Free Claim Construction Opening Brief - District Court of Delaware - Delaware

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IN THE UNITED STATES DISTRICT COURT FOR THE DISTRICT OF DELAWARE

APPLERA CORPORATION, MDS INC., and APPLIED BIOSYSTEMS/MDS SCIEX INSTRUMENTS, Plaintiffs, C.A. No. 04-1230-GMS v. THERMO ELECTRON CORPORATION, Defendant. THERMO FINNIGAN LLC, Plaintiff, v. C.A. No. 05-110-GMS APPLERA CORPORATION, MDS INC., and APPLIED BIOSYSTEMS/MDS SCIEX INSTRUMENTS Defendants. AB/SCIEX'S OPENING CLAIM CONSTRUCTION BRIEF

November 18, 2005

Of Counsel: Walter E. Hanley, Jr. James Galbraith Lewis V. Popovski Jeffrey S. Ginsberg Mark A. Chapman Huiya Wu KENYON & KENYON One Broadway New York, NY 10004 (212) 425-7200

Josy W. Ingersoll (#1088) Karen E. Keller (#4489) YOUNG CONAWAY STARGATT & TAYLOR, LLP The Brandywine Building 1000 West Street, 17th Floor P.O. Box 391 Wilmington, DE 19899-0391 (302) 571-6672 Attorneys for Plaintiffs Applera Corp., MDS, Inc., and Applied Biosystems/ MDS Sciex Instruments

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TABLE OF CONTENTS Page NATURE AND STAGE OF PROCEEDING .................................................................... 1 SUMMARY OF ARGUMENT .......................................................................................... 1 PART I ­ AB/SCIEX'S DOUGLAS '736 PATENT (C.A. 04-1230-GMS)...................... 2 STATEMENT OF FACTS ..................................................................................... 2 A. The '736 Patent and its Technological Background ....................... 2 1. 2. The Mass Spectrometer Described in the '736 Patent................................................................................... 2 The Product of the Pressure and Rod Length (P x L) and Kinetic Energy Operating Parameters of the Ion Guide of the '736 Patent.................. 4

B.

The Original and Reexamination Prosecution of the '736 Patent ...................................................................................... 6 1. 2. The Original Prosecution of the '736 Patent....................... 6 The Reexamination of the '736 Patent................................ 6

C.

The Prior Litigation on the '736 Patent against Micromass....................................................................................... 9 1. 2. The Court's Claim Construction in the Micromass Case .................................................................. 9 Thermo's Challenges to the Court's Claim Construction from the Micromass Case............................ 10

D.

The Accused Thermo Instruments and Thermo's Noninfringement Positions ........................................................... 10 1. 2. 3. Thermo TSQ Quantum Series........................................... 10 Thermo LTQ Series .......................................................... 12 Thermo's Noninfringement Positions............................... 13

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ARGUMENT........................................................................................................ 14 I. DISPUTED TERMS INVOLVING THE PREVIOUSLY DECIDED ISSUE OF WHETHER THE CHAMBERS MUST BE ADJACENT............................................................................ 14 A. B. II. "Separated by a Wall" and "Separated by an Interchamber Orifice" ................................................................... 14 "Located End to End" ................................................................... 17

DISPUTES INVOLVING THE PREVIOUSLY DECIDED IDENTIFICATION OF CORRESPONDING STRUCTURES IN THE CONSTRUCTIONS OF CERTAIN MEANS-PLUS-FUNCTION LIMITATIONS ......................................... 19 A. B. C. "Means . . . for Directing Said Ions Through Said Inlet Orifice" ......................................................................................... 19 "Means for Flowing Gas Through Said Inlet Orifice".................. 23 "Means for Maintaining Kinetic Energies of Ions" ...................... 25

III.

DISPUTED TERMS INVOLVING THE PREVIOUSLY DECIDED ISSUE OF WHAT IS A "ROD SET," AND THE ISSUE OF ROD LENGTH....................................................................... 28 A. B. C. D. E. F. G. "Rod" ............................................................................................ 28 "Rod Means"................................................................................. 30 "Rod Set" ...................................................................................... 31 "Elongated"................................................................................... 32 "Spaced Laterally Apart a Short Distance" .................................. 34 "Space Extending Longitudinally" and "Longitudinally Extending Spaces" ........................................................................ 35 "The Length of Said First Rod Set".............................................. 36

IV.

DISPUTED TERMS AS TO WHICH THERMO RAISES THE ISSUE OF INDEFINITENESS........................................................ 36 A. B. "Means for Applying Essentially an AC-Only Voltage".............. 36 "Means for Applying Both AC and DC Voltages"....................... 40

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V.

OTHER DISPUTED TERMS .................................................................. 42 A. B. C. D. E. "Means for Generating Ions of a Trace Substance"...................... 42 "Extending Along at Least a Substantial Portion of the Length" ......................................................................................... 43 "Essentially an AC-Only Voltage" ............................................... 44 "Mass Filter"................................................................................. 46 "Very Low Pressure for Operation of Said Second Rod Set as a Mass Filter" and "Substantially Lower Pressure . . . for Effective Mass Filter Operation" ...................................... 49 "Whereby to Provide Improved Transmission of Ions Through Said Interchamber Orifice" ............................................ 52

F.

PART II ­ THERMO'S TANG '784 PATENT (C.A. 05-110-GMS).............................. 54 STATEMENT OF FACTS ................................................................................... 54 A. B. C. The '784 Patent and its Technological Background ..................... 54 The Original Prosecution of the '784 Patent................................. 57 The Further Prosecution of the '784 Patent .................................. 58 1. 2. Thermo's Reissue Application for the '784 Patent is Pending Before the Patent Office....................... 58 The Patent Office Is Currently Reexamining the '784 Patent .................................................................. 59

ARGUMENT........................................................................................................ 59 A. B. C. D. "Mass Analyzer"........................................................................... 59 "Adduct Ion(s)"............................................................................. 61 "Multipole Ion Guide" .................................................................. 62 "Means Associated with One or Both Ion Guides for Increasing the Translational Kinetic Energy of the Adduct Ions" (Claim 1)................................................................. 65

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E.

