Wisconsin Alumni Research Foundation

Patent Trials and Appeals Board

Jan 3, 2022

2020004677 (P.T.A.B. Jan. 3, 2022)

UNITED STATES PATENT AND TRADEMARK OFFICE UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 15/154,514 05/13/2016 Joshua J. COON 333538: 86-12A US 3560 81209 7590 01/03/2022 LEYDIG, VOIT & MAYER, LTD. (GS 240-WIS) 4940 PEARL EAST CIRCLE SUITE 200 BOULDER, CO 80301 EXAMINER XU, XIAOYUN ART UNIT PAPER NUMBER 1797 NOTIFICATION DATE DELIVERY MODE 01/03/2022 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address(es): chgpatent@leydig.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE _________ BEFORE THE PATENT TRIAL AND APPEAL BOARD __________ Ex parte JOSHUA J. COON and ALEX HEBERT __________ Appeal 2020-004677 Application 15/154,514 Technology Center 1700 ___________ Before ADRIENE LEPIANE HANLON, BEVERLY A. FRANKLIN, and BRIAN D. RANGE, Administrative Patent Judges. HANLON, Administrative Patent Judge. DECISION ON APPEAL A. STATEMENT OF THE CASE The Appellant1 filed an appeal under 35 U.S.C. § 134(a) from an Examiner’s decision finally rejecting claims 1-18 and 21. We have jurisdiction under 35 U.S.C. § 6(b). We REVERSE. 1 The word “Appellant” refers to “applicant” as defined in 37 C.F.R. § 1.42. The Appellant identifies the real party in interest as Wisconsin Alumni Research Foundation. Appeal Brief dated March 9, 2020 (“Appeal Br.”), at 2. Appeal 2020-004677 Application 15/154,514 2 The claimed subject matter is directed to a method for determining the abundances of an analyte in a plurality of samples. According to the Appellant, the claimed method includes the steps of providing a different isotopic tagging reagent to each sample; chemically reacting the analyte and isotopic tagging reagent of each sample; analyzing the isotopically labeled analytes for each sample using a mass spectrometry analysis technique; and comparing the mass spectrometry signals for the isotopically labeled analytes of each sample. Appeal Br. 3; Spec. ¶ 5. The Appellant explains that “[t]he isotopic tagging reagents provided to the samples have the same chemical formula, but have a different heavy isotope composition and a very slight difference in their exact mass between each sample” (i.e., less than or equal to 300 mDa). Appeal Br. 3; Spec. ¶ 5. Due to the small mass difference, analytes labeled with the isotopic tagging reagents are said to appear as separate peaks under high mass spectrometry resolution (i.e., a resolving power greater than 100,000). Appeal Br. 3; Spec. ¶ 149. Those separate peaks are said to be used to determine the relative abundances of the analyte in each sample. Appeal Br. 3. Claims 1 and 21 are the independent claims on appeal. Claim 1 is reproduced below from the Claims Appendix to the Appeal Brief. The limitations at issue are emphasized. 1. A method for determining the abundances of an analyte in a plurality of samples, said method comprising the steps of: (a) providing said plurality of samples each having said analyte including at least a first sample and a second sample; (b) providing a different isotopic tagging reagent to each sample, wherein each isotopically labeled tagging reagent comprises at least two stable heavy isotopes substituted for light isotopes in a Appeal 2020-004677 Application 15/154,514 3 corresponding unlabeled tagging reagent, wherein at least one of the two heavy isotopes is selected from the group consisting of 15N, 18O, and 34S, wherein said isotopic tagging reagents of each of said samples are isotopologues, and wherein said isotopic tagging reagents are not isobaric tags having a reporter group and a mass balancing group; (c) chemically reacting said analyte and isotopic tagging reagent of each sample, thereby generating a different isotopically labeled analyte for each sample including at least a first isotopically labeled analyte for said first sample and a second isotopically labeled analyte for said second sample; wherein said isotopically labeled analytes of each sample are isotopologues; and wherein the difference of the molecular masses of said first isotopically labeled analyte and said second isotopically labeled analyte is less than or equal to 300 mDa; (d) analyzing said isotopically labeled analytes for each sample using a mass spectrometry analysis technique providing a resolving power equal to or greater than 240,000, thereby generating an independent and distinguishable mass spectrometry signal for the isotopically labeled analytes of each sample; and (e) comparing said mass spectrometry signals for the isotopically labeled analytes of each sample, thereby determining the abundance of the analyte in said plurality of samples. Appeal Br. 15. Similarly, claim 21 recites that “the difference of the molecular masses of said first isotopically labeled analyte and