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 .
DETAILED ACTION
Specification
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant’s cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 10 December 2025 was filed. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 102
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 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.
Claim(s) 1-20 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bauer et al (US 2007/0158542).
Bauer e al disclose the following claimed features:
Regarding claim 1, a computer-implemented method (Figure 3) comprising: receiving a spectrum generated by analysis of a sample with a laboratory analytical instrument, the spectrum comprising a plurality of detected peaks (paragraph [0073]); receiving a list of predicted fragments that are potentially present in the sample (paragraph [0073]); matching the plurality of detected peaks against the list of predicted fragments based on a mass tolerance to generate a list of potential matches (paragraph [0073]); building one or more charge clusters from the list of potential matches based on how well an intensity of each potential match in the list corresponds to an expected intensity of the corresponding predicted fragment (paragraph [0073]); calculating an isotope profile fit for each of the one or more charge clusters (paragraph [0074]); and for each of the one or more charge clusters whose isotope profile fit exceeds a predetermined profile fit threshold, storing the charge cluster in a finalized match set (paragraph [0074]).
Regarding claim 2, further comprising: identifying an ambiguous set of detected peaks capable of being matched to two or more predicted fragments; and flagging the ambiguous set of detected peaks with an indication of the two or more predicted fragments (paragraph [0074]).
Regarding claim 3, further comprising selecting a best fit from the finalized match set based on which charge cluster accounts for the most total intensity of the corresponding detected peak (paragraph [0074]).
Regarding claim 4, further comprising: calculating a quality metric for at least one of the charge clusters stored in the finalized match set, the quality metric comprising one or more of an isotope spacing mean, an isotope spacing median, an isotope spacing deviation, a mass error mean, a mass error median, or a mass error deviation; and displaying the calculated quality metric on a display (paragraph [0074]).
Regarding claim 5, wherein the expected intensity is associated with a threshold value, the threshold value being in the range of 60%-85% (paragraph [0074]).
Regarding claim 6, wherein a first charge cluster and a second charge cluster are matched to a same detected peak, and after the first charge cluster is matched to the detected peak, an intensity of the detected peak is discounted when matching the second charge cluster (paragraph [0074]).
Regarding claim 7, further comprising defining a maximum charge for a precursor ion in the analysis, wherein the list of predicted fragments is limited based on the maximum charge for the precursor ion (paragraphs [0074], [0076]).
Regarding claim 8, a non-transitory computer-readable storage medium, the computer-readable storage medium including instructions that when executed by a computer (paragraphs [0063], [0091], [0092]), cause the computer to: receive a spectrum generated by analysis of a sample with a laboratory analytical instrument, the spectrum comprising a plurality of detected peaks (paragraph [0073]); receive a list of predicted fragments that are potentially present in the sample (paragraph [0073]); match the plurality of detected peaks against the list of predicted fragments based on a mass tolerance to generate a list of potential matches (paragraph [0073]); build one or more charge clusters from the list of potential matches based on how well an intensity of each potential match in the list corresponds to an expected intensity of the corresponding predicted fragment (paragraph [0073]); calculate an isotope profile fit for each of the one or more charge clusters (paragraph [0074]); and for each of the one or more charge clusters whose isotope profile fit exceeds a predetermined profile fit threshold, store the charge cluster in a finalized match set (paragraph [0074]).
Regarding claim 9, further storing instructions for: identifying an ambiguous set of detected peaks capable of being matched to two or more predicted fragments; and flagging the ambiguous set of detected peaks with an indication of the two or more predicted fragments (paragraph [0074]).
Regarding claim 10, further storing instructions for selecting a best fit from the finalized match set based on which charge cluster accounts for the most total intensity of the corresponding detected peak (paragraph [0074]).
Regarding claim 11, further storing instructions for: calculating a quality metric for at least one of the charge clusters stored in the finalized match set, the quality metric comprising one or more of an isotope spacing mean, an isotope spacing median, an isotope spacing deviation, a mass error mean, a mass error median, or a mass error deviation; and displaying the calculated quality metric on a display (paragraph [0074]).
Regarding claim 12, wherein the expected intensity is associated with a threshold value, the threshold value being in the range of 60%-85% (paragraph [0074]).
Regarding claim 13, wherein a first charge cluster and a second charge cluster are matched to a same detected peak, and after the first charge cluster is matched to the detected peak, an intensity of the detected peak is discounted when matching the second charge cluster (paragraph [0074]).
Regarding claim 14, further storing instructions for defining a maximum charge for a precursor ion in the analysis, wherein the list of predicted fragments is limited based on the maximum charge for the precursor ion (paragraphs [0074, [0076]).
Regarding claim 15, a computing apparatus comprising: a processor; and a memory storing instructions (paragraphs [0063], [0092]) that, when executed by the processor, configure the apparatus to: receive a spectrum generated by analysis of a sample with a laboratory analytical instrument, the spectrum comprising a plurality of detected peaks (paragraph [0073]); receive a list of predicted fragments that are potentially present in the sample (paragraph [0073]); match the plurality of detected peaks against the list of predicted fragments based on a mass tolerance to generate a list of potential matches (paragraph [0073]); build one or more charge clusters from the list of potential matches based on how well an intensity of each potential match in the list corresponds to an expected intensity of the corresponding predicted fragment (paragraph [0073]); calculate an isotope profile fit for each of the one or more charge clusters (paragraph [0074]); and for each of the one or more charge clusters whose isotope profile fit exceeds a predetermined profile fit threshold, store the charge cluster in a finalized match set (paragraph [0074]).
Regarding claim 16, the memory further storing instructions for: identifying an ambiguous set of detected peaks capable of being matched to two or more predicted fragments; and flagging the ambiguous set of detected peaks with an indication of the two or more predicted fragments (paragraph [0074]).
Regarding claim 17, the memory further storing instructions for selecting a best fit from the finalized match set based on which charge cluster accounts for the most total intensity of the corresponding detected peak (paragraph [0074]).
Regarding claim 18, the memory further storing instructions for: calculating a quality metric for at least one of the charge clusters stored in the finalized match set, the quality metric comprising one or more of an isotope spacing mean, an isotope spacing median, an isotope spacing deviation, a mass error mean, a mass error median, or a mass error deviation; and displaying the calculated quality metric on a display (paragraph [0074]).
Regarding claim 19, wherein the expected intensity is associated with a threshold value, the threshold value being in the range of 60%-85% (paragraph [0074]).
Regarding claim 20, wherein a first charge cluster and a second charge cluster are matched to a same detected peak, and after the first charge cluster is matched to the detected peak, an intensity of the detected peak is discounted when matching the second charge cluster (paragraph [0074]).
Response to Arguments
Applicant’s arguments, see Applicant’s Remarks, filed 10 December 2025, with respect to the rejection(s) of claim(s) 1-20 under 101 rejection have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of Bauer et al (US 2007/0158542).
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AN H DO whose telephone number is (571)272-2143. The examiner can normally be reached on M-F 7:5:30pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Stephen Meier can be reached on 571-272-2149. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/AN H DO/Primary Examiner, Art Unit 2853