DETAILED ACTION
Final Rejection
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 .
Response to Amendment
Applicant’s amendments, filed 08/21/2025 to claims are accepted. In this amendment, claims1, 8 and 15 have been amended.
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 1-15 are rejected under 35 U.S.C. § 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1
Each of claims 1-15 falls within one of the four statutory categories. See MPEP § 2106.03. For example, each of claim 1-13 and 15 falls within category of machine, i.e., a “concrete thing, consisting of parts, or of certain devices and combination of devices.” Digitech, 758 F.3d at 1348–49, 111 USPQ2d at 1719 (quoting Burr v. Duryee, 68 U.S. 531, 570, 17 L. Ed. 650, 657 (1863)); each of claim 14 fall within category of process.
Regarding Claims 1-13
Step 2A – Prong 1
Exemplary claim 1 is directed to an abstract idea of separating intensity peaks from data.
The abstract idea is set forth or described by the following italicized limitations:
A system for separating intensity peaks from data collected in a separation device coupled mass spectrometry experiment, comprising:
a separation device that separates one or more compounds from a sample over a time period;
an ion source that ionizes the separated one or more compounds received from the separation device, producing an ion beam of one or more precursor ions;
a mass spectrometer that receives the ion beam from the ion source and mass analyzes a mass range of the ion beam at each time of a plurality of times of the time period, producing a three dimensional (3-D) array of intensity measurements measured as a function of m/z and time for the time period; and
a processor in communication with the mass spectrometer that
receives the 3-D array from the mass spectrometer,
converts the 3-D array to an nxm intensity matrix D, wherein the n rows correspond to measured m/z values or values of a mass-related parameter calculated from the measured m/z values and the m columns correspond to the plurality of times or values of a time-related parameter calculated from the plurality of times, and
applies nonnegative matrix factorization (NMF) to the D matrix to solve for an intensity matrix M and an intensity matrix A of the equation D = MA, wherein while solving for the M matrix and the A matrix, the processor enforces nonnegativity of elements of both the M matrix and the A matrix, and wherein the NMF is applied to produce in a row (1) of the A matrix intensity values for a peak (1) in terms of the plurality of times or the values of the time-related parameter that separates the peak (1) from the 3-D array and the NMF 1s applied to produce in column (1) of the M matrix intensity values in terms of the measured m/z values or the values of the mass-related parameter corresponding to the peak (1), and
generates a plot of a peak profile by summing the row (i) and one or more other rows of matrix A..
The italicized limitations above represent a combination of a mathematical concepts (i.e., a process that can be performed by mathematical relationships or rules or idea). Therefore, the italicized limitations fall within the subject matter groupings of abstract ideas enumerated in Section I of the 2019 Revised Patent Subject Matter Eligibility Guidance.
For example, the limitations “ converts the 3-D array […];applies nonnegative matrix factorization (NMF) to the D matrix to solve for an intensity matrix [..] ; generates a plot of a peak profile [..]” are a mathematical concepts (i.e., a process that can be performed by mathematical relationships or rules or idea) , see 2106.04(a)(2). Limitations (a)-(c) are considered together as a single abstract idea for further analysis. (discussing Bilski v. Kappos, 561 U.S. 593 (2010)).
Step 2A – Prong 2
Claims 1 does not include additional elements (when considered individually, as an ordered combination, and/or within the claim as a whole) that are sufficient to integrate the abstract idea into a practical application.
For example, additional first element is “receives the 3-D array from the mass spectrometer”, this additional elements that appears to limit the “collecting data” to be performed, at least in-part, by use of generic sensor component and to be performed, at least in-part, these additional elements appear to only add insignificant extra-solution activity (e.g., data gathering) and only generally link the abstract idea to a particular field. Therefore, this element individually or as a whole does not provide a practical application. See MPEP 2106.05(g)
The 2nd additional element is “A system for separating intensity peaks from data collected in a separation device coupled mass spectrometry experiment, comprising: a separation device that separates one or more compounds from a sample over a time period; an ion source that ionizes the separated one or more compounds received from the separation device, producing an ion beam of one or more precursor ions; a mass spectrometer that receives the ion beam from the ion source and mass analyzes a mass range of the ion beam at each time of a plurality of times of the time period, producing a three dimensional (3-D) array of intensity measurements measured as a function of m/z and time for the time period;”. This element amounts to mere use of a generic mass spectrometry experiment system which is well understood routine and conventional (see background of current discloser and IDS and PTO 892) and this element individually does not provide a practical application. In view of the above, the “additional element” individually or combine does not provide a practical application of the abstract idea. see MPEP 2106.05(d)
The 3rd additional element is “a processor in communication with the mass spectrometer”. This element amounts to mere use of a generic computer component and this element individually does not provide a practical application. In view of the above, the “additional element” individually or combine does not provide a practical application of the abstract idea. See EMPP 2106.05(f).