said second isotopically labeled analyte is less than or equal to 100 mDa.” Appeal Br. 22 (emphasis added). Moreover, claim 21 recites that not only is one of the two heavy isotopes “selected from the group consisting of 15N, 18O, and 34S,” as recited in claim 1, but also another of the two heavy isotopes is “selected from the group consisting of 15N, 13C, 18O, and 34S.” Appeal Br. 21-22. The Examiner maintains the following grounds of rejection on appeal: Appeal 2020-004677 Application 15/154,514 4 (1) claims 1-6, 15, 18, and 21 under 35 U.S.C. § 103(a) as unpatentable over Orlando2 in view of Roussis;3 and (2) claims 7-14, 16, and 17 under 35 U.S.C. § 103(a) as unpatentable over Orlando in view of Roussis, further in view of Kainosho.4 B. DISCUSSION Claims 1 and 21 recite a method for determining the abundances of an analyte in a plurality of samples which includes limitations (1) and (2) identified below. More specifically, the method comprises, inter alia, the step of providing a different isotopic tagging reagent to each sample wherein (1) each isotopically labeled tagging reagent comprises at least two stable heavy isotopes, wherein at least one of the two heavy isotopes is selected from the group consisting of 15N, 18O, and 34S and the isotopic tagging reagents are isotopologues.5 Appeal Br. 15, 21-22. The method further comprises the step of chemically reacting an analyte and the isotopic tagging reagent of each sample, thereby generating a different isotopically labeled analyte for each sample including at least a first isotopically labeled analyte for the first sample and a second isotopically labeled analyte for the second sample. Appeal Br. 15, 22. Claims 1 and 21 recite that (2) the molecular mass difference of the first and second isotopically labeled analytes is “less than or equal to 300 mDa” and “less than or equal to 100 mDa,” respectively. Appeal Br. 15, 22. We interpret claims 1 and 21 as reciting that the isotopic 2 US 2008/0113441 A1, to Orlando et al., published May 15, 2008 (“Orlando”). 3 Stilianos G. Roussis & Richard Proulx, Reduction of Chemical Formulas from the Isotopic Peak Distributions of High-Resolution Mass Spectra, 75 Anal. Chem. 1470-82 (2003) (“Roussis”). 4 US 2005/0084452 A1, to Kainosho et al., published April 21, 2005 (“Kainosho”). 5 According to the Appellant, isotopologues are “molecules having the same chemical formula but different isotope compositions.” Appeal Br. 2. Appeal 2020-004677 Application 15/154,514 5 tagging reagent selections made in the “providing” step (i.e., limitation (1) identified above) determine whether the first and second isotopically labeled analytes have a mass difference falling within the range recited in the “chemically reacting” step (i.e., limitation (2) identified above). The Examiner finds Orlando discloses a method for determining the abundances of an analyte in a plurality of samples. Final Act. 2.6 The Examiner finds Orlando’s method includes the following steps: (b) providing a different isotopic tagging reagent to each sample (par [0007]), wherein each isotopically labeled tagging reagent comprises at least two stable isotopes to be substituted for heavy isotopes in a corresponding unlabeled tagging reagent (par [0030]), wherein at least one of the two heavy isotopes is selected from the group consisting of 15N, 18O, and 34S (par [0030]), wherein said isotopic tagging reagents of each of said samples are isotopologues (par [0030]) . . . ; (c) chemically reacting said analyte and isotopic tagging reagent of each sample, thereby generating a different isotopically labeled analyte for each sample including a first isotopically labeled analyte for said first sample and a second isotopically labeled analyte for said second sample (par [0007]); wherein said isotopically labeled analytes of each sample are isotopologues (par [0030]); and wherein the difference of the molecular masses of said first isotopically labeled analyte and said second isotopically labeled analyte is less than or equal to 300 mDa or 100m Da (par [0032][0034]) . . . . Final Act. 2-3 (emphasis added). Orlando discloses that “[e]mbodiments of the present disclosure include elements that can be used to form isobaric pairs or groups and these elements include, but are not limited to, 1/2H, 15/14 N, 13/12 C, 16/18 O, 32/34 S, 35/37 Cl, and 79/81 Br.” Orlando ¶ 30. Orlando discloses that an exemplar isobaric 6 Final Office Action dated June 19, 2019. Appeal 2020-004677 Application 15/154,514 6 compound group can include (1) 12C3H318O232S35Cl2 (2 heavy isotopes): (2) 12C3H316O234S35Cl2 (1 heavy isotope): (3) 12C3H316O232S37Cl2 (2 heavy isotopes): (4) 13C212C1H316O232S35Cl2 (2 heavy isotopes): (5) 12C3HD218O232S35Cl2 (4 heavy isotopes).7 Orlando ¶ 30; Appeal Br. 8. The Appellant argues that “only two