"Whereby to Increase the Sample Ion Current and Therefore the Sensitivity of the Mass Spectrometer System" (Claim 1)......................................................................... 68 "To Increase the Sample Ion Current and Therefore the Sensitivity of the Mass Spectrometer" (Claim 4) ......................... 68

F.

"Applying a DC Offset Voltage Between a Selected One or Both Lenses and the Succeeding Multipole Ion Guide" (Claim 4)........................................................................... 71 "Ion Lens"..................................................................................... 73 "A DC Offset Voltage . . . Having an Amplitude so as to Provide Translational Kinetic Energy to Said Adduct Ions" (Claim 4) ............................................................................. 77

G. H.

CONCLUSION................................................................................................................. 80

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TABLE OF AUTHORITIES Page(s) Federal Cases ACTV, Inc. v. Walt Disney Co., 346 F.3d 1082 (Fed. Cir. 2003)............................................................................. 49 Altiris, Inc. v. Symantec Corp., 318 F.3d 1363 (Fed. Cir. 2003)............................................................................. 21 Applera Corp. v. Micromass UK Ltd., 186 F. Supp. 2d 487 (D. Del. 2002)............................................................... passim Applera Corp. v. Micromass UK Ltd., 204 F. Supp. 2d 724 (D. Del. 2002).................................................................. 9, 49 Applera Corp. v. Micromass UK Ltd., 60 F.App'x 800 (Fed. Cir. 2003) ........................................................ 10, 15, 18, 54 Asyst Techs., Inc. v. Empak, Inc., 268 F.3d 1364 (Fed. Cir. 2001)...................................................................... passim Atmel Corp. v. Info. Storage Devices, Inc., 198 F.3d 1374 (Fed. Cir. 1999)................................................................. 37, 38, 41 Bailey v. Dunkin Donuts, Inc., 1998 U.S. App. LEXIS 1175 (Fed. Cir. 1998) ..................................................... 45 Budde v. Harley-Davidson, Inc., 250 F.3d 1369 (Fed. Cir. 2001)............................................................................. 20 Burke, Inc. v. Bruno Indep. Living Aids, Inc., 183 F.3d 1334 (Fed. Cir. 1999)....................................................................... 15, 17 Chiuminatta Concrete Concepts, Inc. v. Cardinal Indus., Inc., 145 F.3d 1303 (Fed. Cir. 1998)....................................................................... 19, 42 Default Proof Credit Card Sys., Inc. v. Home Depot U.S.A., Inc., 412 F.3d 1291 (Fed. Cir. 2005)............................................................................. 37 Fonar Corp. v. General Elec. Co., 107 F.3d 1543 (Fed. Cir. 1997)............................................................................. 21 Glaxo Group Ltd. v. Ranbaxy Pharms., Inc., 262 F.3d 1333 (Fed. Cir. 2001)............................................................................. 45 Globetrotter Software, Inc. v. Elan Computer Group, Inc., 236 F.3d 1363 (Fed. Cir. 2001)............................................................................. 21

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In re Dossel, 115 F.3d 942 (Fed. Cir. 1997)................................................................... 39, 40, 41 Interactive Gift Express, Inc. v. CompuServe Inc., 256 F.3d 1323 (Fed. Cir. 2001)............................................................................. 17 Interactive Pictures Corp. v. Infinite Pictures, Inc., 274 F.3d 1371 (Fed. Cir. 2001)............................................................................. 42 Johnson Worldwide Assoc., Inc. v. Zebco Corp., 175 F.3d 985 (Fed. Cir. 1999)............................................................................... 60 KCJ Corp. v. Kinetic Concepts, 223 F.3d 1351 (Fed. Cir. 2000)............................................................................ 16 KX Indus. v. PUR Water Purification Prods., Inc., 108 F. Supp. 2d 380 (D. Del. 2000).......................................................... 20, 24, 25 Markman v. Westview Instr., Inc., 517 U.S. 370 (1996).................................................................................. 20, 24, 25 Mars, Inc. v. H.J. Heinz Co., 377 F.3d 1369 (Fed. Cir. 2004)............................................................................. 49 Micro Chem., Inc. v. Great Plains Chem. Co., 194 F.3d 1250 (Fed. Cir. 1999)............................................................................. 22 Netword, LLC v. Centraal Corp., 242 F.3d 1347 (Fed. Cir. 2001)............................................................................. 17 Northrop Grumman Corp., v. Intel Corp., 325 F.3d 1346 (Fed. Cir. 2003)............................................................................. 19 Phillips Petroleum Co. v. Huntsman Polymers Corp., 157 F.3d 866 (Fed. Cir. 1998)............................................................................... 16 Phillips v. AWH Corp., 415 F.3d 1303 (Fed. Cir. 2005)...................................................................... passim Process Control Corp. v. HydReclaim Corp., 190 F.3d 1350 (Fed. Cir. 1999)............................................................................. 50 Rexnord Corp. v. Laitram Corp., 274 F.3d 1336 (Fed. Cir. 2001)............................................................................. 60 S3 Inc. v. nVIDIA Corp., 259 F.3d 1364 (Fed. Cir. 2001)................................................................. 38, 40, 41

