DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. 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 Arguments
2. Applicant's arguments received 07/27/2026 have been fully considered but they are not persuasive.
Regarding the claim eligibility, Applicant argues that (REMARKS, p.8-9):
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Examiner respectfully disagrees. As illustrated in detail in sections 3-4 below, Examiner asserts that the invention recited in the amended claims 1, 3-4, 7-16 and 18 is directed to an abstract idea (math + mental) of identifying molecular species in a mass spectrum, but without “significantly more”. Specifically, focusing on what the inventors have invented exactly and giving the broadest reasonable interpretation (BRI) to the claims, Examiner maintains that the core of the pending claims 1, 3-4, 7-16 and 18 is directed to an algorithm of optimizing a set of mass spectra coefficients for a set of candidate mass spectra, based on available mass spectrometry data, using the well-known regularized linear regression technique (an extension of the standard linear regression), which falls within a combination of the “Mathematical Concepts” and the “Mental Process” groupings of Abstract Ideas defined by the 2019 PEG. The recited additional limitation relating to obtaining the set of candidate mass spectra for the mass spectrometry data wherein each candidate mass spectrum corresponds to a respective candidate molecular species, under the BRI, encompasses a process of gathering the data/information necessary for performing the abstract idea. The newly incorporated elements in independent claims 1, 16 and 18, such as “wherein the one or molecular species are one or more precursor molecular species, the mass spectrometry data is a fragment mass spectrum derived from the one or more precursor molecular species, and each candidate mass spectrum is a candidate fragment mass spectrum corresponding to a respective candidate molecular species”, are merely data characterization which can be viewed as nothing more than an attempt to generally link the use of the judicial exception to the technological environment of mass spectrometry analysis. They do not meet any of the criteria set forth in MPEP 2106.04(d)(2) and/or MPEP 2106.05(a) to integrate the recited judicial exception into a practical application or reflect any “inventive concept”/”qualified improvement”. Applicant’s arguments in this regard are thus unpersuasive.
Applicant further argues that (REMARKS, p.9-10):
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Examiner respectfully disagrees. Claim 1 of Example 3 of USPTO Subject Matter Eligibility Examples recites a computer-implemented method for halftoning a gray scale image. It is held that the claim is eligible under the 2019 PEG because the claim includes additional limitations (e.g., comparing the blue noise mask to a gray scale image to transform the gray scale image to a binary image array and converting the binary image array into a halftoned image) that tie the mathematical operation (the blue noise mask) to the processor’s ability to process digital images. The claim, when taken as a whole, does not simply describe the generation of a blue noise mask via a mathematical operation and receiving and storing data, but combines the steps of generating a blue noise mask with the steps for comparing the image to the blue noise mask and converting the resulting binary image array to a halftoned image. By this, the claim goes beyond the mere concept of simply retrieving and combining data using a computer.
In the instant case, the representative claim 16 (similarly, the claims 1 and 18) of the present application recites the additional limitations: (S1) obtaining a set of candidate mass spectra for the mass spectrometry data, wherein each candidate mass spectrum corresponds to a respective candidate molecular species, wherein the one or molecular species are one or more precursor molecular species, the mass spectrometry data is a fragment mass spectrum derived from the one or more precursor molecular species, and each candidate mass spectrum is a candidate fragment mass spectrum corresponding to a respective candidate molecular species; and (S3) providing, for one or more of the candidate molecular species, a respective indication of a match in the mass spectrum, based at least in part on the optimized set of mass spectra coefficients. Under the BRI, it is deemed that the additional limitation (S1) encompasses a process of gathering the data/information necessary for performing the abstract idea, while the limitation (S3) encompasses merely an insignificant post-solution activity of outputting the results of the abstract idea (such as printing or displaying the related information). None of the additional limitations (S1) and (S3) of the present application ties the math/mental operation (S2) to the processor’s ability to process such tasks as comparing digital images and converting the resulting binary image array to a halftoned image which “allow the computer to use less memory than required for prior masks, result in faster computation time without sacrificing the quality of the resulting image as occurred in prior processes, and produces an improved digital image.” The decision in USPTO Example 3 is fact specific and accordingly is not analogous to the instant claims of the present application.
