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 .
Response to Amendment
Applicant’s amendments to the claims, filed 12/31/2025, are accepted and appreciated by the examiner.
Response to Arguments
Applicant’s arguments filed 12/31/2025 have been fully considered but they are not persuasive. With respect to the 35 U.S.C.§112(b) Rejection, Applicant’s amendment to change the dependency of claim 7 does not resolve the issue. It is still not clear what sections, the sections is referring to because claim 6 recites four sections, pre-peak section, ascending peak section, post-peak section. With regards to the 35 U.S.C. §103 and the amended limitations, Applicant’s arguments are moot in view of the new grounds of rejection as necessitated by Applicant’s amendments.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 7 is 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 7 recites “the sections”. There is insufficient antecedent basis for this limitation in the claim.
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.
Claim(s) 1-4, 7-10, 13, 15-19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Pfaff (US 2019/0295830 A1) Wright (US 2010/0100336 A1).
With respect to Claim 1 Pfaff teaches A computer-implemented method for detecting at least one interference and/or at least one artefact in at least one chromatogram determined by at least one mass spectrometry device, wherein the at least one chromatogram comprises a plurality of raw data points, the method comprising: (See Abstract A computer implemented method for compressing mass spectrometry data, the method comprising decomposing the mass spectrometry data of a mass stream emitted from a separation device as a function of a separation parameter into a plurality of mass traces, wherein the mass spectrometry data are generated by analysis in a mass spectrometer; identifying erroneous mass traces in the plurality of mass traces by applying an event detection algorithm to each of the plurality of mass traces; and forming a compressed version of the mass spectrometry data from the mass traces and the mass spectrometry data corresponding to the identified erroneous mass traces) retrieving the at least one chromatogram by at least one processing device; (See Fig 1. And Para[0070] The analysis system 150 is arranged to receive the mass spectrometry data 131 generated by the mass spectrometer 130. The analysis system 150 may be (or comprise) one more computer systems, such as a computer system 200 described in more detail shortly with reference to FIG. 2. The analysis system 150 is arranged to generate one or more mass traces 152, based on the mass spectra 132 in the received mass spectrometry data.) applying, by the at least one processing device, at least one peak fit modelling to the at least one chromatogram; (See Para[0030] Optionally, the event may also comprise any of the following properties or measurements determined by the event detection algorithm: one or more peak widths; a measure of the asymmetry of the peak; a measure of the quality of fit to a mod) determining, by the at least one processing device, information about residuals of the raw data points (See Para[0031] Typically erroneous mass traces are ones for which the event detection algorithms fails to detect events, and/or fails to fit a pre-defined model peak to the mass trace with above a threshold degree of certainty (or goodness of fit measure).); and detecting, by the at least one processing device, the at least one interference and/or the at least one artefact by comparing the determined information about the residuals with at least one pre-determined threshold, (See Para[0152]-[0156] A mass trace may be considered to be erroneous if no such event was detected and/or if the event itself is considered erroneous. Typically an erroneous event is one where the goodness of fit of the model peak to the mass trace is below a pre-defined threshold.). However Pfaff is silent to the language of wherein each residual is indicative of a difference between a value of a raw data point at a position of the chromatogram and a value of a final peak fit at the position wherein, if the determined information about the residuals exceed the pre-determined threshold, the at least one interference and/or the at least one artefact is detected Nevertheless Pfaff teaches See Para[0161],[0168]-[0174] It will be appreciated that further processing of the erroneous mass traces may be performed by the compression system. For example, for erroneous mass traces having any of: ….For example, where there are multiple convoluted chromatographic peaks additional mass and time information may be calculated. Where there are m/z deflections due to adjacent mass traces a set of flags (e.g. deflection detected, reference to the interfering peak; mass corrected etc.) may be determined. Therefore it would be obvious to one of ordinary skill in the art where the threshold will determine whether mass traces are kept or discarded and these traces are used to determine