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Specialty Composites v. Cabot Corp., 845 F.2d 981 (Fed. Cir. 1988)......................................................................... 17, 31 Sulzer Textil A.G. v. Pinacol N.V., 358 F.3d 1356 (Fed. Cir. 2004)............................................................................. 32 Tate Access Floors, Inc. v. Interface Architectural Res., Inc., 185 F. Supp. 2d 588 (D. Md. 2002) ...................................................................... 16 Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576 (Fed. Cir. 1996)............................................................................... 61 Wang Labs., Inc. v. Oki Elec. Indus. Co., 15 F. Supp. 2d 166 (D. Mass. 1998) ..................................................................... 16 Warner-Lambert Co. v. Apotex Corp., 316 F.3d 1348 (Fed. Cir. 2003)............................................................................. 72 Wenger Mfg., Inc. v. Coating Mach. Sys., Inc., 239 F.3d 1225 (Fed. Cir. 2001)............................................................................. 31 York Prods. v. Cent. Tractor Farm & Family Ctr., 99 F.3d 1568 (Fed. Cir. 1996)............................................................................... 31 Zenith Lab. v. Bristol-Myers Squibb Co., 19 F.3d 1418 (Fed. Cir. 1994)............................................................................... 45 Statutes 35 U.S.C. § 112 (2005) ..................................................................................................... 19

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Plaintiffs Applera Corporation, MDS Inc., and Applied Biosystems/MDS Sciex Instruments (collectively, "AB/Sciex") respectfully submit this opening claim construction brief setting forth their proposed construction of the disputed terms and phrases in the asserted claims of the patents in these consolidated actions. NATURE AND STAGE OF PROCEEDING On September 7, 2004, AB/Sciex brought an action for infringement of U.S. Patent No. 4,963,736 ("the '736 patent") against Thermo Electron Corporation, which was assigned C.A. No. 04-1230-GMS. The Court construed many of the disputed claim terms and phrases in a prior litigation in which AB/Sciex successfully asserted the '736 patent against Micromass. In response to AB/Sciex's lawsuit, on February 23, 2005, Thermo Finnigan LLC (together with Thermo Electron Corporation, collectively "Thermo") brought an action alleging infringement of U.S. Patent No. 6,528,784 ("the '784 patent") against AB/Sciex, which was assigned C.A. No. 05-110-GMS. On May 9, 2005, the Court ordered opening and answering briefs on claim construction issues to be filed on November 18 and December 12, 2005, respectively, and scheduled a consolidated hearing in both cases on claim construction issues for January 9, 2006. Fact discovery in both cases is scheduled to close on March 17, 2006. A jury trial in both cases is scheduled to begin on December 4, 2006. SUMMARY OF ARGUMENT AB/Sciex has proposed constructions of the disputed terms and phrases in the patents in suit that comport with their ordinary meaning as understood by one of ordinary skill in the art reading the specification and prosecution history. Thermo's proposed constructions of terms in AB/Sciex's '736 patent seek to limit the scope of the invention by impermissibly reading in limitations from the preferred embodiments and by

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distorting the reexamination prosecution history. Thermo also challenges the Court's construction of several claim terms and phrases in the '736 patent from the earlier litigation against Micromass. Thermo takes the opposite approach in its proposed constructions of the terms in Thermo's '784 patent, seeking expansive or vague constructions. Thermo's proposed constructions should be rejected, and the Court should construe the disputed terms and phrases as AB/Sciex proposes. PART I ­ AB/SCIEX'S DOUGLAS '736 PATENT (C.A. 04-1230-GMS) STATEMENT OF FACTS A. The '736 Patent and its Technological Background 1. The Mass Spectrometer Described in the '736 Patent

AB/Sciex's '736 patent relates to a mass spectrometer and its method of operation. JA16, 1:6-12; 1:55-2:39.1 Mass spectrometers are used to analyze trace substances in a sample gas or liquid and obtain information about the molecular weight of compounds or their chemical structures. Id., 1:15-16. A mass spectrometer creates electrically charged particles (called "ions") from a sample compound, and uses electric fields to sort ions by mass-to-charge ratio. In the type of mass spectrometer described in the '736 patent (a "quadrupole mass spectrometer"), the electric fields involved in the mass analysis are produced by applying voltages to a set of four parallel metal rods. The '736 patent illustrates two embodiments of a quadrupole mass spectrometer in Figures 1 and 12. Figure 12, with non-substantive alterations,2 is reproduced below. See JA10.

1

"JA__" refers to the Joint Appendix being filed herewith. "A__" refers to AB/Sciex's Appendix also being filed herewith. The illustration is the mirror image of Figure 12, with the path of ion travel going from left to right, rather than from right to left as shown in the '736 patent, and with shades of blue added from dark to progressively lighter to show the diminishing gas density (i.e., lower pressure).

2

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Molecules in a sample containing a trace substance to be analyzed are vaporized and converted into ions in an ion source 16' at atmospheric pressure. JA17, 4:7-16. Ions, and a much larger number of neutral gas molecules, enter a vacuum chamber 30' containing the ion guide 32' through an inlet orifice 76. JA19, 8:60-68. The ion guide transmits ions entering the vacuum chamber 30' to the vacuum chamber 38' containing a quadrupole mass filter 40' and detector 48'. The ion guide 32' performs the functions of "focussing and separation [of ions] from an accompanying gas." JA16, 1:9; JA17, 4:38-46. It consists of a set of four rods. JA17, 4:21-23. The rods are arranged to form a passageway between them, the longitudinal axis of which is aligned with the inlet and exit orifices of the ion guide. An AC (alternating current) or RF (radio-frequency) voltage is applied to the rods in such a manner that the AC voltage alternates between adjacent pairs of rods so that when one rod is fully positive, the adjacent rod is fully negative. JA17, 4:43-46. Once the ions enter the passageway between the rods, the alternating AC voltage confines the ions, but not neutral gas molecules, within the passageway. Thus, neutral gas molecules are pumped out by the pump (31') while the ions are confined. As ions approach a rod, the repulsive force grows stronger until the ions are re-directed away from the rod. In this way the ions oscillate from one side of the passageway to the other as they travel down the passageway. JA17, 4:43-46 ("An AC RF voltage . . . is applied between the rods of 3

