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 .
Election/Restrictions
Applicant’s election without traverse of Group II (claims 10-16) in the reply filed on 07/13/2026 is acknowledged.
Claims 1-9 and 17-21 are withdrawn.
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 10-16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea (i.e., mental processes and mathematical steps for transforming mass-spectrum data and comparing the transformed data to an expected value to determine a deviation), and the claims do not recite additional elements that integrate the abstract idea into a practical application or amount to significantly more than the judicial exception.
Step 2A, Prong One – Judicial exception (Abstract Idea)
The courts consider a mental process (thinking) that “can be performed in the human mind, or by a human using a pen and paper” to be an abstract idea. CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1372, 99 USPQ2d 1690, 1695 (Fed. Cir. 2011). As the Federal Circuit explained, “methods which can be performed mentally, or which are the equivalent of human mental work, are unpatentable abstract ideas the ‘basic tools of scientific and technological work’ that are open to all.’” 654 F.3d at 1371, 99 USPQ2d at 1694 (citing Gottschalk v. Benson, 409 U.S. 63, 175 USPQ 673 (1972)). See also Mayo Collaborative Servs. v. Prometheus Labs. Inc., 566 U.S. 66, 71, 101 USPQ2d 1961, 1965 ("‘[M]ental processes[] and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work’" (quoting Benson, 409 U.S. at 67, 175 USPQ at 675)); Parker v. Flook, 437 U.S. 584, 589, 198 USPQ 193, 197 (1978) (same). Further, the courts do not distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. As the Federal Circuit has explained, "[c]ourts have examined claims that required the use of a computer and still found that the underlying, patent-ineligible invention could be performed via pen and paper or in a person’s mind." Versata Dev. Group v. SAP Am., Inc., 793 F.3d 1306, 1335, 115 USPQ2d 1681, 1702 (Fed. Cir. 2015). See also Intellectual Ventures I LLC v. Symantec Corp., 838 F.3d 1307, 1318, 120 USPQ2d 1353, 1360 (Fed. Cir. 2016) (‘‘[W]ith the exception of generic computer-implemented steps, there is nothing in the claims themselves that foreclose them from being performed by a human, mentally or with pen and paper.’’); Mortgage Grader, Inc. v. First Choice Loan Servs. Inc., 811 F.3d 1314, 1324, 117 USPQ2d 1693, 1699 (Fed. Cir. 2016) (holding that computer-implemented method for "anonymous loan shopping" was an abstract idea because it could be "performed by humans without a computer").
In the instant case, the independent claims recite limitations that, when considered in their broadest reasonable interpretation, fall within the abstract idea of (i) mental process (concepts formed in the human mind such as observation, evaluation, and judgment) and/or (ii) mathematical concepts (relationships, comparisons, and mathematical operations). For instance, the independent claim 10 recites:
analyzing, by the mass spectrometry instrument, a sample comprising at least one substance having a known molecular weight by means of the mass spectrometry instrument so as to provide a mass spectrum of the sample;
generating, by the mass spectrometry instrument, a wavelet transformation of the mass
spectrum; and
determining, by the mass spectrometry instrument, a deviation of an amplitude of the wavelet transformed mass spectrum from a theoretical amplitude value of the at least one substance at a predetermined period.
These limitations collectively recite mathematically transforming mass-spectrum data and determining a deviation of a transformed amplitude from a theoretical amplitude at a selected period. Mathematical calculations and mathematical relationships fall within the mathematical concepts grouping of abstract ideas. The fact that the calculations are recited by the name of the mathematical technique, i.e., a “wavelet transformation,” does not remove them from that grouping. Such transformations are fundamentally a form of data analysis and mathematical evaluation, activities that have long been performed by humans mentally or with pen and paper and therefore can be characterized as an abstract idea.
Step 2A, Prong Two – Integration into a Practical Application
The claims are not integrated into a practical application because in practice, executing all of the steps is indistinguishable from: (i) mere data acquisition from a conventional instrument environment, and (ii) generic computer implementation of the abstract analysis. That is to say that integration into a practical application is lacking where, as here, the abstract idea has no effect on the material world or the execution of the process.
Although the claims include additional elements, e.g., mass spectrometer instrument having a mass analyzing cell, analyzing a sample containing a substance of known molecular weight to provide a mass spectrum, these additional elements do not integrate the abstract idea into a practical application. The analyzing step merely obtains the spectrum data that is used as input to the wavelet transformation and deviation determination. Obtaining data through testing for subsequent use in a mathematical analysis constitutes insignificant extra-solution data-gathering activity. MPEP§ 2006.05(g) specifically identifies performing tests to obtain input for a calculation and testing system response for use in determination a malfunction as examples of mere data gathering. Further, limiting the source of the data to a mass spectrometry instrument and a substance of known molecular weight merely confines the mathematical analysis to the technological environment or field of mass spectrometry. The instrument is used in its ordinary capacity to generate the data to be analyzed; it does not impose a meaningful limit on how the mathematical concept is performed.