interference, because using only the kept traces would improve accuracy. Furthermore Wright teaches wherein each residual is indicative of a difference between a value of a raw data point at a position of the chromatogram and a value of a final peak fit at the position (See Para[0063]-[0064] The positive residual (the average difference between the current difference spectrum and the synthetic peak function) and chi-squared are calculated and temporarily stored during or after each such constrained fit. As long as chi-squared doesn't grow beyond a certain multiple of its initial value, for instance 3-times its initial value, the search continues until the positive residual decreases to below a certain limit, or until the limit of peak width variation is reached.) It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Pfaff and have a residual such as that of Wright One of ordinary skill would have been motivated to modify Pfaff, in order to get an accurate measurement of the signal to noise. With respect to Claim 2 Pfaff teaches The method according to claim 1, wherein retrieving the at least one chromatogram comprises fully automatically retrieving the at least one chromatogram; wherein applying the at least one peak fit modelling to the at least one chromatogram comprises fully automatically applying the at least one peak fit modelling to the at least one chromatogram; wherein determining the information about residuals of the raw data points comprises fully automatically determining the information about residuals of the raw data points; and wherein detecting the at least one interference and/or the at least one artefact comprises fully automatically detecting the at least one interference and/or the at least one artefact. (See Para[0007] The number of individual mass spectra produced by such combined separation/mass spectrometry techniques is often very large (for a typical LC/MS analysis it can be of the order of thousands of mass spectra). This means, in turn the number of mass traces identified is often correspondingly large (e.g. of the order of around 1,000 to 1,000,000 mass traces). Given this, the generation of mass traces typically requires automation.) With respect to Claim 3 Pfaff teaches The method according to claim 1, further comprising measuring the at least one chromatogram using the mass spectrometry device. (See Para[0007] The number of individual mass spectra produced by such combined separation/mass spectrometry techniques is often very large (for a typical LC/MS analysis it can be of the order of thousands of mass spectra). This means, in turn the number of mass traces identified is often correspondingly large (e.g. of the order of around 1,000 to 1,000,000 mass traces). Given this, the generation of mass traces typically requires automation.) With respect to Claim 4 Pfaff teaches The method according to claim 1, further comprising determining a position of the at least one interference and/or the at least one artefact in the at least one chromatogram. ( See Para[0168]-[0174]) With respect to Claim 8 Pfaff teaches The method according to claim 1, wherein the information about the residuals is one or more of the residuals, a mean of the residuals, a median of the residuals, a sum of the residuals, a product of the residuals, and/or an integral of the residuals. (See Para[0153]) With respect to Claim 7 Pfaff teaches The method according to claim 4, wherein determining the position of the at least one interference and/or the at least one artefact in the at least one chromatogram comprises: determining the information about the residuals of the raw data points and comparing the information about the residuals with the at least one pre-determined threshold for each of the sections. (See Para[0031] Typically erroneous mass traces are ones for which the event detection algorithms fails to detect events, and/or fails to fit a pre-defined model peak to the mass trace with above a threshold degree of certainty (or goodness of fit measure).); With respect to Claim 9 Pfaff teaches The method according to claim 1, wherein applying the at least one peak fit modelling to the at least one chromatogram comprises applying one or more of at least one polynomial interpolation, at least one exponentially modified Gaussian function, at least one Gauss-Newton algorithm, and at least one Fourier-Transformation. (See Para[0108],[0149],[0177]) With respect to Claim 10 Pfaff teaches The method according to claim 1, further comprising at least one preprocessing step comprising one or more of: selecting at least one region of interest in the at least one chromatogram; selecting at least one predefined retention time interval; performing at least one smoothing by applying one or more of a moving average filter, a Gaussian filter, a discrete wavelet de-noising, a Savitzky-Golay smoothing, a Loess smoothing; and/or performing at least one background subtraction by applying one or more of an asymmetric weighted least squares fit with regularization, a morphological top hat filter, a discrete or continuous wavelet base background determination, and/or a moving average minimum. (See Para[0014]-[0019])