Claim 2 of USPTO Example 48 recites the additional limitation step (f) “synthesizing speech waveforms from the masked clusters, wherein each speech waveform corresponds to a different source sn”. This step requires converting the result of step (e) into separate speech signals in the time domain. Claim 2 of USPTO Example 48 further recites the additional limitation step (g) “combining the speech waveforms to generate a mixed speech signal x' by stitching together the speech waveforms corresponding to the different sources sn, excluding the speech waveform from a target source ss such that the mixed speech signal x' includes speech signals from the different sources sn, where n ∈ {1, . . . N}, and excludes the speech signal from the target source ss” which combines the speech waveforms to generate a mixed speech signal by stitching together speech waveforms corresponding to the different sources excluding the speech signal from a target source. It is held that, while on their own steps (b)-(e) recite judicial exceptions, steps (f) and (g) are directed to creating a new speech signal that no longer contains extraneous speech signals from unwanted sources thus integrate the abstract idea into a practical application. Further, claim 2 of Example 48 reflects the improvement as discussed in the disclosure by reciting details of how the DNN aids in the cluster assignments to correspond to the sources identified in the mixed speech signal, which are then synthesized into separate speech waveforms in the time domain and converted into a mixed speech signal, excluding audio from the undesired source. Accordingly, Examiner asserts that the decision in claim 2 of Example 48 is fact specific and not analogous to the instant claims of the present application.
Applicant further argues that (REMARKS, p.10):
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Examiner respectfully disagrees. The examiner’s position is that the claims at issue are directed to a judicial exception reciting a series of mathematical concepts and mental process, which falls within a combination of the “Mental Process” and “Mathematical Concepts” groupings of Abstract Ideas defined by the 2019 PEG. The courts have concluded that these abstract ideas can be performed by a human using a pen and paper or with a general purpose computer being used to automate well-known manual processes. The courts noted that even though the claimed method may require the use of a computer, methods that can be performed mentally with the aid of pen and paper, or which are the equivalent of human mental work, are unpatentable abstract ideas "even when performed by a computer". Also, the courts have decided that storing and retrieving information in memory as well-understood, routine, conventional activity as a computer function when claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (MPEP § 2106.05(d)(II)). Moreover, the courts have decided that receiving or transmitting data over a network as well-understood, routine, conventional activity when claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (MPEP § 2106.05(d)(II) other types of activities example i. receiving or transmitting data over a network, OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015) (sending messages over a network). Accordingly, Applicant’s arguments in this regards are unpersuasive.
Regarding the 102/103 rejection, Applicant argues (REMARKS, p.13):
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Examiner respectfully disagrees. With the BRI to the claims, Examiner asserts that Peckner teaches an objective function defined as: “We consider a library precursor to be identified by Specter if this elution profile contains a peak (local maximum) of at least five consecutive coefficients that are greater than 1 …. This is a physical constraint that recognizes that total ion intensities less than 1 cannot possibly correspond to meaningful signal” (see Page 9, right column, 3rd paragraph); wherein the objective function relates a linear combination of the candidate mass spectra (“S = c1× L1+ c2 × L2 +…+ cm × Lm + N”), according to the mass spectra coefficients (c1 c2 … cm), to the mass spectrometry data (see Page 9, left column, 2nd to last paragraph – Page 9, right column, 1st paragraph). Further, Peckner’s objective function contains a regularization term: “Each library spectrum is normalized so that its total ion intensity is 1, and these normalized spectra are arranged as the columns of a matrix L whose number of rows equals the length of S” (Page 9, left column, 3rd paragraph). This regularization term constrains (or, defines) the total number (i.e., the length m of the linear regression equation S) of non-zero mass spectra coefficient values (c1 c2 … cm) (Page 9, right column, 2nd, 3rd and last paragraphs). As such, this regularization term adds a penalty to the objective function to stop the linear regression model from becoming too complex or overfitting the data. That is, the optimization of the set of mass spectra coefficients by varying their values through the least-squares fitting process is subject to or dependent on the regularization term of the objective function as claimed. Accordingly, Applicant’s arguments in this regard are not persuasive.
The rest of the Applicant’s arguments are reliant upon the issues discussed above and are deemed unpersuasive as well. The rejections are therefore maintained.
Claim Rejections - 35 USC § 101
3. The following is a quotation of the appropriate paragraphs of 35 U.S.C. 101 that form the basis for the rejections under this section made in this Office action:
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.
