Ex Parte SatulovskyDownload PDFPatent Trial and Appeal BoardOct 30, 201412466045 (P.T.A.B. Oct. 30, 2014) Copy Citation UNITED STATES PATENT AND TRADEMARK OFFICE ____________ BEFORE THE PATENT TRIAL AND APPEAL BOARD ____________ Ex parte JAVIER E. SATULOVSKY ____________ Appeal 2012-007900 Application 12/466,045 Technology Center 2800 ____________ Before CHUNG K. PAK, LINDA M. GAUDETTE, and KAREN M. HASTINGS, Administrative Patent Judges. GAUDETTE, Administrative Patent Judge. DECISION ON APPEAL Appeal 2012-007900 Application 12/466,045 2 Appellant appeals under 35 U.S.C. § 134(a) from the Examiner’s decision1 finally rejecting claims 1–20.2 We have jurisdiction under 35 U.S.C. § 6(b). We REVERSE. “[M]ass spectrometers measure mass-to-charge ratios of charged samples, enabling contents of the samples to be identified.” See Spec.3 [0001]. Ions of a protein in a sample are volatilized and provided to a mass analyzer of the mass spectrometer. Id. The proteins and peptides are then identified, for example, by matching the measured mass-to-charge ratios to a database of mass-to-charge ratios of known proteins and peptides. Id. “Tandem mass spectrometry (MS/MS) provides multiple stage measurements of a sample, for example, using separate analyzers corresponding to the multiple stages, or using a single analyzer to analyze the sample multiple times.” Id. The present invention relates to a system for performing tandem mass spectrometry analysis which is said to provide a more efficient identification of peptides as compared to prior art systems. See id. at [0012]. Of the appealed claims, claims 1, 14, and 20 are independent. Claim 1 is representative of the claimed invention, and is reproduced below from the Claims Appendix to the Appeal Brief: 1. A system for performing tandem mass spectrometry (MS/MS) analysis of a sample, the system comprising: 1 Final Office Action mailed August 18, 2011 (“Final Act.”). 2 Appeal Brief filed January 17, 2012 (“App. Br.”). 3 Specification filed May 14, 2009. Appeal 2012-007900 Application 12/466,045 3 a mass spectrometer configured to perform a mass spectrometry (MS) scan of an ionized sample to provide a mass of an observed peak corresponding to a precursor ion; and a processor configured to perform operations comprising: determining whether the mass of the observed peak matches a mass of at least one of a plurality of expected peptides on a dynamic watch list, the expected peptides corresponding to a protein in the sample; and calculating a score of an accuracy of the determination when the mass of the observed peak is determined to match the mass of at least one of the plurality of expected peptides, wherein the peptide is excluded from the dynamic watch list and is excluded from a full tandem mass spectrometry (MS/MS) scan by the mass spectrometer when the accuracy score indicates that the determination is accurate. The Examiner maintains the following grounds of rejection4: 1. claims 1–8 and 11–20 under 35 U.S.C. § 103(a) as unpatentable over Freitas et al. (U.S. Patent App. Pub. No. 2007/0282537 A1, published Dec. 6, 2007) in view of Le Blanc (U.S. Patent App. Pub. No. 2004/0251409 A1, published Dec. 16, 2004); 2. claim 9 under 35 U.S.C. § 103(a) as unpatentable over Freitas as modified by Le Blanc and further in view of Geromanos et al. (U.S. Patent App. Pub. No. 2007/0009898 A1, published Jan. 11, 2007). 3. claim 10 under 35 U.S.C. § 103(a) as unpatentable over Freitas as modified by Le Blanc and further in view of Schulzknappe et al. (U.S. Patent App. Pub. No. 2010/0167267 A1, published July 1, 2010). 4 The Examiner has withdrawn the rejection of claim 2 under 35 U.S.C. §112, second paragraph. Examiner’s Answer mailed February 13, 2012 (“Ans.”), 4. Appeal 2012-007900 Application 12/466,045 4 Freitas discloses “a program that matches tandem mass spectra created automatically and simultaneously to theoretical peptide sequences derived from a protein database.” Freitas [0019]. Freitas discloses use of a special data structure, referred to as “peprecord,” that “consists of nested matrices used in the MS/MS database search program to store all the peptides that has [sic] been searched.” Id. at [0186]. According to Freitas, [w]hen [a] new peptide sequence is to be searched, the MS/MS