With respect to Claim 13 Pfaff teaches A processing system for automatic detection of at least one interference and/or at least one artefact in at least one chromatogram determined by at least one mass spectrometry device, wherein the at least one chromatogram comprises a plurality of raw data points, the processing system comprising: (See Abstract A computer implemented method for compressing mass spectrometry data, the method comprising decomposing the mass spectrometry data of a mass stream emitted from a separation device as a function of a separation parameter into a plurality of mass traces, wherein the mass spectrometry data are generated by analysis in a mass spectrometer; identifying erroneous mass traces in the plurality of mass traces by applying an event detection algorithm to each of the plurality of mass traces; and forming a compressed version of the mass spectrometry data from the mass traces and the mass spectrometry data corresponding to the identified erroneous mass traces) at least one data collector configured to retrieve the at least one chromatogram; (See Fig 1. And Para[0070] The analysis system 150 is arranged to receive the mass spectrometry data 131 generated by the mass spectrometer 130. The analysis system 150 may be (or comprise) one more computer systems, such as a computer system 200 described in more detail shortly with reference to FIG. 2. The analysis system 150 is arranged to generate one or more mass traces 152, based on the mass spectra 132 in the received mass spectrometry data.) at least one fitting unit configured to apply at least one peak fit modelling to the at least one chromatogram; (See Para[0030] Optionally, the event may also comprise any of the following properties or measurements determined by the event detection algorithm: one or more peak widths; a measure of the asymmetry of the peak; a measure of the quality of fit to a mod) at least one mathematical unit configured to determine information about residuals of the raw data points; and (See Para[0031] Typically erroneous mass traces are ones for which the event detection algorithms fails to detect events, and/or fails to fit a pre-defined model peak to the mass trace with above a threshold degree of certainty (or goodness of fit measure).); at least one identification unit configured to detect the at least one interference and/or the at least one artefact by comparing the determined information about the residuals with at least one pre-determined threshold (See Para[0152]-[0156] A mass trace may be considered to be erroneous if no such event was detected and/or if the event itself is considered erroneous. Typically an erroneous event is one where the goodness of fit of the model peak to the mass trace is below a pre-defined threshold.)., However Pfaff is silent to the language of wherein each residual is indicative of a difference between a value of a raw data point at a position of the chromatogram and a value of a final peak fit at the position wherein, if the determined information about the residuals exceed the pre-determined threshold, the at least one interference and/or the at least one artefact is detected Nevertheless Pfaff teaches See Para[0161],[0168]-[0174] It will be appreciated that further processing of the erroneous mass traces may be performed by the compression system. For example, for erroneous mass traces having any of: ….For example, where there are multiple convoluted chromatographic peaks additional mass and time information may be calculated. Where there are m/z deflections due to adjacent mass traces a set of flags (e.g. deflection detected, reference to the interfering peak; mass corrected etc.) may be determined. Therefore it would be obvious to one of ordinary skill in the art where the threshold will determine whether mass traces are kept or discarded and these traces are used to determine interference, because using only the kept traces would improve accuracy. Furthermore Wright teaches wherein each residual is indicative of a difference between a value of a raw data point at a position of the chromatogram and a value of a final peak fit at the position (See Para[0063]-[0064] The positive residual (the average difference between the current difference spectrum and the synthetic peak function) and chi-squared are calculated and temporarily stored during or after each such constrained fit. As long as chi-squared doesn't grow beyond a certain multiple of its initial value, for instance 3-times its initial value, the search continues until the positive residual decreases to below a certain limit, or until the limit of peak width variation is reached.) It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Pfaff and have a residual such as that of Wright One of ordinary skill would have been motivated to modify Pfaff, in order to get an accurate measurement of the signal to noise.