4. Claims 1, 3-4, 7-16 and 18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Under the 2019 PEG (now been incorporated into MPEP 2106), the revised procedure for determining whether a claim is "directed to" a judicial exception requires a two-prong inquiry into whether the claim recites: (1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human interactions such as a fundamental economic practice, or mental processes); and (2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim: (3) adds a specific limitation beyond the judicial exception that is not "well-understood, routine, conventional" in the field (see MPEP § 2106.0S(d)); or (4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception.
Claims 1, 3-4, 7-16 and 18 are directed to an abstract idea of identifying molecular species in a mass spectrum.
Specifically, representative claim 16 recites:
A system for identifying one or more molecular species represented in mass spectrometry data, comprising:
a storage medium; and
a processing coupled to the storage medium, wherein the storage medium comprises processor-executable instructions for:
(S1) obtaining a set of candidate mass spectra for the mass spectrometry data, wherein each candidate mass spectrum corresponds to a respective candidate molecular species, wherein the one or molecular species are one or more precursor molecular species, the mass spectrometry data is a fragment mass spectrum derived from the one or more precursor molecular species, and each candidate mass spectrum is a candidate fragment mass spectrum corresponding to a respective candidate molecular species;
(S2) optimizing a set of mass spectra coefficients for the set of candidate mass spectra, based on the mass spectrometry data, wherein said optimizing comprises: varying the mass spectra coefficient values based on an objective function, wherein the objective function relates a linear combination of the candidate mass spectra, according to the mass spectra coefficients, to the mass spectrometry data, subject to a regularization term of the objective function constraining the number of non-zero mass spectra coefficient values; and
(S3) providing, for one or more of the candidate molecular species, a respective indication of a match in the mass spectrum, based at least in part on the optimized set of mass spectra coefficients.
The claim limitations in the abstract idea have been highlighted in bold above; the remaining limitations are “additional elements”.
The highlighted portion of the claim constitutes an abstract idea under the 2019 Revised Patent Subject Matter Eligibility Guidance and the additional elements are NOT sufficient to amount to significantly more than the judicial exceptions, as analyzed below:
Step
Analysis
1. Statutory Category ?
Yes.
System/Apparatus
2A - Prong 1: Judicial Exception Recited?
Yes.
See the bolded portion as listed above.
Under its broadest reasonable interpretation (BRI), the limitations (S2) recited in the bolded portion encompasses mathematical concepts and/or calculations, namely a series of calculations leading to one or more numerical results or answers, which also encompasses mental processes, i.e. data manipulation, evaluation and judgment, that can be performed in the human mind or by a human using a pen and paper.
Nothing in the bolded portion precludes this limitation from practically being performed in the mind and/or with the aid of pen/paper. Note, 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. See CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1372, 99 USPQ2d 1690, 1695 (Fed. Cir. 2011). See also to MPEP 2106.04(a)(2).III
Therefore, the bolded portion of instant claim 16, reciting a series of mathematical concepts and mental process, amounts to an abstract idea falling within a combination of the “Mental Process” and “Mathematical Concepts” groupings of Abstract Ideas defined by the 2019 PEG.
2A - Prong 2: Integrated into a Practical Application?
No.
Representative claim 16 recites “a storage medium; and
a processor coupled to the storage medium, wherein the storage medium comprises processor-executable instructions” at a high level of generality. Under the BRI, the combination of the processor and the storage medium reads on a general-purpose computer performing a generic computer function of processing data. The generic processor limitation is no more than mere instructions to apply the abstract idea using the general-purpose computer. It is held that performing an abstract idea using a general-purpose computer system would not amount to significantly more than the abstract algorithm itself. See, for example, Whitserve LLC v. Dropbox, Inc. and MPEP 2106.05(f).
The limitation of “mass spectrometry data” is recited broadly. The claim does not require any particular devices or sensors to obtain the “mass spectrometry data”. It could just as easily relate to the acquisition of the “mass spectrometry data” from, e.g., look-up tables as opposed to the generation of actual measurement data in real-time. Thus claim 16 would monopolize the abstract idea across a wide range of applications
Under its BRI, the limitation (S1) encompasses a process of gathering the data/information necessary for performing the abstract idea. Thus, it does not impose any other meaningful limits on the claim. See MPEP 2106.05(g)(3): … that were described as mere data gathering in conjunction with a law of nature or abstract idea. See also Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 13863, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015).