isotopically labeled compounds [i.e., compounds (1)-(5) identified in the previous paragraph] have at least two heavy isotopes, where one of the isotopes is also selected from the group consisting of 15N, 18O and 34S” as recited in claims 1 and 21. Appeal Br. 8. The Appellant argues that those compounds “result in a mass difference of greater than 2 Da and therefore fail to provide a mass difference less than or equal to 300 mDa or 100 mDa as required by claims 1 and 21, respectively.” Appeal Br. 8. In response, the Examiner finds that 12C3H318O232S35Cl2 (compound (1) identified above) and 12C3H316O232S37Cl2 (compound (3) identified above) have a mass difference of 14.4 mDa, which is “far less” than the upper limits recited in claims 1 and 21. Ans. 10.8 Likewise, the Examiner finds that 12C3H316O234S35Cl2 (compound (2) identified above) and 13C212CH316O232S35Cl2 (compound (4) identified above) have a mass difference of 10.9 mDa, which is also “far less” than the upper limits recited in claims 1 and 21. Ans. 10-11. To satisfy limitation (1) identified above, both of the compounds in either of the two exemplary pairs identified by the Examiner (i.e., compounds (1) and (3) or compounds (2) and (4)) must have at least one heavy isotope selected from the group consisting of 15N, 18O, and 34S. However, the heavy isotope in compound (3) 7 Throughout this Decision, heavy isotopes are identified in bold. 8 Examiner’s Answer dated April 8, 2020. Appeal 2020-004677 Application 15/154,514 7 is 37Cl2 and the heavy isotope in compound (4) is 13C2, neither of which is “selected from the group consisting of 15N, 18O, and 34S” as recited in claims 1 and 21.9 The Examiner also contends that “for C3H3O2SCl2, the two heavy isotope substitutes can be 13C3H318O16OSCl2 and 12C3D318O16OSCl2.” Ans. 5 (emphasis added). The Examiner finds that each of the two compounds have at least one of the heavy isotopes recited in claims 1 and 21 (i.e., 18O) and have a mass difference of 8.5 mDa, which is “far less” than the upper limits recited in claims 1 and 21. Ans. 5. Similarly, the Examiner finds that another pair of compounds can be 13C3H316O234SCl2 and 12C3D316O234SCl2. Ans. 12. Each of those two compounds is also said to have at least one of the heavy isotopes recited in claims 1 and 21 (i.e., 34S) and a mass difference within the ranges recited in claims 1 and 21 (i.e., 8.5 mDa). Ans. 12. Notably, however, the Examiner does not direct us to any portion of Orlando expressly disclosing either of the two pairs of compounds. See Reply Br. 510 (contending that the compounds identified by the Examiner “are not disclosed anywhere in Orlando et al. as examples of their isotopic tagging reagents”). The Appellant argues that there is no guidance in Orlando that would have directed one of ordinary skill in the art to select isotopic compounds having a mass difference less than 300 mDa as claimed. Reply Br. 5; see also Appeal Br. 9 (arguing that “there is no disclosure [in Orlando] that the tagging reagents based on C3H3O2SCl2 should be or could be modified to have a mass difference less than 300 mDa”). The Appellant’s argument is persuasive of reversible error. 9 Claims 1 and 21 also recite that each isotopically labeled reagent comprises at least two heavy isotopes. Compound (2) only comprises one heavy isotope (i.e., 34S). 10 Reply Brief dated June 3, 2020. Appeal 2020-004677 Application 15/154,514 8 The Examiner directs our attention to the following disclosure in paragraph 32 of Orlando to support the conclusion of obviousness. Ans. 10. Embodiments of the present disclosure include a number of advantages. Many of the advantages derive from the fact that the isobaric ions appear at the same nominal mass to charge ratio. This characteristic leads to increased ion intensity since ions from both samples are not distributed between isotopic species having different m/z values.[11] In addition, the small mass difference between these isobars allows the two species to be simultaneously selected for MSn analysis, which permits the relative quantitation of isomeric compounds. Orlando ¶ 32 (emphasis added). The Examiner finds that isotopic tags having the same nominal mass inherently have a mass difference less than 300 mDa. Ans. 19. The Examiner bases that finding on the additional finding that “nominal mass” describes tagging reagents having the same number of neutrons. Ans. 12. To illustrate, the Examiner finds that 12C3H318O232S35Cl2 (compound (1) identified above) and 12C3H316O232S37Cl2 (compound (3) identified above) have the same nominal mass (i.e., 177) “because both tags are added 4 neutrons.” The Examiner finds that “[t]he mass difference between the two compounds is 14.4 mDa, which is far less than 300 mDa.” Ans. 19. Notably, the Examiner does not provide any evidentiary support