With respect to Claim 15 Pfaff teaches A mass spectrometry system comprising the processing system of claim 13, and further comprising at least one mass spectrometry device comprising at least one mass filter and at least one detector. (See Para[0059])
With respect to Claim 16 Pfaff teaches One or more non-transitory machine-readable storage media comprising a plurality of instructions stored thereon that, in response to execution by at least processing device, causes a computing system to: (See Abstract A computer implemented method for compressing mass spectrometry data, the method comprising decomposing the mass spectrometry data of a mass stream emitted from a separation device as a function of a separation parameter into a plurality of mass traces, wherein the mass spectrometry data are generated by analysis in a mass spectrometer; identifying erroneous mass traces in the plurality of mass traces by applying an event detection algorithm to each of the plurality of mass traces; and forming a compressed version of the mass spectrometry data from the mass traces and the mass spectrometry data corresponding to the identified erroneous mass traces) retrieve at least one chromatogram, wherein the at least one chromatogram comprises a plurality of raw data points; (See Fig 1. And Para[0070] The analysis system 150 is arranged to receive the mass spectrometry data 131 generated by the mass spectrometer 130. The analysis system 150 may be (or comprise) one more computer systems, such as a computer system 200 described in more detail shortly with reference to FIG. 2. The analysis system 150 is arranged to generate one or more mass traces 152, based on the mass spectra 132 in the received mass spectrometry data.) apply at least one peak fit modelling to the at least one chromatogram; (See Para[0030] Optionally, the event may also comprise any of the following properties or measurements determined by the event detection algorithm: one or more peak widths; a measure of the asymmetry of the peak; a measure of the quality of fit to a mod) determine information about residuals of the raw data points; and (See Para[0031] Typically erroneous mass traces are ones for which the event detection algorithms fails to detect events, and/or fails to fit a pre-defined model peak to the mass trace with above a threshold degree of certainty (or goodness of fit measure).); detect at least one interference and/or at least one artefact in the at least one chromatogram by comparing the determined information about the residuals with at least one pre-determined threshold, (See Para[0152]-[0156] A mass trace may be considered to be erroneous if no such event was detected and/or if the event itself is considered erroneous. Typically an erroneous event is one where the goodness of fit of the model peak to the mass trace is below a pre-defined threshold.). However Pfaff is silent to the language of wherein each residual is indicative of a difference between a value of a raw data point at a position of the chromatogram and a value of a final peak fit at the position wherein, if the determined information about the residuals exceed the pre-determined threshold, the at least one interference and/or the at least one artefact is detected Nevertheless Pfaff teaches See Para[0161],[0168]-[0174] It will be appreciated that further processing of the erroneous mass traces may be performed by the compression system. For example, for erroneous mass traces having any of: ….For example, where there are multiple convoluted chromatographic peaks additional mass and time information may be calculated. Where there are m/z deflections due to adjacent mass traces a set of flags (e.g. deflection detected, reference to the interfering peak; mass corrected etc.) may be determined. Therefore it would be obvious to one of ordinary skill in the art where the threshold will determine whether mass traces are kept or discarded and these traces are used to determine interference, because using only the kept traces would improve accuracy. Furthermore Wright teaches wherein each residual is indicative of a difference between a value of a raw data point at a position of the chromatogram and a value of a final peak fit at the position (See Para[0063]-[0064] The positive residual (the average difference between the current difference spectrum and the synthetic peak function) and chi-squared are calculated and temporarily stored during or after each such constrained fit. As long as chi-squared doesn't grow beyond a certain multiple of its initial value, for instance 3-times its initial value, the search continues until the positive residual decreases to below a certain limit, or until the limit of peak width variation is reached.) It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Pfaff and have a residual such as that of Wright One of ordinary skill would have been motivated to modify Pfaff, in order to get an accurate measurement of the signal to noise. With respect to Claim 17 Pfaff is silent to the language of The method according to claim 1, further comprising determining, by the at least one processing device, a curve of the residuals as a function of time. Nevertheless Wright teaches further comprising determining, by the at least one processing device, a curve of the residuals as a function of time. (See Fig.4 and Para[0046]) It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Pfaff and determine a curve such as that of Wright. One of ordinary skill would have been motivated to modify Pfaff, in order to get a proper baseline.