database search program checks the sequence against peprecord to see if it has been searched before. If that is the case, the peptide will be skipped and not be searched by the MS/MS database search program again. Otherwise the peptide sequence will be added into peprecord and searched by the MS/MS database search program. A modified hashing and binary searching algorithm is used to accelerate the check/storage process. Id. at [0187]. Le Blanc discloses “a method of obtaining mass spectrographic data of a substance.” Le Blanc [0010]. “The ion (or ions) having the fastest rising mass signal(s) is/are then identified by comparing the current mass spectrum against a spectrographic background which may comprise one or more previously acquired mass spectrums of the output.” Id. “[T]he identified ion may be placed on a dynamic exclusion list. This ion will then not be considered as the fastest rising mass signal thereby enabling the identification and selected [sic] of the next-fastest rising ion for a secondary mass analysis.” Id. at [0012]. The Examiner finds Freitas discloses the invention as claimed in the independent claims with the exception of a processor configured to exclude a peptide from the dynamic watch list as recited in claim 1, and from a full tandem mass spectrometry scan in the manner recited in claims 1, 14, and Appeal 2012-007900 Application 12/466,045 5 20. Ans. 5–6. The Examiner finds Le Blanc teaches the principle of excluding ions from a dynamic watch list and a full tandem mass spectrometry scan when an ion is accurately identified. Id. at 6, 14. The Examiner determines that, in view of the teaching of LeBlanc it would have been obvious to one of ordinary skill in the art at the time the invention was made to exclude a peptide from Freitas’ dynamic watch list and from a full tandem mass spectrometry scan by the mass spectrometer when the accuracy score indicates that the determination is accurate, because this would result in increased speed and efficiency, while also reducing the processing power required for mass determination. Id. at 6. Appellant contends Freitas seeks to improve mass accuracy, e.g., by reducing noise peaks, but does not disclose or suggest taking any action based on accuracy scoring as required by the appealed claims. See Reply Br.5 5-6. Appellant argues the Examiner has failed to identify evidence which supports a finding that one of ordinary skill in the art would have been motivated to modify Freitas’ system to exclude peptides from a watch list or a full MS/MS scan based on accuracy scoring in the manner recited in the appealed claims. See App. Br. 13. In this regard, Appellant contends the Examiner erred in finding LeBlanc discloses a processor configured to: (1) exclude ions from a full MS/MS scan based on an accuracy score; and (2) exclude ions from a dynamic watch list. App. Br. 12-13. We agree with Appellant that, in the paragraphs cited by the Examiner, LeBlanc describes a system configured to perform the opposite of the claimed functions, i.e., LeBlanc performs a full MS/MS scan on an ion based on a “best match,” and then includes the ion on a dynamic exclusion list. LeBlanc ¶¶ [0010-0012]. 5 Reply Brief filed April 13, 2012. Appeal 2012-007900 Application 12/466,045 6 The Examiner has not explained adequately how, or why, one of ordinary skill in the art would have configured Freitas’ system, wherein peptides are added to a search (watch) list, such that peptides are also excluded from the list and a full MS/MS scan, based on LeBlanc which describes adding ions to (not excluding them from) a list after performing a full scan. The Examiner has not directed us to disclosure in LeBlanc, or identified other evidence, which supports a finding that one of ordinary skill in the art would have found it “highly desirable” to modify Freitas in the manner claimed, in order to “increase the speed and efficiency of the [system] while also reducing the processing power required for mass determination.” Ans. 6. In view of the foregoing, we agree with Appellant that the Examiner’s obviousness determination is based on improper hindsight reasoning. See App. Br. 13. Therefore, the Examiner’s decision to reject claims 1–20 is: REVERSED cdc Copy with citationCopy as parenthetical citation