, analogous to melting point, solubility, or binding affinity, and because the method relies on intrinsic properties of the sample without external input.
The Examiner is not persuaded.
(a) “Derived” Analytical Values Remain Abstract
While Applicant argues that binding affinity is also a derived value, courts have made clear that deriving a numerical value from collected data does not itself constitute a practical application unless the claim improves a technical process or effects a transformation beyond data analysis. See Parker v. Flook, 437 U.S. 584 (1978).
Here, the claimed molecular assembly index is not used to control a process, alter a physical state, or improve an analytical instrument. The claim merely produces a numerical result, which is insufficient to integrate the abstract idea into a practical application.
(b) Conventional Instrumentation Does Not Supply Integration
Applicant relies on the use of MS/MS, NMR, or IR instrumentation to argue practical application. However, the recited spectroscopic techniques are well-understood, routine, and conventional, and are used only to generate input data for the abstract calculation.
As held in Electric Power Group, “merely collecting information, analyzing it, and displaying results” does not amount to patent-eligible subject matter, even when performed using physical sensors or instruments.
(c) “Intrinsic Properties” and “Without External Input” Are Insufficient
Applicant asserts that estimating complexity based on intrinsic properties and without external input constitutes a technical improvement.
The Examiner disagrees. These limitations describe the source of the data, not a technological improvement. The claim does not:
improve the operation of a mass spectrometer, NMR, or IR instrument;
improve spectral resolution or peak detection;
change how data is acquired or processed at a technical level; or
produce a transformation of the sample.
Functional language disclaiming “external input” does not convert an abstract data analysis into a patent-eligible application.
Step 2B: “Significantly More”
Even if claim 1 were considered to involve a judicial exception, the claim fails to recite additional elements that amount to significantly more.
Scaling the number of peaks by a magnitude (m) is a routine mathematical operation.
Determining peaks from spectra is a conventional analytical practice.
The claim does not include a non-conventional algorithm, a new data structure, or a technical improvement to instrumentation.
Thus, the claim merely instructs the practitioner to apply an abstract idea using conventional tools, which is insufficient under Alice and Flook.
Preemption
Applicant suggests that requiring a specific downstream use would be unduly limiting. However, the absence of such limitations underscores that the claim preempts the abstract idea of estimating molecular complexity from spectral features, rather than claiming a specific technological application.
See Gottschalk v. Benson, 409 U.S. 63 (1972).
Conclusion
Claim 1 is directed to an abstract idea—collecting spectral data and mathematically analyzing it to produce a numerical index—and does not integrate that idea into a practical application or recite significantly more. Accordingly, the rejection under 35 U.S.C. § 101 is maintained.
Regarding 112 rejection
Applicant’s arguments have been fully considered but are not persuasive.
Applicant argues that the molecular assembly index is definite because claim 1 recites scaling the number of unique peaks by a magnitude (m), thereby allegedly establishing an objective mathematical relationship.
The Examiner is not persuaded. Although claim 1 recites “scaling,” the claim fails to define the scope and bounds of the molecular assembly index. Specifically, the claim does not specify:
whether the scaling is linear, affine, logarithmic, or otherwise;
whether the molecular assembly index must be an integer or a real number;
whether different values of (m) yield different molecular assembly indices for the same sample; or
whether two practitioners using different scaling magnitudes would arrive at the same claimed result.
Because the claim encompasses multiple materially different calculations, the term “molecular assembly index” lacks objective boundaries and remains indefinite. See Nautilus, Inc. v. Biosig Instruments, Inc., 572 U.S. 898, 910 (2014).
Applicant asserts that the magnitude (m) is a conventional scaling factor and that allowing flexibility does not render the claim indefinite.
The Examiner disagrees. While analytical chemistry may employ scaling factors, claim 1 provides no constraint whatsoever on the magnitude (m). The claim does not specify whether (m) is:
fixed or variable,
selected empirically or arbitrarily,
dependent on instrument type or sample type, or
required to be consistent across measurements.
As a result, the scope of the claim changes depending on the subjective choice of the practitioner. This lack of objective limitation renders the claim indefinite, as one of ordinary skill in the art cannot determine the metes and bounds of the claimed invention. Breadth does not excuse the absence of definitional boundaries.
