Thermo Fisher Scientific (Bremen) GmbH

Patent Trials and Appeals Board

Jan 13, 2022

2021002950 (P.T.A.B. Jan. 13, 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. 15/600,996 05/22/2017 Mikhail BELOV TP20106US1-NAT 4843 44064 7590 01/13/2022 THERMO FISHER SCIENTIFIC INC. Attn: IP Department 5823 Newton Drive Carlsbad, CA 92008 EXAMINER MCCORMACK, JASON L ART UNIT PAPER NUMBER 2881 NOTIFICATION DATE DELIVERY MODE 01/13/2022 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): PatentDocketing@thermofisher.com pair_thermofisher@firsttofile.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE ____________ BEFORE THE PATENT TRIAL AND APPEAL BOARD ____________ Ex parte MIKHAIL BELOV, EDUARD DENISOV, GREGOR QUIRING, and DMITRY GRINFELD ____________ Appeal 2021-002050 Application 15/600,996 Technology Center 2800 ____________ Before ADRIENE LEPIANE HANLON, JEFFREY B. ROBERTSON, and JANE E. INGLESE, Administrative Patent Judges. INGLESE, Administrative Patent Judge. DECISION ON APPEAL The Appellant1 requests review under 35 U.S.C. § 134(a) of the Examiner’s final rejection of claims 1-10 and 12-22.2 We have jurisdiction under 35 U.S.C. § 6(b). We REVERSE. 1 “Appellant” refers to the “applicant” as defined in 37 C.F.R. § 1.42. The Appellant identifies Thermo Fisher Scientific (Bremen) GmbH as the real party in interest. Appeal Brief filed September 14, 2020 (“Appeal Br.”), 3. 2 Final Office Action entered September 12, 2019 (“Final Act.”), 1. Appeal 2021-002950 Application 15/600,996 2 CLAIMED SUBJECT MATTER The Appellant claims a method of injecting ions into an orbital electrostatic trap (independent claim 1) and a mass spectrometer (independent claim 22). Supplemental Appeal Brief filed November 24, 2020, 3-4. Independent claims 1 and 22 illustrate the subject matter on appeal, and read as follows: 1. A method of injecting ions into an orbital electrostatic trap, comprising: applying an ejection potential to an ion storage device, to cause ions stored in the ion storage device to be ejected towards and injected into the orbital electrostatic trap; and applying synchronous injection potentials to a central electrode of the orbital electrostatic trap and a deflector electrode associated with the orbital electrostatic trap during injection of ions into the orbital electrostatic trap, to cause the ions ejected from the ion storage device to be captured by the electrostatic trap such that they orbit the central electrode; wherein the steps of applying the ejection potential and applying the synchronous injection potentials are each started at respective different times, the difference in times being selected based on desired values of mass-to-charge ratios of ions to be captured by the orbital electrostatic trap. 22. A mass spectrometer, comprising: an ion storage device, configured to receive ions for analysis, store the received ions and eject the stored ions; an orbital electrostatic trap, having a central electrode and a deflector electrode and being arranged to receive the ions ejected from the ion storage device; and a controller, configured to perform steps of: applying an ejection potential to the ion storage device, to cause ions stored in the ion storage device to be ejected towards the orbital electrostatic trap and injected into the orbital electrostatic trap; and applying during injection of ions into the orbital electrostatic trap synchronous injection potentials to the Appeal 2021-002950 Application 15/600,996 3 central electrode of the orbital electrostatic trap and the deflector electrode, to cause the ions ejected from the ion storage device to be captured by the electrostatic trap such that they orbit the central electrode; wherein the steps of applying the ejection potential and applying the synchronous injection potentials are each started at respective different times, the difference in times being selected based on desired values of mass- to-charge ratios of ions to be captured by the orbital electrostatic trap. Appeal Br. 9, 12 (Claims Appendix) (emphasis added and spacing altered). REJECTIONS The Examiner maintains the following rejections in the Examiner’s Answer entered November 1, 2019 (“Ans.”): I. Claims 1, 2, 8, 10, 12-18, and 20-22 under 35 U.S.C. § 102(a)(1) as anticipated by Markarov I;3 II. Claims 3-6 under 35 U.S.C. § 103 as unpatentable over Makarov I in view of Campbell;4 III. Claims 7 and 9 under 35 U.S.C. § 103 as unpatentable over Makarov I; and IV. Claim 19 under 35 U.S.C. § 103 as unpatentable over Makarov II5 in view of Makarov I. FACTUAL FINDINGS AND ANALYSIS Upon consideration of the evidence relied upon in this appeal and each of the Appellant’s contentions, we reverse the Examiner’s rejection of 3 US 2004/0108450 A1, published June 10, 2004. 