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 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 1-5, 7-8, 10, 12, 14-24 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 collecting spectral information, analyzing the information and presenting the analyzed results for user review), 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 1 recites (independent claim 15 recites similar limitations):
receiving the charge series spectrum, the charge series spectrum including a plurality of charge series peaks;
determining one or more reconstructed mass values based at least in part on the received charge series spectrum;
displaying the one or more reconstructed mass values on a first portion of a display;
receiving a selection of one of the displayed reconstructed mass values; and
displaying a plurality of icons on a second portion of the display, each icon including a marker and a corresponding charge series peak thereof, the marker identifying a charge of the charge series spectrum.
These limitations collectively recite the abstract idea of collecting spectral information, analyzing the information to identify reconstructed mass values and corresponding charge-state peak information, and presenting the analyzed information for user review. These steps are mental processes and information-display steps that could be performed by a person using the spectrum data, or are merely implemented using generic computer/display components, and therefore can be characterized as an abstract idea.
Likewise, the independent claim 24 recites:
receiving the charge series spectrum, the charge series spectrum including a plurality of charge series peaks;
generating one or more reconstructed mass values based at least in part on the received charge series spectrum; and
for each reconstructed mass value:
generating a plurality of markers, each marker corresponding to a charge of the charge series and having a corresponding charge series peak thereof from the charge series spectrum; and
determining that the reconstructed mass value is a probable artifact when a difference between at least one of the plurality of markers and a local maximum of the corresponding charge series peak thereof is greater than a threshold.
These limitations collectively recite the abstract idea of mathematically analyzing spectral data by calculating reconstructed mass values and charge-state marker positions, comparing the calculated marker positions to observed local maxima, and classifying a reconstructed mass value as a probable artifact when the difference exceeds a threshold. Thus, claim 24 recites both mathematical concepts and mental-process steps of observation, comparison, and classification, 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, such as a display device, data receiver, and a processor, these additional elements do not integrate the abstract idea into a practical application. For example, although a display is physical hardware, the claim uses the display only to present calculated information to a user. The claimed display operations merely show the results of the abstract data analysis in a particular format. The claim does not improve the display device itself, does not change how the display operates, and does not require a particular graphical-interface technology beyond presenting information on different portions of a display. The specification confirms that the alleged improvement is reducing the user’s manual zooming and saving analysis time by providing thumbnail/icon views of charge-state peaks and markers (see Spec. para. [0020]). That benefit is an improvement to information presentation and user review workflow, not an improvement to the functioning of the computer, display, mass spectrometer, or other technology. The additional hardware elements, e.g., a data receiver, processor, and memory, are generic computer/display components. These components are merely invoked as tools to perform the abstract receiving, calculating, selecting, and displaying steps. They do not impose a meaningful technological limitation.
Therefore, the claims as a whole are 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 additional elements of claim 1—a display, first and second display portions, user selection, icons, markers, and corresponding peaks—are used in a conventional manner to present information. The claim does not recite a specific unconventional display structure or a technical improvement to graphical rendering. The icons merely provide a visual arrangement of the calculated/selected spectral information.
The additional elements of claim 15—data receiver, display device, processor, and memory—are generic computer components performing their ordinary functions of receiving data, processing data, storing instructions, and displaying results. Merely implementing the abstract idea on generic computer hardware does not provide significantly more.
The dependent claims do not cure the deficiency. Claims 2–5, 16–17, and 22 further specify what is displayed or how it is displayed, such as displaying the charge-series spectrum, enlarged icons, a reconstructed spectrum, or a list of reconstructed mass values and intensities. These limitations further organize and present information, but do not improve computer/display technology. Claims 7, 10, 12, 18, and 21 further specify determining non-coincidence or artifact status based on separation, peak width, or FWHM. These limitations are additional data comparisons or mathematical evaluations. Claims 8, 19, and 20 omit artifacts from displayed spectra/lists, which is merely displaying filtered information. Claims 14 and 23 specify arranging icons so that a central icon corresponds to the highest signal intensity, which is another information-presentation rule.