Considering as a whole, claim 10 does not require using the determine deviation to adjust, calibrate, repair, or control the mass spectrometry instrument; alter a voltage applied to a mass analyzing cell; modify the handling of ions; correct a subsequent acquired spectrum; or otherwise change a physical operation of the instrument. Thus, the claim does not apply mathematical results to effect a particular technological action,
Therefore, claim 10 does not integrate the recited mathematical concept into a practical application and is directed to an abstract idea.
Step 2B– Significant More (Inventive Concept)
The claims do not include additional elements, either individually or as an ordered combination, that amount to significant more than the abstract idea. The mass spectrometry instrument, mass analyzing cell, and step of analyzing a sample to produce a mass spectrum are recited at a high level of generality and perform their ordinary data-acquisition functions. The specification itself describes mass spectrometry as a known analytical technique and describes a “typical” mass-spectrometry procedure in which a sample is ionized, ions are separated and detected, and results are presented as a mass spectrum. As an ordered combination, claim 10 merely acquires spectrum data using a conventionally operated mass spectrometry instrument and then perform the abstract mathematical analysis on the data. Accordingly, the additional elements, individually and in combination, do not amount to significantly more than the judicial exception.
Claim 11 further recites creating a heatmap which merely organizes or visually presents the results of the mathematical analysis. Claim 12 further recites determining the deviation depending on wave power, which is itself a mathematical property of the wavelet-transformation data. Claim 13 further recites determining an improper status of the instrument when the deviation exceeds a predetermined threshold, which merely makes a comparison and assigns a classification of “improper,” and does not require any corrective or controlling action in response to that classification. Claim 14 recites performing the analysis for more than one generic analyzing cells. Claims 15-16 further recite performing the analysis as a specified time, which merely narrows the timing or operating environment in which the abstract idea is applied.
Taken alone or as ordered combination, claims 10-16 fail to recite patent eligible subject matter.
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 10-16 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.
Claim 10 recites comparing an amplitude of the wavelet transformed mass spectrum to “a theoretical amplitude value of the at least one substance.” It is unclear whether the value is an amplitude theoretically inherent to the substance an expected amplitude obtained from a reference spectrum, an amplitude expected from a properly operating instrument, or some other value. Although the specification repeatedly refers to a theoretical amplitude value, it does not clearly define the source or nature of that value. Thus, the claim does not reasonably identify the reference value from which the claimed deviation is determined.
Claim 12 recites “determining… the deviation of the amplitude at the predetermined period depending on a wavelet power,” which does not clearly define the relationship between the claimed amplitude and the wavelet power. The specification defines “wavelet power” as the amplitude of a certain period associated with a particular position in the wavelet-transformed spectrum. Thus, claim 12 appears to require determining a deviation of an amplitude “depending on” an amplitude, without specifying whether the wavelet power is the measured amplitude, the theoretical amplitude, or another quantity used in calculating the deviation.
Claim 16 recites “wherein at least one of the predetermined points of time comprises a start of the mass spectrometry instrument,” which does not clearly identify the event constitutes the claimed “start.” It is unclear whether “a start” refers to applying power to the instrument, beginning an initiation or calibration sequence, commencing acquisition of a mass spectrum, beginning analysis of a sample, or another operational event. The speciation merely repeats that the points of time may include a start of the instrument and states that the status may be checked at regular intervals, without clarifying which startup event defines the claimed point in time.
Claims 11-16 are also vague and indefinite by virtue of their dependencies on claim 10.
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.
Claims 10-13 are rejected under 35 U.S.C. 103 as being unpatentable over Du, P., et al., (2006). Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics, 22(17), 2059–2065. [hereinafter Du] in view of US20240068997A1 [hereinafter Ivosev].
Regarding Claim 10:
Under BRI, the limitation of “a theoretical amplitude value” is interpreted as an expected, target, ideal, or reference wavelet-amplitude value associated with the substance at the predetermined period, against which the amplitude obtained from the measured, wavelet-transformed mass spectrum is compared. The specification defines amplitude as wavelet power at a particular period and m/z position but does not prescribe an equation, model, data source, or procedure for generating the theoretical amplitude value. Thus, this term is not limited to a value derived by any particular technique. Accordingly, this limitation is reasonably interpreted as encompassing any predetermined expected, ideal, normal, or reference wavelet-amplitude value associated with substance at the selected period, provided that the value is used as the reference for determining the claimed derivation.