4 US 2015/0235828 A1, published August 20, 2015. 5 US 2015/0348767 A1, published December 3, 2015. Appeal 2021-002950 Application 15/600,996 4 claims 1, 2, 8, 10, 12-18, and 20-22 under 35 U.S.C. § 102(a)(1), and rejections of claims 3-7, 9, and 19 under 35 U.S.C. § 103, for reasons set forth in the Appeal Brief and below. Rejection I We turn first to the Examiner’s rejection of claims 1, 2, 8, 10, 12-18, and 20-22 as anticipated by Markarov I. Independent claims 1 and 22 recite steps of, or a controller configured to perform steps of, applying an ejection potential to an ion storage device, and applying synchronous injection potentials to a central electrode of an orbital electrostatic trap and a deflector associated with the orbital electrostatic trap, where the steps of applying the ejection potential and applying the synchronous injection potentials are each started at respective different times, and the difference in times is selected based on desired values of mass-to-charge ratios of ions to be captured by the orbital electrostatic trap. The Examiner finds that Markarov I discloses a method of injecting ions into orbital electrostatic trap 130 by ramping voltage applied to exit electrode 70 of ion storage device 30 so as to apply a single pulse or successive pulses to electrode 70 (applying an ejection potential), to cause ions stored in ion storage device 30 to be ejected out of device 30 and into orbital electrostatic trap 130. Final Act. 4 (citing Markarov I Abstr., ¶ 78). The Examiner finds that Markarov I discloses ramping voltages applied to central electrode 140 of orbital electrostatic trap 130 and field compensator 200 (applying synchronous injection potentials) during injection of ions into orbital electrostatic trap 130, to cause ions ejected from ion storage device 30 to be captured by electrostatic trap 130. Final Act. 4-5 (citing Markarov Appeal 2021-002950 Application 15/600,996 5 I ¶¶ 61, 78). The Examiner finds that Markarov I discloses that field compensator 200 acts as a deflector associated with orbital electrostatic trap 130. Final Act. 4 (citing Markarov I ¶ 78). The Examiner finds that Markarov I discloses that a “data acquisition system starts to ramp the voltage applied to the central electrode 140 in the orbitrap 130 and, simultaneously, applies a voltage pulse to the exit electrode 70 of the linear trap 30,” such that “the ramping of the voltages on the central electrode [140] of the orbitrap 130 and the exit electrode 70 of the linear trap [30] are timed to each other.” Final Act. 5 (citing Markarov I ¶ 61). The Examiner finds that this disclosure indicates that “the steps of applying the ejection potential and applying the synchronous injection potentials are each started at respective different times” because “the voltage is only applied to electrode 140 after voltage has been applied to perform storage in trap 30.” Id. The Examiner finds that Markarov I discloses that “the delay between successive pulses [applied to exit electrode 70] is chosen in such a way that all of the mass range of interest arrives into the orbitrap 130 during the correct phase of the voltage applied to the central electrode 140 thereof as it is ramped,” which the Examiner finds indicates that “the difference in times [is] selected based on desired values of mass-to-charge ratios of ions to be captured by the orbital electrostatic trap.” Id. The Appellant argues that, contrary to the Examiner’s findings, paragraph 61 of Markarov I does not disclose selecting relative start times of ejection and synchronous injection potentials based on desired mass-to- charge ratios of ions to be analyzed. Appeal Br. 6. The Appellant’s arguments identify reversible error in the Examiner’s rejection, for reasons that follow. Appeal 2021-002950 Application 15/600,996 6 Markarov I discloses mass spectrometer 10 that includes pulsed ion source 12, quadrupole mass filter 24, linear ion trap 30 bounded by entrance 80 and exit 70 electrodes, electrostatic orbitrap 130 having central electrode 140, and a data acquisition system that controls voltages applied to components of spectrometer 10. Markarov I ¶¶ 46, 48, 50, 53, 55, 58; Fig. 1. Markarov I discloses that during operation of spectrometer 10, ions from ion source 12 enter quadrupole mass filter 24, which “extracts only those ions within a window of m/z [mass-to-charge ratio] of interest and the chosen ions are then released to a linear ion trap 30.” Markarov I ¶ 48; see also ¶ 11 (“mass-to-charge ratio m/z”). Markarov I discloses supplying entrance 80 and exit 70 electrodes of linear ion trap 30 with