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rod set 32, as is well known, to permit rod set 32 to perform its guiding and focusing function."). Ions that strike a rod have their charges extinguished, i.e., are neutralized, and thus can no longer be influenced and directed by the electric fields in the instrument nor detected by the detector. At the end of the passageway between the rods, the ions encounter a wall having an orifice (34'). In the embodiments described in the '736 patent, the orifice leads directly to the mass analyzer section (ref. 38'); that is, there is no intermediate pressure stage. As the ions exit the passageway, they will either make contact with the wall or pass through orifice 34'. JA20, 10:52-66. Because the size of the orifice (34') is smaller than that of the passageway formed by the rods, some ions will contact the wall and be neutralized and not pass through the orifice. Just like ions that strike a rod, the ions that contact the wall are thus lost for purposes of analysis. The mass analyzer section illustrated schematically in the '736 patent (38') includes a single quadrupole rod set that has both an AC voltage and a DC voltage applied between rods. JA17, 4:46-50. The DC voltage destabilizes the trajectory of all ions except the ions of interest, thereby ejecting the unwanted ions between the rods or into the rods themselves. In the mass filter embodiments described in the '736 patent, ions that have been "selected" by the mass filter proceed to the detector section where they are detected. Id. 2. The Product of the Pressure and Rod Length (P x L) and Kinetic Energy Operating Parameters of the Ion Guide of the '736 Patent

Maximizing the transfer efficiency of an ion guide is desirable because the more ions that are available to be analyzed, the greater the sensitivity of the device. Prior to the invention of the '736 patent, it was believed that an ion guide should be operated at a "low" pressure, typically 10-4 torr or less, to maximize the transmission of ions from the 4

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ion source to the mass filter.3 JA17-18, 4:56-5:2. The belief at that time was that as the pressure in the ion guide increased, ion transmission would decrease, since the greater abundance of inert gas molecules would cause more collisions between the ions and gas molecules and cause the ions to "scatter." JA18, 5:16-40. A scattered ion undergoes a change in trajectory, which increases the probability that the ion will contact either the rods or a wall of the ion guide and be lost. Id. Through a series of experiments performed on two different mass spectrometers, depicted schematically in Figures 1 and 12 of the '736 patent, inventors Dr. Donald Douglas and Dr. John Barry French discovered that increasing the pressure in the ion guide unexpectedly caused an increase in ion transmission. JA18, 5:41-50. The increased ion transmission increased the sensitivity of the mass spectrometer because more ions were available for detection. These benefits are obtained through the use of what the '736 patent calls "collisional focusing" ­ using low energy collisions within a focusing field to concentrate or "focus" the ions into a dense beam along the centerline of the passageway. JA18-19, 6:62-7:9; JA19, 7:58-62. The highly concentrated beam transmits more ions through the relatively small orifice leading out of the ion guide than otherwise might be possible. The inventors determined that: [t]he significant parameter, then, is the pressure in chamber 30, 30' times the length of the AC-only rods 32, 32'. This product . . . will be called the PL product and is expressed in torr-cm.

3

The '736 patent refers to two papers that exemplify the use of low pressures in the ion guide sections of a mass spectrometer: (1) Richard D. Smith, On-Line Mass Spectrometric Detection for Capillary Zone Electrophoresis, 59 Anal. Chem. 1230 (1987) (A1-3) ("the first Smith reference"); and (2) Richard D. Smith, Capillary Zone Electrophoresis ­ Mass Spectrometry Using an Electrospray Ionization Interface, 60 Anal. Chem. 436 (1988) (A4-9) ("the second Smith reference"). JA18, 5:3-15.

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JA22, 13:27-31 (emphasis added). Based on their experiments, they concluded that improved ion transmission would be obtained at a P x L at or above 2.25 x 10-2 torr cm. Id., 13:32-35. At various ion guide pressures within the range explored in their experiments, the inventors also varied the DC difference voltage between the inlet orifice and the rod set to examine the effect of ion kinetic energy on the ion signal. JA21, 12:30-63. They discovered that it is important for the kinetic energies of the ions moving between the inlet to the passageway defined by the rods of the ion guide to be maintained relatively low, and, in particular, below the level at which significant fragmentation of the ions would occur through collision induced dissociation. Id., 12:44-49. B. The Original and Reexamination Prosecution of the '736 Patent 1. The Original Prosecution of the '736 Patent

The application that issued as the '736 patent was filed on November 15, 1989, claiming priority from a Canadian application filed on December 12, 1988.4 On May 8, 1990, in the first Office Action, the Examiner allowed all the claims as originally filed. The '736 patent issued on October 16, 1990 with twenty-four claims, of which claims 1 and 14 are independent. 2. The Reexamination of the '736 Patent

On September 30, 1997, patent owner MDS Health Group, Inc., now plaintiff MDS Inc. ("MDS"), requested reexamination of the '736 patent in light of eight prior art references that had not been considered during the original prosecution.5 Four of the references disclosed "ion traps"--the Schaaf article, the Vedel article, the Stafford article

4 5

A copy of the original prosecution file history is included in the Joint Appendix at Tab 3. A copy of the reexamination file history is included in the Joint Appendix at Tab 4.