Du teaches a method for characterization of a mass spectrometry instrument comprising at least one mass analyzing cell (Abstract: “a continuous wavelet transform (CWT)-based peak detection algorithm… was evaluated with SELDI-TOF spectra”), the method comprising:
analyzing, by the mass spectrometry instrument, a sample comprising at least one substance having a known molecular weight by means of the mass spectrometry instrument so as to provide a mass spectrum of the sample (Pages 2 and 4: “the algorithm was evaluated with MS spectra with known polypeptide compositions and positions.” “There are seven polypeptides in the sample with the m/z values of …Figure 3 shows the result of one MS spectrum”);
generating, by the mass spectrometry instrument, a wavelet transformation of the mass spectrum (Pages 2 and 3: “we directly apply the CWT over the raw spectrum and utilize the information over the 2D CWT coefficients matrix, which provides additional information on how the CWT coefficients change over scales.” More specifically, Du “performed the CWT at 33 scale levels (from 1 to 64 at an interval of 2) directly over the raw MS spectrum”); and
Du further teaches determining an amplitude of the wavelet-transformed mass spectrum at a selected wavelet scale corresponding to the claimed predetermined period, and presents the amplitude of the CWT coefficients as a third dimension and determines the maximum CWT coefficient along the ridge (Page 2: “the amplitude of the local maximum gradually increases as the CWT scale increases, reaches a maximum when the scale best matches the peak width, and gradually decreases later… this is just like a ridge if we visualize the 2D CWT coefficients with the amplitude of the CWT coefficients as the third dimension”).
However, Du does not expressly teach determining, by the mass spectrometry instrument, a deviation of an amplitude of the wavelet transformed mass spectrum from a theoretical amplitude value.
Ivosev teaches generating and using a wavelet response intensity for a mass spectrometry output signal by generating a wavelet scale-space response of the signal at multiple scales (paras. [0039-0041]). Since the wavelet response intensity represents the strength of a component produced by a wavelet transformation at a particular scale, it corresponds to the claimed “amplitude,” which is described in the specification as the wavelet power at a selected period at a particular spectrum position.
Specifically, Ivosev teaches determining, by the mass spectrometry instrument, a deviation of an amplitude of the wavelet transformed [mass-spectrometry signal] from a theoretical amplitude value of the at least one substance at a predetermined period (paras. [0036-0045]: Ivosev teaches determining an optimum wavelet scale, generating an ideal signal “based on the optimum scale…via smoothing and/or modelling” the measured signal, generating a wavelet scale-space response of both the measured signal and ideal signal and representing wavelet-response intensity by gray level. Ivosev also teaches analyzing the responses at selected low wavelet scales (“predetermined period”), e.g., scales 1-3, concluded “a wavelet scale can depict signal irregularity or deviation from ideal” and further comparing/correlating the original signal response with the ideal response).
As such, adding Ivosev to Du would result in a modified method where the amplitude of the Du’s wavelet-transform mass spectrum at a selected scale is compared with a corresponding expected or ideal wavelet-response amplitude at the that scale to determine a deviation.
Du teaches determining CWT-coefficient amplitudes to identify and characterize peaks in a measured mass spectrum. Ivosev teaches that the measure wavelet response alone can be evaluated more meaningfully by comparing it with the corresponding response of an ideal or expected signal since their difference indicates signal irregularity or departure from ideal. Therefore, it would have been obvious for an ordinary skilled person in the art, before the effective time of filing, to modify Du’s method to further compare the measured CWT-coefficient amplitude with a corresponding expected or ideal amplitude, as taught by Ivosev, to determine whether the spectral response represented by the measured coefficient amplitude departs from an expected response and thereby distinguish a normal spectral feature from signal irregularity or distortion. Applying such a known comparison step to Du would have therefore supplemented Du’s peak characterization with a quantities assessment of deviation from an expected spectral response.
Regarding Claim 11:
Du in view of Ivosev teaches the method of claim 10.
Du further teaches creating, by the mass spectrometry instrument, a heatmap of the wavelet transformed mass spectrum (Fig. 2(b) and Pages 2 -3: “directly apply the CWT over the raw spectrum and utilize the information over the 2D CWT coefficients matrix…visualizing the 2D CWT coefficients as a false color image.” Du explains that in the false color image (“heatmap”) “yellow color represents the high amplitude and green represents low”):
Du also teaches determine the amplitude at the selected scale in the heatmap by “linking the local maxima of CWT coefficients at each scale level… link these local maxima as lines… the signal strength of a peak is defined as the maximum CWT coefficient on the ridge line within a certain scale range”.