Under its BRI, the limitation (S3) encompasses a process of outputting the results of the abstract idea (such as printing or displaying the related information) which is treated as insignificant post-solution activity.
The claim as a whole does not meet any of the following criteria to integrate the abstract idea into a practical application:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to affect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception.
Various considerations are used to determine whether the additional elements are sufficient to integrate the abstract idea into a practical application. However, in all of these respects, the claim fails to recite additional elements which might possibly integrate the claim into a particular practical application. At most, it only generally links the judicial exception to a particular technological environment or field of use. See MPEP 2106.04(d)(2).
2B: Claim provides an Inventive Concept?
No.
As analyzed in Step 2A - Prong 2, the claim does not recite any additional element that amounts to be “significantly more” to integrate the abstract idea into a practical application. Further, it is deemed that none of the recited additional limitations/elements reflect an inventive concept or a qualified improvement. See MPEP 2106.05.
The claim is therefore ineligible under 35 USC 101.
Claims 1 and 18 are treated as ineligible subject matter under 35 U.S.C. § 101 for the same reasons as for claim 16 set forth above. 1, 3-4, 7-16 and 18
The dependent claims 3-4 and 7-15 inherit attributes of the independent claim 1, but does not add anything which would render the claimed invention a patent eligible application of the abstract idea. The claim merely extends (or narrows) the abstract idea which does not amount for "significantly more" because it merely adds details to the algorithm which forms the abstract idea as discussed above. In particular, limitations of the various physical parameters/variables recited in dependent claims 3-4 and 7-15, under the BRI, encompass merely data characterization which can be viewed as nothing more than an attempt to generally link the use of the judicial exception to the relevant technological environment or field of use.
Claim Rejections - 35 USC § 102
5. 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; or
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
6. Claims 1, 3-4, 8-9, 12-14, 16 and 18 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Peckner et al. (Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics, Nature Methods, 15(5): 371-378 (2018)).
Regarding claims 1, 16 and 18, Peckner discloses a system, a method, and computer program product, for identifying one or more molecular species represented in mass spectrometry data (Page 1, Abstract; Page 4, right column: “Specter identified both of the positional isomers … The peptide … is a constituent of the cytoskeletal cross-linking protein plectin … ”), comprising a storage medium and a processor coupled to the storage medium, wherein the storage medium comprises processor-executable instructions (Page 2, left column: “Specter is built on the open-source distributed computing framework Apache Spark”; see also discussion of the “open-source software tool” on Pages 1, 12 and 14) for:
obtaining a set of candidate mass spectra (L1, L2, …) for the mass spectrometry data (Page 9, left column, 1st paragraph: “ … The set of library members used to analyze S is determined by the following conditions (where L denotes a candidate library precursor): …”), wherein the one or more molecular species are one or more precursor molecular species, the mass spectrometry data is a fragment mass spectrum derived from the one or more precursor molecular species (Page 1, right column, last paragraph), and each candidate mass spectrum is a candidate fragment mass spectrum corresponding to a respective candidate molecular species (Page 9, left column, 1st paragraph; Page 9, right column, 2nd paragraph);
optimizing a set of mass spectra coefficients (c1, c2, …) for the set of candidate mass spectra, based on the mass spectrometry data (Page 2, left column, last paragraph: “These algebraic coefficients are then analyzed further to determine the final identifications and quantifications of library members”; Page 9, left column: “Finding the optimal combination. …”; Page 9, right column, 2nd, 3rd and last paragraphs), wherein said optimizing comprises:
varying the mass spectra coefficient values (Page 9, left column, 2nd to the last paragraph: “Finding the optimal combination. … Our aim is to find the non-negative linear combination of the columns of L (the normalized library spectra) that best explains S, that is, is closest to it in terms of Euclidean distance; Page 9, right column, 1st paragraph: “… of the corresponding non-negative least-squares problem, which finds the vector c of length m (where m is the number of spectral library members), all of whose entries are non-negative, such that the matrix product of L with c is as close as possible to S in the Euclidean norm among all such non-negative vectors”) based on an objective function (Page 9, right column, 3rd paragraph: “We consider a library precursor to be identified by Specter if this elution profile contains a peak (local maximum) of at least five consecutive coefficients that are greater than 1 …. This is a physical constraint that recognizes that total ion intensities less than 1 cannot possibly correspond to meaningful signal”; see also discussion of the “Specter coefficient cj” on Page 9, right column, 2nd and last paragraphs), wherein the objective function relates (i.e., to make or show a connection between) a linear combination (“S = c1× L1+ c2 × L2 +…+ cm × Lm + N”) of the candidate mass spectra, according to the mass spectra coefficients, to the mass spectrometry data, subject to a regularization term (“the library spectra are normalized to have a total ion intensity of 1”) of the objective function constraining (i.e., limiting) the number of non-zero mass spectra coefficient values (Page 9, right column, 2nd, 3rd and last paragraphs); and
providing, for one or more of the candidate molecular species, a respective indication of a match in the mass spectrum, based at least in part on the optimized set of mass spectra coefficients (Page 2, left column, last paragraph: “These algebraic coefficients are then analyzed further to determine the final identifications and quantifications of library members”; Page 9, right column, last paragraph: “we used several chromatographic peak scores to rank the quality of our identifications … The four scores associated with the precursor were then …”).