for the meaning of “nominal mass.” The Appellant, on the other hand, contends that [a]s is used in the art, the “nominal mass” of an [sic, a] molecule refers to the isotope mass of the most naturally abundant isotope of each constituent element rounded to the nearest integer value and multiplied by the number of atoms of each element. Applicant respectfully believes that this definition is consistent with the 11 We understand “m/z” to refer to the mass to charge ratio. Appeal 2020-004677 Application 15/154,514 9 definition from the International Union of Pure and Applied Chemistry (IUPAC) as well as most textbooks on mass spectrometry. Thus, in the context of paragraph [0030] of Orlando, all of the different isotope combinations of C3H3O2SCl2 (e.g., 12C3H316O234S35Cl2 and 12C3H316O232S37Cl2) would have the same nominal mass (173) corresponding to the molecule having the most naturally abundant isotope of each element (e.g., 12C, 1H, 16O, 32S and 35Cl) rounded to the nearest integers. This interpretation is supported by the portion of paragraph [0030] of Orlando et al. following the description of the C3H3O2SCl2 isotopic compounds which states that “In this regard, various combinations of isobars can be constructed so that the isobar labels have the same nominal mass, but differ in their exact mass.” This statement indicates that all of the isotopic compounds of C3H3O2SCl2 described in paragraph [0030] are intended as having the same nominal mass but have different exact masses. Reply Br. 6-7. A preponderance of the evidence supports the Appellant’s definition of “nominal mass.”12 Thus, the Examiner’s finding of inherency is not supported by the record. To illustrate, 12C3H318O232S35Cl2 (compound (1) identified above) and 12C3HD218O232S35Cl2 (compound (5) identified above)13 have the same nominal mass and are the only two compounds disclosed in paragraph 30 of Orlando that each have an isotope selected from the group consisting of 15N, 18O and 34S” (i.e., 18O2) as recited in claims 1 and 21. However, those two compounds have a mass 12 According to mass-spec.lsu.edu/msterms/index.php/Nominal_mass (last visited Dec. 27, 2021), “nominal mass” is defined as “[m]ass of a molecular ion or molecule calculated using the isotope mass of the most abundant constituent element isotope of each element rounded to the nearest integer value and multiplied by the number of atoms of each element”). This definition is said to be from “Definitions of Terms Relating to Mass Spectrometry (IUPAC Recommendations 2013).” Id. 13 See Orlando ¶ 30. Appeal 2020-004677 Application 15/154,514 10 difference greater than 2 Da, which is outside the ranges recited in claims 1 and 21. See Appeal Br. 8; Reply Br. 9 (contending that the mass difference of compounds (1) and (5) is greater than 2 Da using “exact mass” or “monoisotopic mass”). We recognize that Orlando also discloses there is a “small mass difference” between isobars. Orlando ¶ 32. However, the Examiner does not direct us to any disclosure in Orlando that quantifies a “small mass difference.”14 In sum, the Examiner does not direct us to any disclosure in Orlando that would have led one of ordinary skill in the art to generate different isotopically labeled analytes using the isotopic tagging reagents recited in the claimed “providing” step (i.e., step (b)), wherein first and second isotopically labeled analytes have a mass difference within the range recited in the claimed “chemically reacting” step (i.e., step (c)).15 The Examiner does not rely on Roussis and/or Kainosho to cure the deficiencies in Orlando. Therefore, the obviousness rejections on appeal are not sustained. C. CONCLUSION The Examiner’s decision is reversed. 14 We note Orlando discloses that differentially labeled analytes may be separated at a resolution of ~30,000 m/µm. Orlando ¶ 49. In contrast, claims 1 and 21 recite a substantially higher resolving power, i.e., equal to or greater than 240,000. Appeal Br. 15, 22; see also Final Act. 4 (relying on Roussis to teach the claimed resolving power). The Appellant contends that Orlando “generally teaches that it is more beneficial to increase the mass difference between samples labeled with different isotopic tagging reagents since doing so would allow smaller resolutions to be used during MS [mass spectroscopy] analysis.” 15 As discussed above, claim 1 recites that the molecular mass difference is “less than or equal to 300 mDa,” and claim 21 recites that the molecular mass difference is “less than or equal to 100 mDa.” Appeal Br. 15, 22. Appeal 2020-004677 Application 15/154,514 11 In summary: Claims Rejected 35 U.S.C. § Reference(s)/Basis Affirmed Reversed 1-6, 15, 18, 21 103(a) Orlando, Roussis 1-6, 15, 18, 21 7-14, 16, 17 103(a) Orlando, Roussis, Kainosho 7-14, 16, 17 Overall Outcome 1-18, 21 REVERSED