With respect to Claim 18 Pfaff is silent to the language of The method according to claim 17, further comprising determining, by the at least one processing device, an area under the curve of the residuals. Nevertheless Wright teaches determining, by the at least one processing device, an area under the curve of the residuals. (See Fig 3) It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Pfaff and determine an area under a curve such as that of Wright. One of ordinary skill would have been motivated to modify Pfaff, in order to get a proper baseline.
With respect to Claim 19 Pfaff is silent to the language of The method of according to claim 18, further comprising normalizing, by the at least one processing device, the area under the curve to a peak area of a fitted analyte. Nevertheless Wright teaches normalizing, by the at least one processing device, the area under the curve to a peak area of a fitted analyte. (See Fig 3 and Para[0055], [0066]-[0070]) It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Pfaff and normalize as that of Wright. One of ordinary skill would have been motivated to modify Pfaff, in order to get a proper baseline.
Claim(s) 5, 6, is/are rejected under 35 U.S.C. 103 as being unpatentable over Pfaff (US 2019/0295830 A1) in view of Wright (US 2010/0100336 A1) and Garczarek (US 2006/0080040 A1).
With respect to Claim 5 Pfaff is silent to the language of The method according to claim 4, further comprising dividing the at least one chromatogram into at least two sections. Nevertheless Garczarek teaches further comprising dividing the at least one chromatogram into at least two sections. (See Para[0002] ) It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Pfaff and divide the at least one chromatogram into at least two sections such as that of Garczarek. One of ordinary skill would have been motivated to modify Pfaff, because dividing into sections would allow one to focus on each feature and separate different items. With respect to Claim 6 Pfaff is silent to the language of The method according to claim 4, wherein the at least one chromatogram is divided into four sections, wherein the at least one chromatogram is divided into a pre-peak section defined between peak start and peak start minus full width at half maximum, an ascending peak section defined between peak start and peak maximum, a descending peak section defined between retention time and peak end and a post-peak section defined between peak end and peak end plus full width at half maximum. Nevertheless Garczarek teaches wherein the at least one chromatogram is divided into four sections, wherein the at least one chromatogram is divided into a pre-peak section defined between peak start and peak start minus full width at half maximum, an ascending peak section defined between peak start and peak maximum, a descending peak section defined between retention time and peak end and a post-peak section defined between peak end and peak end plus full width at half maximum. (See Para[0076]-[0084] Examiner notes It would,have been an obvious matter of design choice to have such sections,since such a modification would have involved a mere change in the size of a component. A change in size is generally recognized as being within the level of ordinary skill in the art. In re Rose, 105 USPQ 237 (CCPA 1955). Examiner further notes implementing the sections in a novel way to determine the interference may overcome the presented prior art) It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Pfaff wherein the at least one chromatogram is divided into four sections, wherein the at least one chromatogram is divided into a pre-peak section defined between peak start and peak start minus full width at half maximum, an ascending peak section defined between peak start and peak maximum, a descending peak section defined between retention time and peak end and a post-peak section defined between peak end and peak end plus full width at half maximum such as that of Garczarek. One of ordinary skill would have been motivated to modify Pfaff, because dividing into four sections would allow one to focus on each feature and separate different items.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YOSHIHISA ISHIZUKA whose telephone number is (571)270-7050. The examiner can normally be reached M-F 11:00-7:00.
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YOSHIHISA . ISHIZUKA
Examiner
Art Unit 2857
/YOSHIHISA ISHIZUKA/Primary Examiner, Art Unit 2857
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