Regarding claims 3-4, Peckner discloses: wherein the step of providing comprises identifying the one or more candidate molecular species as sample molecular species represented in a chimeric mass spectrum (Page 4, left column, 2nd paragraph: “We analyzed three families of synthetic peptides, each consisting of precursors whose spectra were highly similar and whose m/z (in charge state +2) fell into the same isolation windows for DIA (Fig. 4 and Supplementary Tables 1 and 2)”; Page 7, left column, 2nd paragraph) based on the optimized set of fragment mass spectra coefficients (Page 9, right column, 2nd, 3rd and last paragraphs); wherein the precursor molecular species represented in one or more candidate fragment mass spectra are peptides or peptide precursors (Page 1, right column, last paragraph).
Regarding claim 8, Peckner discloses: wherein the respective indication comprises a quantity (e.g., a consecutive series of at least five candidates) of the corresponding candidate molecular species present in the mass spectrum (Page 9, right column, last paragraph).
Regarding claim 9, Peckner discloses: identifying the mass spectrometry data as a chimeric mass spectrum based on the optimized set of mass spectra coefficients based on the optimized set of fragment mass spectra coefficients (Page 4, left column, 2nd paragraph: “We analyzed three families of synthetic peptides, each consisting of precursors whose spectra were highly similar and whose m/z (in charge state +2) fell into the same isolation windows for DIA (Fig. 4 and Supplementary Tables 1 and 2)”; Page 7, left column, 2nd paragraph; see also Page 9, right column, 2nd, 3rd and last paragraphs).
Regarding claim 12, Peckner discloses: wherein the mass spectrometry data is part of a series of mass spectrometry data for a separation parameter wherein the regularization term comprises a constraint enforcing a relation between the mass spectra coefficient for a given candidate mass spectrum and a mass spectra coefficient of the same candidate mass spectrum determined for further mass spectrometry data of the series (Page 9, right column, 2nd paragraphs: “the library spectra are normalized to have a total ion intensity of 1 (Supplementary Note 3): when such a normalized spectrum L is multiplied by a coefficient c (meaning that the intensities of all of its peaks are multiplied by this constant), the total ion intensity of the resulting scaled spectrum c × L can be nothing other than c”; see also Page 9, right column, 3rd paragraph).
Regarding claim 13, Peckner discloses: wherein the regularization term comprises an L1 norm (e.g., at least five consecutive coefficients) of the mass spectra coefficient values, wherein optionally the regularization term comprises an L2 norm (coefficients must be greater than 1) of the mass spectra coefficient values (Page 9, right column, 3rd paragraph).
Regarding claim 14, Peckner discloses: wherein the optimizing step further comprises varying a parameter (e.g., the number of the “consecutive Coefficients” must be equal to or greater than five, “where coefficients are considered consecutive only if they are calculated relative to sequential MS2 spectra for which the precursor satisfies the conditions”) specifying a degree of regularization of the regularization term (Page 9, right column, 3rd and last paragraphs: by inherency, more number of “consecutive Coefficients” reflects higher degree of regularization of the regularization term).