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and the Stafford application.6 The other four references disclosed "tandem mass spectrometers" and included a prior patent application of inventor Dr. French ("the French application"). JA171-72. An ion trap that is exemplary of those described in the four references that were cited in the Reexamination Request appears in Figure 1 of the Stafford article, reproduced below:

As the caption indicates, the structure includes a "ring electrode" and two "end cap electrodes," shown in cross section in the Figure. In the Reexamination Request, MDS distinguished the ion trap references on several grounds. First, MDS distinguished the references on the basis that they did not disclose any of the following elements of the claimed mass spectrometer or method: first and second vacuum chambers; first and second rod sets; an inlet orifice; an interchamber orifice; the application of an AC-only voltage to a first rod set; the application of AC and
H. Schaaf , U. Schmeling & G. Werth, Trapped Ion Density Distribution in the Presence of He-Buffer Gas, 25 Applied Physics 249 (1981) ("Schaaf article") (JA249-51); F. Vedel & J. Andre, Influence of Space Charge on the Computed Statistical Properties of Stored Ions Cooled by a Buffer Gas in a Quadrupole RF Trap, 29 Physical Rev. 2098 (1984) ("Vedel article") (JA252-54); G.C. Stafford, P.E. Kelley, J.E.P. Syka, W.E. Reynolds & J.F.J. Todd, Recent Improvements in and Analytical Applications of Advanced Ion Trap Technology, 60 Int'l J. of Mass Spectrometry & Ion Processes 85 (1984) ("Stafford article") (JA255-68); and Stafford et al., European Patent Application, Publication No. 0 0113207, July 11, 1984 ("Stafford application") (JA270-301).
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DC voltages to a second rod set; the product of the pressure in the first vacuum chamber and the length of the first rod set of at least 2.25 x 10-2 torr cm; and maintaining the kinetic energies of ions at a relatively low level as they travel from an inlet orifice to a first rod set. JA175 (Schaaf); JA176 (Vedel); JA177-78 (Stafford article); JA178-79 (Stafford application). Second, MDS further distinguished Schaaf on the ground that the AC-only rod set (ion guide) in the claimed invention does not trap ions for analysis but rather guides the ions through the ion guide into the mass analyzer. JA173-75. Third, MDS further distinguished Schaaf and Vedel on the ground that it would not have been obvious to use a high-pressure gas in the claimed ion guide because the ion trap references suggest that this would cause ion losses due to scattering. JA174 (Schaaf); JA176 (Vedel). On November 20, 1997, the examiner granted MDS's Reexamination Request, stating that the French application, considered with other tandem mass spectrometer references, raised a substantial new question of patentability. JA378. The examiner did not find that any of the ion trap references raised a substantial new question of patentability. In the first Office Action, dated February 3, 1998, the examiner rejected the claims essentially on the grounds set forth in the reexamination grant, relying primarily on the French application. See JA383. After an in-person interview with inventor Dr. Douglas and MDS's attorney, followed by submission of an Amendment and a Declaration of Dr. French addressing the pertinence of the French application, the examiner issued a final Office Action confirming the validity of the original claims 1 to

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24. JA434-35.7 On May 25, 1999, the Patent Office issued Reexamination Certificate No. B1 4,963,736. JA24-25. C. The Prior Litigation on the '736 Patent against Micromass 1. The Court's Claim Construction in the Micromass Case

Prior to filing this suit against Thermo, AB/Sciex successfully asserted the '736 patent in the Court against the Quattro Ultima mass spectrometer made by Micromass UK Ltd. and sold in the U.S. by Micromass Inc. (collectively, "Micromass"). After extensive briefing and a Markman hearing, the Court construed almost every claim term of the '736 patent. The Court's thorough claim construction opinion is reported at Applera Corp. v. Micromass UK Ltd., 186 F. Supp. 2d 487 (D. Del. 2002) (JA485-528). After a ten-day jury trial on infringement, invalidity and damages issues, the jury found the '736 patent valid and infringed by Micromass's Quattro Ultima mass spectrometers and awarded AB/Sciex $47.5 million in damages. The Court denied Micromass's post-trial motions and dismissed its antitrust counterclaims. Moreover, after a one-day bench trial, the Court rejected Micromass's inequitable conduct and equitable estoppel defenses. The Court's post-trial opinion is reported at Applera Corp. v. Micromass UK Ltd., 204 F. Supp. 2d 724 (D. Del. 2002) (JA529-89).8 Micromass appealed to the Federal Circuit, challenging the Court's construction of the claim terms "end to end," "separated by a wall," "interchamber orifice," "second rod set," and "second vacuum chamber." Micromass also argued that the Court erred by failing to construe the claim term "improved transmission of ions" and proposed its own

7

The examiner, however, rejected newly added claims 25-30. After submission of further amendments, these claims were also allowed. The Court also denied Micromass's motion for reconsideration of certain aspects of its claim construction. See id. at 747-49 (JA552-54).

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construction. Finally, Micromass also challenged the infringement and damages verdicts on a number of additional grounds. In a brief per curiam order issued about a week after oral argument, the Federal Circuit rejected every one of Micromass's arguments by affirming the judgment "on the basis" of the Court's claim construction and post-trial opinions. Applera Corp. v. Micromass UK Ltd., 60 F.App'x 800 (Fed. Cir. 2003) (JA590). 2. Thermo's Challenges to the Court's Claim Construction from the Micromass Case

As explained below in more detail, despite the Court's thorough claim construction analysis in the Micromass case and the Federal Circuit's affirmance, Thermo seeks to challenge the Court's prior claim construction of the following claim terms: (1) "separated by a wall," (2) "interchamber orifice," (3) "located end to end," (4) "means. . . for directing said ions through said inlet orifice into said first vacuum chamber," (5) "means for flowing gas through said inlet orifice into said first space," (6) "means for maintaining the kinetic energies of ions moving from said inlet orifice to said first rod set at a relatively low level," and (7) "whereby to provide improved transmission of ions through said interchamber orifice." D. The Accused Thermo Instruments and Thermo's Noninfringement Positions AB/Sciex has accused the Thermo TSQ Quantum and LTQ series of mass spectrometers of infringement of the '736 patent. 1. Thermo TSQ Quantum Series

The Thermo TSQ Quantum series9 of mass spectrometers have all the components of the embodiment shown in Figures 1 and 12 of the '736 patent, including
9

The Thermo TSQ Quantum series includes the TSQ Quantum, TSQ Quantum Ultra and TSQ Quantum Discovery mass spectrometers.