Therefore, the claims as a whole amount to no more than receiving spectral data, calculating/analyzing expected charge-state relationships, comparing calculated positions to observed peak positions, and displaying or classifying the results using generic computer/display components. The claims do not recite significantly more than the abstract idea.
Taken alone or as ordered combination, claims 1–5, 7–8, 10, 12, and 14–24 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 8, 10, 12, 14, and 19-20 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 8 and 19 each recites “displaying a reconstructed spectrum on the display without the artifact.” There is insufficient antecedent basis for this limitation in the claim. For the purposes of compact prosecution, they will be interpreted as dependent on claims 7 and 18, respectively.
Claims 10 and 12 each recites “wherein determining that the marker does not coincide with the local maximum…” There is insufficient antecedent basis for this limitation in the claim. Both claims are dependent on claim 1, and that determining concept appears in claim 7. For the purposes of compact prosecution, they will be interpreted as dependent on claim 7.
Claim 14 recites “wherein a corresponding peak of the central icon has a highest signal intensity…”. There is insufficient antecedent basis for this limitation in the claim.
Claim 20 recites “the list omitting the artifact.” There is insufficient antecedent basis for this limitation in the claim. For the purposes of compact prosecution, it will be interpreted as dependent on claim 15, respectively.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-5, 7-8, 15-20, 22, and 24 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by US20210335589A1 [hereinafter Bern].
Regarding Claim 1:
Bern teaches a method of displaying a charge series spectrum (Abstract: “a graphical user interactive displays for use in MS-based analysis”), the method comprising:
receiving the charge series spectrum, the charge series spectrum including a plurality of charge series peaks (para. [0033]: “receiving a data file comprising mass spectrometry (MS) data for a sample comprising a molecule,” that mass spectrometry analyzes ions based on their mass/charge ratios (m/z) to produce a mass spectrum, e.g., the MS1 spectrum);
determining one or more reconstructed mass values based at least in part on the received charge series spectrum (Figs. 10A (1)-(3) and para. [0011]: “allow the user to select one or more points or regions of a deconvolved mass spectrum, and immediately and interactively show corresponding points (e.g., peaks) corresponding to the selected charged states to look at the deconvolved mass. The peaks may be displayed...and may be shown in multiple views.”);
displaying the one or more reconstructed mass values on a first portion of a display (Figs. 10A (1)-(3) and para. [0124]: FIGS. 10A (1)-(3) show an example of a dashboard showing multiple windows, including a mass listing 1001, an MS1 plot 1005 and a deconvolved mass spectrum 1007);
receiving a selection of one of the displayed reconstructed mass values (para. [0124]: “In the example shown in FIGS. 10A (1) -10A (3), three masses (two are visible in the mass listing 1001) have been selected”); and
displaying a plurality of icons on a second portion of the display, each icon including a marker and a corresponding charge series peak thereof, the marker identifying a charge of the charge series spectrum (Fig. 10B and paras. [0013, 0124]: “the user interface may ... highlight, (e.g., in the MS1 or other window (s), the resulting predicted peaks as colored dots or points on the graphs (e.g., spectra spectra) displayed in each window.” For example, Fig. 10B shows an MS1 spectrum with multiple displayed marker circles/dots over corresponding charge-series peaks. Each marker corresponds to an experimental MS1 peak and identifies the charge state of that peak using charge labels such as z=52 through z=43).
Regarding Claim 15:
Claim 15 recites a mass spectrometry data display apparatus comprising: a data receiver; a display device functionally coupled to the data receiver, the display device comprising a display screen; a processor operatively coupled to the data receiver and to the display device; and a memory coupled to the processor, the memory storing instructions that, when executed by the processor, perform a set of operations including the identical method steps recited in claim 1. Since all structure components of the mass spectrometry data display apparatus are merely generic components, and Bern teaches “a graphical user-interactive displays for use in MS-based analysis of protein impurities, as well as methods and software for generating and using such” and claim 1, Bern also teaches the mass spectrometry data display apparatus as recited in claim 15.