Claim Rejections - 35 USC § 103
7. 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 of this title, 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.
8. Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Peckner et al. in view of Wang et al. (US 20060255258 A1).
Regarding claim 15, Peckner does not mention explicitly: wherein the objective function provides a measure of difference between the linear combination of the candidate mass spectra and the mass spectrometry data, optionally wherein the step of varying is carried out to obtain an extremum value of the objective function.
Wang discloses a computer-implemented system and method for identifying one or more molecular species represented in mass spectrometry data (para. 0016, 0048, 0060: “performing chromatographic peak detection using known peak shape functions with regression analysis; reporting regression coefficients from the regression analysis as one of peak area and peak location”) by optimizing a set of mass spectra coefficients for a linear combination (para. 0119: “r=Kc+e”) of a set of candidate mass spectra (para. 0121: “The components arranged in the columns of matrix K will be referred to as peak components, which may optionally include any baseline of known functionality …”) based on measured mass spectrometry data (para. 0119-0122), wherein said optimizing comprises: varying the mass spectra coefficient values (inherent to the least squares fitting process discussed in para. 0198, 0126 and 0132) based on an objective function (e.g., the residual sum of squares RSS, which is calculated as the sum of the squared residuals across all data points, wherein the RSS is minimized by finding the optimal coefficients that minimize the objective function, ensuring an efficient fit to the data), wherein the objective function relates a linear combination (para. 0119: “r=Kc+e”) of the candidate mass spectra, according to the mass spectra coefficients, to the mass spectrometry data, and wherein the objective function provides a measure of difference between the linear combination of the candidate mass spectra and the mass spectrometry data, optionally wherein the step of varying is carried out to obtain an extremum value (i.e., a minimum of the RSS) of the objective function (para. 0126, 0132).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to incorporate Wang’s teaching of linear regression fitting technique into Peckner to provide an alternative mechanism for identifying one or more molecular species represented in mass spectrometry data. The skilled person would conceive and apply such modification, as intended use of known inventions, without needing inventive skill but depending on practical considerations and according to the dictates of the circumstances. Further, one of ordinary skill in the art would have recognized that the results of such a combination were predictable for performing chromatographic peak detection since the use of that known technique provides the rationale to arrive at a conclusion of obviousness.
Examiner’s Note
9. While there are related references that discuss identifying molecular species in a mass spectrum, the prior art of record does not specifically provide teachings for the claimed limitations including: wherein for a given candidate mass spectrum: a spectrum similarity score is calculated between the given candidate mass spectrum and a further mass spectrum, wherein the further mass spectrum is generated by subtracting each of the other candidate mass spectra from the mass spectrometry data according to the optimized set of mass spectra coefficients (as recited in claim 7); wherein the step of providing further comprises generating reporter ion intensities for one or more of candidate mass spectra and generating corrected reporter ion intensities for at least one of the precursor molecular species based on a difference between a reporter ion intensity for the precursor molecular species generated from the mass spectrometry data and the reporter ion intensities for the one or more candidate mass spectra scaled by the corresponding optimized mass spectra coefficients (as recited in claim 10), obtaining a respective set of reporter ion intensities for each item of mass spectrometry data, each reporter ion intensity of the set corresponding to a respective isobarically labelled sample of the mixed sample, and calculating, for at least one of the peptide precursors, a fraction of the abundance of the peptide in the mixed sample corresponding to one of the samples, based on the sets of reporter ion intensities and the sets of optimized mass spectra coefficients (as recited in claim 11). It is these limitations, as they are claimed in the combination in independent claim 1, that would make these claims distinguish over the prior art of record. As such, pending claims 7, 10 and 11 would be allowable if rewritten in independent form including all the limitations of the base claim and any intervening claims and to overcome the rejection under 35 USC 101 as set forth in sections 3-4 above in this Office action.
Conclusion
10. THIS ACTION IS MADE FINAL. 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 extension fee 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.
Contact Information
11. Any inquiry concerning this communication or earlier communications from the examiner should be directed to XIUQIN SUN whose telephone number is (571)272-2280. The examiner can normally be reached 9:30am-6:00pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Shelby A. Turner can be reached on (571) 272-6334. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/X.S/Examiner, Art Unit 2857
/SHELBY A TURNER/Supervisory Patent Examiner, Art Unit 2857
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