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an ion source, an ion guide comprising an AC-only rod set in a vacuum chamber, and a mass filter comprising an AC-DC rod set in a vacuum chamber. Unlike Figure 12, the TSQ Quantum has two ion guide stages instead of one, and, since it is a tandem mass spectrometer, it also includes a collision cell and a second mass filter. A schematic of the mass spectrometer components of the TSQ Quantum from one of Thermo's manuals is shown below. A34.

The two-stage ion guide of the TSQ Quantum includes two vacuum chambers (depicted as "Q00" and "Q0"), each of which includes an AC-only quadrupole rod set, i.e., a set of four rods, arranged to provide a passageway through which ions are guided. Id. The Q00 chamber corresponds to the claimed "first vacuum chamber" with a "first rod set" of the '736 patent, i.e., the ion guide. The product of the rod length and the pressure of the first ion guide stage (Q00) exceeds the 2.25 x 10-2 torr cm threshold of the '736 patent. Ions exit the Q00 chamber through an orifice, travel through the second ion guide stage (Q0) and then pass into the mass analyzer section, which is a tandem mass analyzer that includes three stages: a first mass filter stage (depicted as "Q1"), a collision 11

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cell (depicted as "Q2"), and a second mass filter stage (depicted as "Q3"). A38. The first mass filter stage (Q1) includes an AC-DC quadrupole rod set that defines a passageway for the ions. A39. The Q1 chamber corresponds to the claimed "second vacuum chamber" with a "second rod set" of the '736 patent, i.e., the mass analyzer chamber. 2. Thermo LTQ Series

The Thermo LTQ series10 of mass spectrometers also have all the components of the embodiment shown in Figures 1 and 12 of the '736 patent, including an ion source, an ion guide comprising an AC-only rod set in a vacuum chamber, and a mass filter comprising an AC-DC rod set in a vacuum chamber. Unlike Figure 12, the LTQ has three ion-guide stages instead of one, and, since it is a linear ion trap mass spectrometer, it uses a linear ion trap as the mass filter. A schematic of the ion guide and mass filter components of the LTQ from one of Thermo's manuals is shown below. A89.

The three-stage ion guide of the LTQ includes three vacuum chambers, the first two of which (depicted as "Q00" and "Q0") each includes an AC-only quadrupole rod set arranged to provide a passageway through which the ions are guided, and the last of which (depicted as "Q1") includes an AC-only octapole rod set, i.e., a set of eight rods.
10

The Thermo LTQ series includes the LTQ, LTQ FT and LTQ Orbitrap mass spectrometers.

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A89-91. The Q00 chamber corresponds to the claimed "first vacuum chamber" with a "first rod set" of the '736 patent, i.e., the ion guide. The product of the rod length and the pressure of the first ion guide stage (Q00) exceeds the 2.25 x 10-2 torr cm threshold of the '736 patent. Ions exit the Q00 chamber through an orifice, travel into the second and third ion guide stages (Q0 and Q1) and pass into the mass analyzer section. The mass analyzer section of the LTQ is a linear ion trap which includes an AC-DC quadrupole rod set, as shown below in one of Thermo's manuals. A91-92.

The linear ion trap chamber corresponds to the claimed "second vacuum chamber" with a "second rod set" of the '736 patent, i.e., the mass analyzer chamber. 3. Thermo's Noninfringement Positions

Thermo's noninfringement positions are based on unduly narrow claim constructions that are impermissibly based on importing limitations from the preferred embodiments of the specification and distorting the reexamination prosecution history. Some of Thermo's interpretations seek to limit the claims to the specific structural arrangement of the preferred embodiments. Others seek to limit the claims to certain operating parameters based on alleged disclaimers during the reexamination. Some are also inconsistent with the Court's prior constructions in the Micromass case. As

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explained below, Thermo's narrow litigation-motivated constructions are not supported by the claim language, specification or prosecution history, and should be rejected. ARGUMENT I. A. DISPUTED TERMS INVOLVING THE PREVIOUSLY DECIDED ISSUE OF WHETHER THE CHAMBERS MUST BE ADJACENT "Separated by a Wall" and "Separated by an Interchamber Orifice" Proposed Construction: "Separated by a Wall"--At least a wall between the first and second vacuum chambers. "Separated by an Interchamber Orifice"--An orifice in a wall between the first and second vacuum chambers. In the Micromass litigation, Micromass proposed constructions of several phrases in independent claims 1 and 14 of the '736 patent that would have limited the claims to mass spectrometer systems in which the "first" and "second" vacuum chambers housing the "first rod set" (ion guide) and "second rod set" (mass filter), respectively, are adjacent to each other. Micromass sought to exclude from the scope of the claims its Quattro Ultima mass spectrometer, which included an additional vacuum chamber and ion guide between the "first" and "second" vacuum chambers. Micromass thus asked the Court to construe the phrase "first and second vacuum chambers separated by a wall" in claim 1 to require that no structure other than the recited wall be between the two chambers and the phrase "first and second spaces . . . separated by an interchamber orifice" in claim 14 to require that the interchamber orifice join or link the two chambers. Applera, 186 F. Supp. 2d at 509-10 (JA507-08). The Court correctly rejected Micromass's constructions as seeking to import limitations from the preferred embodiments in the specification into the claims. Id. The Court construed the phrase "separated by a wall" in accordance with its ordinary meaning to mean that there is "at least a wall between the first and second vacuum chambers" and 14