Regarding Claim 2:
Bern teaches the method of claim 1. Bern further teaches displaying the charge series spectrum on a third portion of the display (para. [0033]: “receiving a data file comprising mass spectrometry (MS) ... simultaneously displaying a plurality of visual representations derived from the received data... comprising: a first visual representation comprising estimated or calculated masses...a second visual representation comprising a distribution of mass/charge (m/z) ... and a third visual representation comprising a deconvolved mass spectrum”).
Regarding Claim 3 and 22:
Bern teaches the method of claim 1 and apparatus of claim 15, respectively. Bern further teaches wherein displaying the plurality of icons comprises displaying each icon with an enlarged view of the marker and of the corresponding peak thereof compared to the charge series spectrum (Fig. 10B and para. [0086]: “the three different types of plot (MS1, MS2, and XIC) allow panning, zooming, and resetting the level of zoom.” For example, Fig. 10B as an enlarged view of the labeled MS1 window).
Regarding Claim 4 and 16:
Bern teaches the method of claim 1 and apparatus of claim 15, respectively. Bern further teaches wherein displaying the one or more reconstructed mass values comprises displaying a reconstructed spectrum, the reconstructed spectrum including reconstructed peaks corresponding to the one or more reconstructed mass values (Fig. 10A (2) and para. [0124]: Fig. 10A (2) shows the deconvolved mass spectrum 1007, “Peaks representing each of these masses (e.g., Mass ID 80 and mass ID 88) are then plotted on both the MS1 and deconvolved mass spectrum windows/plots”).
Regarding Claim 5 and 17:
Bern teaches the method of claim 1 and apparatus of claim 15, respectively. Bern further teaches wherein displaying the one or more reconstructed mass values comprises displaying a list of the one or more reconstructed mass values and their corresponding signal intensities (Fig. 10A (1) and para. [0124]: Fig. 10A (1) shows a mass listing 1001 including three masses (two are visible in the listing)).
Regarding Claim 7 and 18:
Bern teaches the method of claim 1 and apparatus of claim 15, respectively. Bern further teaches determining that the selected reconstructed mass value is a probable artifact when the marker does not coincide with a local maximum of the corresponding charge series peak thereof in at least one of the plurality of icons (para. [0124]: “In the MS1 window, each mass selected results in a series of ‘peaks’ or values... As shown in greater detail in FIG. 10B... first series 1015 ... correspond to a subset of peaks in the m/z plot...the second series 1017 ... corresponds to a second set of peaks ...the third series 1019 does not consistently appear to correspond to a peak, and is likely to be erroneous. This may correspond to an ‘off by one’ error in the resulting charge”).
Regarding Claim 8 and 19:
Bern teaches the method of claim 1 and apparatus of claim 15, respectively. Bern further teaches displaying a reconstructed spectrum on the display without the artifact (paras. [0124, 0128]: Bern teaches distinguishing actual signal from noise and identifying erroneous/off-by-one charge results and “the selectable control may include toggling on/off the markers, charge labels, etc.”. Thus, once a mass/peak is determined erroneous or false-positive, it can be omitted from a deconvolved/reconstructed display).
Regarding Claim 20:
Bern teaches the apparatus of claim 15. Bern further teaches wherein the set of operations further comprise displaying a list of the one or more reconstructed mass values, the list omitting the artifact, as discussed in claim 8/19. Bern further teaches display the corresponding signal intensities (para. [0128]: Bern’s selectable control may “limit the intensity of the markers (‘limit visible circles by maximum intensity,’ where the maximum intensity is selectable)”, indicating that the displayed mass-to-m/z markers have associated intensity values).
Regarding Claim 24:
Bern teaches a method of evaluating a quality of a charge series spectrum, the method comprising: receiving the charge series spectrum, the charge series spectrum including a plurality of charge series peaks; generating one or more reconstructed mass values based at least in part on the received charge series spectrum, as discussed in claim 1.