In view of the above three, the “additional elements” individually does not provide a practical application of the abstract idea. Furthermore, the “additional elements” in combination amount to a generic system with extra solution activity with high level of software, where such computers, database and software amount to mere instructions to implement the abstract idea on a computer(s) and/or mere use of a generic computer component(s) as a tool to perform the abstract idea. Therefore, these elements in combination do not provide a practical application. The combination of additional elements does no more than generally link the use of the abstract idea to a particular technological environment, and for this additional reason, the combination of additional elements does not provide a practical application of the abstract idea.
Step 2B
Claims1 does not include additional elements, when considered individually and as an ordered combination, that are sufficient to amount to significantly more than the abstract idea. For example, the limitation of Claim 1 is an additional element that is, i.e. “A system for separating intensity peaks from data collected in a separation device coupled mass spectrometry experiment, comprising: a separation device that separates one or more compounds from a sample over a time period; an ion source that ionizes the separated one or more compounds received from the separation device, producing an ion beam of one or more precursor ions; a mass spectrometer that receives the ion beam from the ion source and mass analyzes a mass range of the ion beam at each time of a plurality of times of the time period, producing a three dimensional (3-D) array of intensity measurements measured as a function of m/z and time for the time period;”, generic device, which is well understood, routine and convention (see background of current discloser and IDS and PTO 892) and MPEP 2106.05(d)).
The reasons for reaching this conclusion are substantially the same as the reasons given above in § Step 2A – Prong 2. For brevity only, those reasons are not repeated in this section. See MPEP §§ 2106.05(g) and MPEP §§2106.05(II).
.
Dependent Claims 2-13
Dependent claims 2-13 fail to cure this deficiency of independent claim 1 (set forth above) and are rejected accordingly. Particularly, claims 2-10 recite limitations that represent (in addition to the limitations already noted above) either the abstract idea or an additional element that is merely extra-solution activity, mere use of instructions and/or generic computer component(s) as a tool to implement the abstract idea, and/or merely limits the abstract idea to a particular technological environment.
For example, the limitations of Claims 2-6 and 8--13 are a combination of mathematical steps with mental steps.
For example, the limitations of claim 7: these additional elements appear to only add insignificant extra-solution activity (e.g., data gathering) and only generally link the abstract idea
Independent Claim 14-15
Claims 14-15 contains language similar to claims 1 as discussed in the preceding paragraphs, and for reasons similar to those discussed above, claims 14-15 are also rejected under 35 U.S.C. § 101(abstract idea).
Response to Argument
Applicant’s arguments with respect 101 rejection, specially claims 1, 14 and 15 , the applicant did not agree with it., see pages 7-12.