As such, the combined references teach determining, by the mass spectrometry instrument, the deviation of the amplitude at the predetermined period in the heatmap.
Regarding Claim 12:
The specification describes “wavelet power” as “a broad term and is to be given its ordinary and customary meaning” and may refer to “the amplitude of a certain period associated with a certain position in the definition range of a wavelet transformed mass spectrum” (Spec. Page 11: Para.4). Therefore, claim 12 is interpreted as not requiring a separate calculation distinct from the amplitude recited in claim 10. It merely clarifies that the deviation of claim 10 is determined using the wavelet-domain amplitude at the predetermined period.
Du in view of Ivosev teaches the method of claim 10. The combined references further teach determining, by the mass spectrometry instrument, the deviation of the amplitude at the predetermined period depending on a wavelet power (Du teaches determines CWT-coefficient amplitude of a mass spectrum at a selected scale while Ivosev teaches the comparison with the expected or ideal value).
Regarding Claim 13:
Du in view of Ivosev teaches the method of claim 10. Ivosev further comprising determining, by the mass spectrometry instrument, an improper status of the mass spectrometry instrument if the determined deviation of the amplitude exceeds a predetermined amplitude threshold (Claims 1-2 and paras. [0045-0047]: generating a signal quality metric at least based on the wavelet scale-space response and the correlation of the measured signal and ideal signal, and adjust the mass analyzer operational parameter “according to the comparison of the signal quality metric to the expected value”).
Claims 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over Du in view of Ivosev, further in view of US20220246412A1 [hereinafter Quint].
Regarding Claim 14:
Du in view of Ivosev teaches the method of claim 10. However, the combined references do not expressly teach wherein the mass spectrometry instrument comprises more than one mass analyzing cell, wherein analyzing the sample, generating the wavelet transformation, and determining the deviation of the amplitude are performed for each mass analyzing cell of the more than one mass analyzing cell.
Quint teaches a mass spectrometer comprising a first mass filter and a second mass filter and performing a first full-scan MS measurement for the first mass filter and a second full-scan MS measurement for the second mass filter to obtain respective measurement data, which are compared with respective reference data to determine whether a calibration condition is out of speciation (Abstract).
As such, adding Quint to the combined Du-Ivosev would result in a modified method where a mass spectrum is generated for each first and second mass analyzing cell/mass filter, and applying the wavelet transformation and amplitude-deviation analysis to the respective mass spectrum generated for each mass analyzing cell for calibration, as recited in claim 14.
Therefore, it would have been obvious for an ordinary skilled person in the art, before the effective time of filing, to perform Du-Ivosev’s wavelet-based characterization for each of the first and second mass filter taught by Quint, so that each mass analyzing cell may independently affect the mass spectrum generated using that cell, and separately characterizing the respective spectra would allow the source of an irregular spectral response to be identified and the corresponding mass analyzing cell to be adjusted.
Regarding Claim 15:
Du in view of Ivosev teaches the method of claim 10. However, the combined references do not expressly teach wherein analyzing the sample, generating the wavelet transformation, and determining the deviation of the amplitude are performed at predetermined points of time
Quint teaches the mass-axis checking procedure that may be scheduled by a scheduler, performed repeatedly at regular time interval, such as once every hour or once every day, or performed after a predetermined number of analyzed samples (paras. [0057, 0060]).
As such, adding Quint to the combined Du-Ivosev would result in performing the wavelet-based characterization at predetermined scheduled time, including regular time interval after predetermined number of samples have been analyzed.
Therefore, it would have been obvious for an ordinary skilled person in the art, before the effective time of filing, to perform Du-Ivosev’s wavelet-based characterization at the predetermined ties taught by Quint, to periodically identify degradation or irregularities in the mass spectrometry instrument and permit an operational parameter to be adjusted before the irregularity materially affects subsequent sample measurements.
Regarding Claim 16:
Du in view of Ivosev and Quint teaches the method of claim 15. Quint further teaches wherein at least one of the predetermined points of time comprises a start of the mass spectrometry instrument (para. [0056]: “a mass axis checking technique starts 201 with a trigger event. The trigger event can be that a particular routine or operation is carried out in the analyzer system or the mass spectrometer. For example… during a start-up procedure of the mass spectrometer or of an analyzer including the mass spectrometer”).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JING WANG whose telephone number is (571)272-2504. The examiner can normally be reached M-F 7:30-17:00.
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/JING WANG/Examiner, Art Unit 2881
/WYATT A STOFFA/Primary Examiner, Art Unit 2881
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