Bern further teaches
for each reconstructed mass value: generating a plurality of markers, each marker corresponding to a charge of the charge series and having a corresponding charge series peak thereof from the charge series spectrum (Fig. 10B and paras. [0013, 0124]: “the user interface may ... highlight, (e.g., in the MS1 or other window (s), the resulting predicted peaks as colored dots or points on the graphs (e.g., spectra spectra) displayed in each window.” For example, Fig. 10B shows an MS1 spectrum with multiple displayed marker circles/dots over corresponding charge-series peaks. Each marker corresponds to an experimental MS1 peak and identifies the charge state of that peak using charge labels such as z=52 through z=43); and
determining that the reconstructed mass value is a probable artifact when a difference between at least one of the plurality of markers and a local maximum of the corresponding charge series peak thereof is greater than a threshold (Claim 10 and paras. [0124]: Bern teaches determining whether a selected mass value is erroneous by determining whether there is a peak within a predetermined range of a predicted marker position. Thus, Bern also teaches determining an artifact based on whether the distance between a nearby experimental peak/local maximum and the estimated marker position is greater than a predetermined range value, i.e., a threshold).
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, 12, and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Bern in view of US 20250379043 A1[hereinafter Roder].
Regarding Claims 10 and 21:
Bern teaches the method of claim 1 and apparatus of claim 20. Bern further teaches determining whether a predicted mass-to-m/z marker corresponds to an actual experimental peak by identifying a maximum-amplitude peak within a predetermined m/z range around the predicted marker position. However, Bern does not specially note that predetermined m/z range is a percentage of a width (claim 10) or a width (claim 21) of the corresponding charge series peak.
Roder teaches identifying/cluster-grouping candidate peaks based on whether their peak centers are within a predetermined distance, and expressly says that predetermined distance may be a half peak width (para. [0121]).
Therefore, it would have been obvious for an ordinary skilled person in the art, before the effective time of filing, to define Bern’s predetermined m/z range/threshold as half of the peak width, as taught in Roder, since Roder explains that peak width provides a suitable distance/tolerance measure for determining whether nearby spectral peak positions correspond to the same peak/alignment feature.
Regarding Claim 12:
Bern teaches the method of claim 1. Bern further teaches determining whether a predicted mass-to-m/z marker corresponds to an actual experimental peak by identifying a maximum-amplitude peak within a predetermined m/z range around the predicted marker position. However, Bern does not specially note that predetermined m/z range is a percentage of a full width at half-maximum of the corresponding charge series peak.
Roder teaches “Peak candidates to be fit were estimated using a peak finding algorithm based on the convolution of the Fine structure with the peak-shape. Peak candidate locations were estimated using the MATLAB function …with a prominence window equal to the width of the FWHM of a peak and a minimum separation of peaks equal to ¼ of the peak FWHM at the m/z location”) (para. [0112]).
Therefore, it would have been obvious for an ordinary skilled person in the art, before the effective time of filing, to define Bern’s predetermined m/z range/threshold as the width of the FWHM of the peak, as taught in Roder, since Roder demonstrates that FWHM is a known quantitively measure of spectra peal width for peak detection/separation in mass-spectra data.
Claims 14 and 23 are rejected under 35 U.S.C. 103 as being unpatentable over Bern.
Regarding Claims 14 and 23
Bern teaches the method of claim 1 and apparatus of claim 15, respectively. Bern does not specially teach proximity to the central icon; and a corresponding charge series peak of the central icon has a highest signal intensity compared to corresponding charge series peaks of the other icons.
Bern’s Fig. 10B teaches displaying a plurality of charge-identifying markers/icons corresponding to charge-series peaks, where the markers are displayed in the MS1 spectrum according to their actual m/z positions from low m/z to high m/z. The instant application displays the same type of charge-series marker/peak information, but places the marker/icon corresponding to the highest-intensity m/z peak in a central position and arranges the other related markers/icons around it (See. Fig. 2 of the instant application). Because the specification does not associate this rearrangement with any technical improvement to the m/z-position matching or artifact-detection process, the central placement is merely an obvious user-interface design choice for emphasizing the strongest peak as a convenient visual reference while presenting the remaining related peaks in proximity thereto. Therefore, it would have been obvious to arrange Bern’s displayed charged series markers/icons so that the highest-intensity peak is positioned centrally, as recited in claims 14 and 23, since a central placement of the strongest peak would emphasize the most visually significant peak as a convenient reference while presenting the remaining related charge series peaks nearby.
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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