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the term "interchamber orifice" to mean that there is "an orifice in a wall that is between the first and second vacuum chambers," thus allowing for the presence of other structures in addition to the recited wall that also separate the two chambers. Id. at 510 (JA508). On appeal, Micromass argued for reversal of the judgment on the basis that the Court's constructions of "separated by a wall" and "separated by an interchamber orifice" were erroneous. A149-53. The Federal Circuit rejected Micromass's proposed constructions and confirmed the correctness of the Court's constructions by affirming the judgment below "on the basis" of the Court's analysis. Applera, 60 F.App'x 800 (JA590). Thermo proposes constructions of "separated by a wall" and "separated by an interchamber orifice" that are substantively the same as those proposed by Micromass and rejected by the Court and the Federal Circuit, and for exactly the same reason. Thermo proposes that "separated by a wall" be construed to mean "that a wall defines a common boundary of each of the first and second vacuum chambers," i.e., that the two chambers are separated only by a wall and no other structures. Each of the accused TSQ Quantum series instruments has an additional vacuum chamber and ion guide between the "first" (ion guide) and "second" (mass filter) vacuum chambers, just as Micromass's infringing Quattro Ultima instrument did. The accused LTQ instrument has two additional ion guides. Thermo's constructions seek to limit the claims to the preferred embodiments in order to exclude its mass spectrometers. In view of the Court's prior construction and the Federal Circuit's affirmance, Thermo's constructions should be rejected under the doctrine of stare decisis. See Burke, Inc. v. Bruno Indep. Living Aids, Inc., 183 F.3d 1334, 1341-42 (Fed. Cir. 1999) (reversing grant of summary judgment of noninfringement based on a claim construction that was

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inconsistent with the construction adopted by the Federal Circuit in a prior nonprecedential opinion in another case); Tate Access Floors, Inc. v. Interface Architectural Res., Inc., 185 F. Supp. 2d 588, 595 n.4 (D. Md. 2002) ("Prior claim constructions [by the Federal Circuit], when on point, are given deference under the doctrine of stare decisis in the interest of uniformity and consistency in claim interpretation"); Wang Labs., Inc. v. Oki Elec. Indus. Co., 15 F. Supp. 2d 166, 176 (D. Mass. 1998) ("Despite its inability to participate in the [prior] litigation, [the accused infringer] is nevertheless bound by the rule of law established in [the Federal Circuit's claim construction in the prior suit]"). Thermo's constructions should also be rejected because they are incorrect. The claim language does not exclude structure in addition to a wall between the first and second vacuum chambers. Claims 1 and 14 define the mass spectrometer system and method as "comprising" the elements that follow, and, therefore, do not exclude the presence of other structures. See, e.g., Phillips Petroleum Co. v. Huntsman Polymers Corp., 157 F.3d 866, 874 (Fed. Cir. 1998). The use of the indefinite article "a" in the phrase "separated by a wall" further supports a construction that permits other structures to be between the first and second vacuum chambers. See KCJ Corp. v. Kinetic Concepts, 223 F.3d 1351, 1356 (Fed. Cir. 2000) ("This Court has repeatedly emphasized that an indefinite article `a' or `an' in patent parlance carries the meaning of `one or more' in open-ended claims containing the transitional phrase `comprising.'"). The phrase "separated by a wall" does not appear in the specification. Although the preferred embodiments shown schematically in Figures 1 and 12 show the ion guide chamber being separated from the mass filter chamber by only a wall, the specification does not describe any functional constraint (other than the necessity that ions be able to

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travel from the first vacuum chamber to the second vacuum chamber, and the necessity that the ion guide chamber and the mass filter chamber be at different pressures, as discussed above) that would preclude the presence of other structures between the first and second vacuum chambers. There is no basis for limiting the claims to the preferred embodiments described in the specification. "[A]lthough the specification often describes very specific embodiments of the invention, we have repeatedly warned against confining the claims to those embodiments." Phillips v. AWH Corp., 415 F.3d 1303, 1323 (Fed. Cir. 2005); see also Specialty Composites v. Cabot Corp., 845 F.2d 981, 987 (Fed. Cir. 1988); Interactive Gift Express, Inc. v. CompuServe Inc., 256 F.3d 1323, 1340 (Fed. Cir. 2001); Netword, LLC v. Centraal Corp., 242 F.3d 1347, 1352 (Fed. Cir. 2001); Burke, 183 F.3d at 1341. Finally, nothing in the original or reexamination prosecution history provides a basis for restricting the meaning of the phrase "separated by a wall" to "separated only by a wall." No prior art was distinguished on the basis that the claims required that the first and second vacuum chambers be separated only by a wall. There is simply no support for Thermo's construction. B. "Located End to End" Proposed Construction: The rod sets and spaces must be arranged in a manner that ions may be successfully transmitted from the end of the first rod set or the first space to the end of the second rod set of the second space.

Thermo also opposes the construction of the phrase "located end to end" in claims 1 and 14 that was adopted by the Court in the Micromass litigation and affirmed by the Federal Circuit. In claim 1, the phrase refers to the arrangement of the rod sets: "said first rod set being located end to end with said second rod set." In claim 14, the phrase

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refers to the corresponding arrangement of the spaces defined by the rod sets: "first and second spaces respectively located end-to-end with each other." In the Micromass litigation, the Court construed "located end to end" to mean that "the rod sets and spaces must be arranged in a manner that ions may be successfully transmitted from the end of the first rod set or the first space to the end of the second rod set or second space." Applera, 186 F. Supp. 2d at 513-14 (JA511-12). The Court rejected the construction Micromass proposed that would have required that the end of one rod set or space be placed against the end of the other rod set or space. Id. at 511 (JA509), 514 (JA512). Micromass's construction was yet another attempt to have the claims confined to the preferred embodiments, in which the chambers are adjacent to each other. Micromass challenged the Court's construction of "end to end" on appeal, but the Federal Circuit implicitly rejected Micromass's proposed construction and confirmed the correctness of the Court's construction by affirming the judgment below "on the basis" of the Court's analysis. Applera, 60 F.App'x 800 (JA590). Thermo does not propose a contrary construction of "located end to end." Instead, it contends that no construction is necessary in view of the construction of "aligned," on which the parties agree (and which was adopted by the Court in the Micromass litigation). Claim 1 recites: "said first rod set being located end to end with said second rod set so that said first and second spaces are aligned." The construction of "aligned" ­ "being in or coming into precise adjustment or correct relative position" ­ will tell the jury that the spaces must be in "correct relative position" but does not itself explain what that means in this context. The construction of "located end to end" provides that explanation ­ that "the rod sets and spaces must be arranged in a manner that ions may be successfully transmitted from the end of the first rod set or the first