1) Applicant argus that “applies nonnegative matrix factorization (NMF) to the D matrix to solve for an intensity matrix M and an intensity matrix A of the equation D = MA", "wherein the NMF is applied to produce in a row (i) of the A matrix intensity values for a peak (i) in terms of the plurality of times or the values of the time-related parameter that separates the peak (i) from the 3-D array" and "generates a plot of a peak profile by summing the row (i) and one or more other rows of matrix A." Claim 14 now recites, inter alia, "applying nonnegative matrix factorization (NMF) to the D matrix to solve for an intensity matrix M and an intensity matrix A of the equation D = MA using the processor", "wherein the NMF is applied to produce in a row (i) of the A matrix intensity values for a peak (i) in terms of the plurality of times or the values of the time-related parameter that separates the peak (i) from the 3-D array" and "generating a plot of a peak profile by summing the row (i) and one or more other rows of matrix A." Claim 15 now recites, inter alia, "[a] non-transitory and tangible computer-readable storage medium whose contents include a computer program with instructions being executed on a processor to perform a method for separating intensity peaks from data collected in a separation device coupled mass spectrometry experiment, the method comprising", "applying nonnegative matrix factorization (NMF) to the D matrix to solve for an intensity matrix M and an intensity matrix A of the equation D = MA using the analysis module ... wherein the NMF is applied to produce in a row (i) of the A matrix intensity values for a peak (i) in terms of the plurality of times or the values of the time-related parameter that separates the peak (i) from the 3-D array" and "generating a plot of a peak profile by summing the row (i) and one or more other rows of matrix A. Support for the amendments can be found in the originally filed application at, for example, claim 7 and paragraph [0085] of the Specification. Applicant respectfully submits that such actions cannot be practically performed by mathematical concepts. For example, applying, using a processor, nonnegative matrix factorization (NMF) to a D matrix to solve for a M matrix and an A matrix, wherein while solving for the M matrix and the A matrix, the NMF is applied to produce in a row (i) of the A matrix intensity values for a peak (i) in terms of the plurality of times or the values of the time- related parameter that separates the peak (i) from the 3-D array and generating a plot of a peak profile by summing the row (i) and one or more other rows of matrix A cannot be performed by mathematical concepts. Rather, a machine (i.e., a computer) must be employed to apply, using a processor, nonnegative matrix factorization (NMF) to a D matrix to solve for a M matrix and an A matrix, wherein while solving for the M matrix and the A matrix, the NMF is applied to produce in a row (i) of the A matrix intensity values for a peak (i) in terms of the plurality of times or the values of the time-related parameter that separates the peak (i) from the 3-D array and generate a plot of a peak profile by summing the row (i) and one or more other rows of matrix A. Accordingly, the claims are not directed toward mathematical concepts Since the pending claims are not directed toward mathematical concepts, Applicant respectfully requests reconsideration and withdrawal of the rejection.”(page 7-8).
In response, the Examiner respectfully disagree because limitations above represent a combination of a mathematical concepts (i.e., a process that can be performed by mathematical relationships or rules or idea). Therefore, the italicized limitations fall within the subject matter groupings of abstract ideas enumerated in Section I of the 2019 Revised Patent Subject Matter Eligibility Guidance (see, fig. 4; [0081-[0085]])and processors acts as a generic computer component(s) as a tool to perform the abstract idea. (see, [0087]: Processor 640 can be, but is not limited to, a controller, a computer, a microprocessor, the computer system of Figure 1, or any device capable of sending and receiving control signals and processing data)
2) Applicant argus that the claims recite additional elements demonstrating that the claim as a whole integrates the exception into a practical application.
“another way to demonstrate such integration into a practical application is when the claimed invention improves the functioning of a computer or improves another technology or technical field…”.(see page 8-9)
“Limitations that qualify as "significantly more" when recited in a claim include specific limitations other than what is well-understood, routine, conventional activity in the field, or unconventional steps that confine the claim to a particular useful application, e.g., a non- conventional and non-generic arrangement of various computer components for filtering internet content, as discussed in BASCOMGlobal Internet v. AT&TMobility LLC, 827 F.3d 1341, 1350- 51 (Fed. Cir. 2016). MPEP § 2106.05.”(page 11)
In response, the Examiner respectfully disagree because in view of the three “additional elements” (see rejection above) individually does not provide a practical application of the abstract idea. Furthermore, the “additional elements” in combination amount to a generic system with extra solution activity with high level of software, where such computers, database and software amount to mere instructions to implement the abstract idea on a computer(s) and/or mere use of a generic computer component(s) as a tool to perform the abstract idea. Therefore, these elements in combination do not provide a practical application. The combination of additional elements does no more than generally link the use of the abstract idea to a particular technological environment, and for this additional reason, the combination of additional elements does not provide a practical application of the abstract idea. The claim recites only the idea of a solution or outcome, i.e., the claim fails to recite details of how a solution to a problem is accomplished. see MPEP 2106.05(a).
3) Applicant further argus that Claims 1, 14, and 15 include the limitations of the required combination of limitations including the "additional elements" is "significantly more" as the required combination is not well-understood, routine, and conventional activity. I.e., it is not well-understood, routine, or conventional that Claims 1, 14, and 15 include the elements ofapplying, using a processor, nonnegative matrix factorization (NMF) to a D matrix to solve for a M matrix and an A matrix, wherein while solving for the M matrix and the A matrix, the NMF is applied to produce in a row (i) of the A matrix intensity values for a peak (i) in terms of the plurality of times or the values of the time- related parameter that separates the peak (i) from the 3-D array and generating a plot of a peak profile by summing the row (i) and one or more other rows of matrix A(see, page 11).