DC voltages, and choosing the pressure inside linear ion trap 30, so that ions within the trap accumulate near the bottom of an axial potential well, where the ions are stored. Markarov I ¶¶ 59, 60; Fig. 4a. Markarov I discloses that “[a]t the end of storage, the data acquisition system starts to ramp the voltage applied to the central electrode 140 in the orbitrap 130 and, simultaneously, applies a voltage pulse to the exit electrode 70 of the linear trap 30.” Markarov I ¶ 61. Markarov I discloses that although a single pulse is preferably applied “to empty the linear trap,” multiple pulses may instead be applied to exit electrode 70. Id. Markarov I discloses that in such case, “the delay between successive pulses is chosen in such a way that all of the mass range of interest arrives into the orbitrap 130 during the correct phase of the voltage applied to the central electrode 140 thereof as it is ramped.” Id. Markarov I discloses that “[a]lthough the ramping of the voltages on the central electrode [140] of the orbitrap 130 and the exit electrode 70 of Appeal 2021-002950 Application 15/600,996 7 the linear trap [30] are timed to each other, they do not however need to be synchronous,” and “the voltage applied to the central electrode 140 of the orbitrap 130 may start to ramp before the pulse is applied to the exit electrode 70 on the linear trap, and may continue to ramp for a period (e.g. tens of microseconds) after the linear trap has been emptied.” Id. The relied-upon disclosures of Markarov I thus describe applying voltage to central electrode 140 of orbitrap 130 (applying an injection potential) before applying voltage pulses to exit electrode 70 of linear ion trap 30 (applying an ejection potential), and choosing a delay between application of successive pulses to exit electrode 70 in order to empty ion trap 30 so that the mass range of interest previously extracted by quadrupole mass filter 24 arrives into orbitrap 130 during the correct phase of the voltage applied to central electrode 140. The Examiner does not explain why this disclosure of choosing a delay between application of successive pulses to exit electrode 70 of linear ion trap 30 (ion storage device)-so that the mass range of interest arrives into orbitrap 130 during the correct phase of the voltage applied to central electrode 140-constitutes an explicit or inherent disclosure of selecting a difference in start times for applying ejection and injection voltages based on desired values of mass-to-charge ratios of ions to be captured by orbitrap 130, as required by claims 1 and 22. Consequently, on the record before us, the Examiner does not provide a sufficient factual basis to establish that Markarov I discloses selecting different start times for application of voltage to central electrode 140 of orbitrap 130 (orbital electrostatic trap) and exit electrode 70 of linear ion trap 30 (ion storage device) based on desired values of mass-to-charge ratios of ions to be captured by orbitrap 130 (orbital electrostatic trap). The Appeal 2021-002950 Application 15/600,996 8 Examiner, therefore, does not establish that Markarov discloses applying an ejection potential to an ion storage device, and applying synchronous injection potentials to a central electrode of an orbital electrostatic trap and a deflector associated with the orbital electrostatic trap, where the steps of applying the ejection potential and applying the synchronous injection potentials are each started at respective different times, and the difference in times is selected based on desired values of mass-to-charge ratios of ions to be captured by the orbital electrostatic trap, as required by claims 1 and 22. We, accordingly, do not sustain the Examiner’s rejection of these claims under 35 U.S.C. § 102(a)(1). Nor do we sustain the Examiner’s rejection of claims 2, 8, 10, 12-18, 20, and 21, which each depend from claim 1, under 35 U.S.C. § 102(a)(1). Rejections II-IV We do not sustain the Examiner’s rejections of claims 3-7, 9, and 19 under 35 U.S.C. § 103 as unpatentable over Makarov I alone, or in combination with Campbell or Makarov II, because the Examiner does not rely on any disclosure in Campbell or Makarov II that remedies the Examiner’s reliance on Makarov I, discussed above. Final Act. 12-19. DECISION SUMMARY Claims Rejected 35 U.S.C. § Reference(s)/ Basis Affirmed Reversed 1, 2, 8, 10, 12-18, 20-22 102(a)(1) Makarov I 1, 2, 8, 10, 12-18, 20-22 3-6 103 Makarov I, Campbell 3-6 7, 9 103 Makarov I 7, 9 Appeal 2021-002950 Application 15/600,996 9 Claims Rejected 35 U.S.C. § Reference(s)/ Basis Affirmed Reversed 19 103 Makarov II, Makarov I 19 Overall Outcome 1-10, 12-22 REVERSED