Applicant argues that “unique peaks” is a well-understood term of art and further asserts that the Office’s reliance on “unique peaks” in the §103 rejection is inconsistent with a §112(b) rejection.
The Examiner is not persuaded. The claim itself does not define what constitutes a “unique peak.” In particular, the claim does not specify whether a peak is “unique”:
relative to noise,
relative to other peaks in a single spectrum,
relative to other components in a mixture, or
relative to a reference spectrum or database.
While the specification provides examples, claim 1 does not incorporate these limitations. A claim is indefinite when the scope is unclear from the claim language itself, even if examples are provided elsewhere in the specification.
Further, reliance on a term in the prior art for purposes of obviousness does not require that the term be definite in Applicant’s claim. The legal standards for §103 and §112(b) are distinct.
Applicant argues that “without external input” excludes reliance on reference databases, molecular identity, or prior knowledge.
The Examiner is not persuaded. Claim 1 does not define what constitutes “external input,” nor does it exclude:
user-defined peak thresholds,
instrument calibration parameters,
selection of parent ions,
selection of spectral acquisition conditions, or
selection of the magnitude (m).
Thus, the phrase “without external input” is ambiguous and subjective, and does not impose a clear structural or procedural limitation on the claim. Functional language that merely states an intended result or advantage, without objective boundaries, renders a claim indefinite. See Halliburton Energy Servs., Inc. v. M-I LLC, 514 F.3d 1244, 1255 (Fed. Cir. 2008).
Applicant argues that inclusion of MS/MS, NMR, and IR does not create indefiniteness.
The Examiner disagrees. Claim 1 applies the same undefined concepts of “unique peaks,” “scaling,” and “molecular assembly index” across analytical techniques governed by different physical principles, without specifying:
whether the same magnitude (m) applies across all modalities;
how peak counts from different modalities are normalized or compared; or
whether modality-specific criteria are required.
As a result, the scope of the claim varies depending on the chosen analytical technique, further contributing to indefiniteness.
Conclusion
For the reasons set forth above, claim 1 fails to inform those skilled in the art, with reasonable certainty, of the scope of the claimed invention. Accordingly, the rejection of claim 1 under 35 U.S.C. § 112(b) is maintained.
Regarding 103 rejection
The amendment clarifies that the molecular assembly index is obtained by scaling the number of unique peaks by a magnitude (m). However, this modification merely recites a linear mathematical operation applied to counted features and does not materially distinguish the claimed subject matter from the teachings of the prior art.
As previously explained, Marshall teaches quantifying complexity by reducing observable features of an object into a numerical complexity measure. Merwin teaches obtaining molecular features experimentally via MS/MS, NMR, or IR, including identification of spectral peaks. Applying a scaling factor to a counted feature set represents a routine mathematical adjustment that would have been obvious to a person of ordinary skill in the art in implementing any quantitative metric. See KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398 (2007). For example, Merwin teaches scaling the number of unique peaks in the resulting MS2, NMR or IR spectrum by a magnitude (m) (par [0155]).
Applicant now recites that the method estimates molecular complexity “based on the intrinsic properties of the sample and without external input.” This limitation does not render the claim non-obvious.
As discussed previously, both the claimed method and the prior art inherently require human-defined parameters and analytical choices, including but not limited to:
selection of spectral acquisition conditions;
determination of what constitutes a “unique peak”;
selection of peak detection thresholds; and
selection of the scaling magnitude (m).
Accordingly, the method is not free from external input, and the recited limitation does not meaningfully distinguish over the combined teachings of Marshall and Merwin. Functional language disclaiming “external input” does not negate the obviousness of the underlying steps where such input is implicit and unavoidable.
Thus, Marshall teaches the concept of quantifying complexity as a numerical index derived from object features, and Merwin teaches experimentally obtaining molecular features via spectroscopy and scaling the number of spectral peaks by a magnitude (m). Therefore, claim 1 remains obvious over Marshall in view of Merwin.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to XIAOYUN R XU, Ph. D. whose telephone number is (571)270-5560. The examiner can normally be reached M-F 8am-5pm.
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/XIAOYUN R XU, Ph.D./ Primary Examiner, Art Unit 1797