“The required combination of limitations including the "additional elements" is "significantly more" as the required combination is not well-understood, routine, and conventional activity. I.e., it is not well-understood, routine, or conventional that Claims 1, 14, and 15 include the elements of applying, using a processor, nonnegative matrix factorization (NMF) to a D matrix to solve for a M matrix and an A matrix, wherein while solving for the M matrix and the A matrix, the NMF is applied to produce in a row (i) of the A matrix intensity values for a peak (i) in terms of the plurality of times or the values of the time-related parameter that separates the peak (i) from the 3-D array and generating a plot of a peak profile by summing the row (i) and one or more other rows of matrix A”(see, page 12)
In response, the Examiner respectfully disagree because current claims amendment further directed to details of abstract idea of mathematical concepts. In view of the above, the “additional element” individually or combine does not provide a practical application of the abstract idea. See MPEP 2106.05(f).. This element amounts to mere instructions to implement the abstract idea (i.e. separating intensity peaks from data and generates a plot) on a computer and/or mere use of a generic computer component with generic data collection system as tool to perform the abstract idea. Therefore, this element individually does not provide a practical application. see MPEP 2106.05(d). In view of the above, the “additional elements” individually do not provide a practical application of the abstract idea. Furthermore, the “additional elements” in combination amount to a plurality of generic devices associated with computer with software, where such generic data colleting device with computers and software amount to mere instructions to implement the abstract idea on a computer(s) and/or mere use of a generic computer component(s) as a tool to perform the abstract idea. Therefore, these elements in combination do not provide a practical application. (The claim recites only the idea of a solution or outcome, i.e., the claim fails to recite details of how a solution to a problem is accomplished).
As such 101 rejection is maintained.
Applicant’s arguments with respect 103 rejection based on amended limitation are persuasive and withdrawn.
Examiner Notes
Regarding claims 1-15, specifically claims 1, 14 and 15, There is no prior art rejection over claim, however there is 101 rejections. Closes prior arts fail to teach the limitations of “applies nonnegative matrix factorization (NMF) to the D matrix to solve for an intensity matrix M and an intensity matrix A of the equation D = MA, wherein while solving for the M matrix and the A matrix, the processor enforces nonnegativity of elements of both the M matrix and the A matrix, and wherein the NMF is applied to produce in a row (1) of the A matrix intensity values for a peak (1) in terms of the plurality of times or the values of the time-related parameter that separates the peak (1) from the 3-D array and the NMF 1s applied to produce in column (1) of the M matrix intensity values in terms of the measured m/z values or the values of the mass-related parameter corresponding to the peak (1), and generates a plot of a peak profile by summing the row (i) and one or more other rows of matrix A”
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
a) Ivosev et al. (US 2021/0166159) disclose a positive mode MALDI-FT-ICR mass spectrum of one spot containing guanosine (go) and 9-aminoacridine (9A) as the matrix compound. Automated analysis of each spot used 4× averaging of 1-second acquisitions. Guanosine ions (2, 3, 4, 5, in red) are present, along with two protonated matrix peaks (1, 6, in blue). Matrix (b) graphically shows the intensity of the protonated matrix (peak 1) at m/z=195.0916±0.001 for a MALDI plate with 1024 independent mixture spots. Protonated aminoacridine is positively identified in 1020 spots (99.6%).
b) Ivosev et al. (US 2019/0228957) disclose matrix multiplication equation showing an experimental example of how corresponding precursor ions are determined from a product ion QIT, in accordanc, fig. 9.
c) Cappadona et al. (US 2010/0161238) disclose The method comprises the steps of: providing an intensity column vector (SIC) representative of the elution values at a specific mass value (m/z) of the measurement signal (11);
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MOHAMMAD K ISLAM whose telephone number is (571)270-0328. The examiner can normally be reached M-F 9:00 a.m. - 5:00 p.m..
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/MOHAMMAD K ISLAM/Primary Examiner, Art Unit 2857