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space to the end of the second rod set or second space." Moreover, the term "aligned" does not appear in claim 14 but the phrase "located end to end" does. The construction of "aligned" in claim 1 will not help the jury understand what "located end to end" means in claim 14. Therefore, the construction of "located end to end" will assist the jury and should be included. II. DISPUTES INVOLVING THE PREVIOUSLY DECIDED IDENTIFICATION OF CORRESPONDING STRUCTURES IN THE CONSTRUCTIONS OF CERTAIN MEANS-PLUS-FUNCTION LIMITATIONS "Means . . . for Directing Said Ions Through Said Inlet Orifice" Proposed Construction: The function of the element is "directing said ions through said inlet orifice into said vacuum chamber." The corresponding structure, material, or acts described in the specification is either, or both, of two independent operating parameters: (1) the application of appropriate DC potential between the inlet orifice and the rod set in the first vacuum chamber; and/or (2) a difference in the pressures on either side of the inlet orifice. AB/Sciex and Thermo agree that the phrase "means . . . for directing said ions through said inlet orifice into said first vacuum chamber" in element (b) of claim 1 is a means-plus-function element subject to 35 U.S.C. § 112, ¶ 6. A means-plus-function limitation is one which recites a function to be performed rather than the structure or materials for performing that function. Northrop Grumman Corp., v. Intel Corp., 325 F.3d 1346, 1350 (Fed. Cir. 2003). "Such a limitation is construed `to cover the corresponding structure, materials, or acts described in the specification and equivalents thereof.'" Id. (citing 35 U.S.C. § 112, ¶ 6; Chiuminatta Concrete Concepts, Inc. v. Cardinal Indus., Inc., 145 F.3d 1303, 1309-09 (Fed. Cir. 1998)). "The first step in construing a means-plus-function limitation is to identify the 19

A.

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function explicitly recited in the claim." Asyst Techs., Inc. v. Empak, Inc., 268 F.3d 1364, 1369 (Fed. Cir. 2001) (citing Budde v. Harley-Davidson, Inc., 250 F.3d 1369, 1376 (Fed. Cir. 2001)). The next step is to identify the corresponding "structure, materials, or acts" set forth in the written description that performs the particular function set forth in the claim. Asyst Techs., 268 F.3d at 1369. AB/Sciex and Thermo agree that the function for this means-plus-function limitation is "directing said ions through said inlet orifice into said first vacuum chamber." However, AB/Sciex and Thermo disagree on the corresponding structure disclosed in the specification for performing this function. AB/Sciex's proposed construction of the corresponding structure was adopted by the Court in the Micromass case.11 Applera, 186 F. Supp. 2d at 519 (JA517), 530 (JA528). Since claim construction is a matter of law, the Court's prior construction should be given deference. Markman v. Westview Instr., Inc., 517 U.S. 370, 391 (1996) (stare decisis should promote uniformity in the claim construction of a given patent); KX Indus. v. PUR Water Purification Prods., Inc., 108 F. Supp. 2d 380, 387 (D. Del. 2000), aff'd, 18 F.App'x 871 (Fed. Cir. 2001) ("[T]o the extent the parties do not raise new arguments, the court will defer to its previous construction of the claims."). The construction adopted in the Micromass litigation is compelled by the specification, as understood by those skilled in the art. There are two corresponding structures identified in the specification for directing the ions though an inlet orifice into

11

The Court used the statutory language "corresponding structure, material or acts" in its constructions of the means-plus-function limitations in its Markman opinion in the Micromass litigation. Therefore, AB/Sciex uses that formulation here.

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a first vacuum chamber. The first is the DC potential voltage12 applied between the inlet orifice and the first rod set in the first vacuum chamber. With reference to the Figure 1 embodiment, the specification recites that "[i]ons produced in the ionization chamber 16 are drifted by appropriate DC potentials on plates 22, 28, and on the AC-only rod set 32 through opening 20 and orifice 26," into the first vacuum chamber. JA17, 4:38-41 (emphasis added). With reference to the Figure 12 embodiment, the specification states that: [i]t was found that with the physical arrangement shown in FIG. 12, the ion to gas ratio entering the AC-only rods 32' increased by a factor of about two to four . . . when an appropriate DC voltage difference voltage (preferably about 1 to 15 volts) existed between skimmer plate 72 and AConly rods 32'. JA20, 9:34-41 (emphasis added). The other corresponding structure identified in the specification for directing ions though an inlet orifice into a first vacuum chamber is a difference in the pressures on either side of the inlet orifice. The specification discloses repeatedly that pressure differentials exist between the first vacuum chamber and the preceding chambers. For example, Figure 1 shows that a pump 31 is used for evacuating chamber 30. The pump 31 causes a pressure difference between chamber 24 (which is at about atmospheric pressure or slightly higher) and chamber 30. JA17, 4:19-21; JA2, Fig. 1. Similarly, Figure 12 depicts a pressure difference between a rod-less vacuum chamber 70 held at

12

The corresponding structure for a means-plus-function claim element does not need to be hardware or a solid object. See, e.g., Fonar Corp. v. General Elec. Co., 107 F.3d 1543, 1551-52 (Fed. Cir. 1997) (finding a "generic gradient waveform" to be the corresponding structure); Altiris, Inc. v. Symantec Corp., 318 F.3d 1363, 1377 (Fed. Cir. 2003) (finding "the normal operating system on the computer, another automation operating system, a customized or a normal MBR ["Master Boot Record"], and communications software" each to be the corresponding structures); Globetrotter Software, Inc. v. Elan Computer Group, Inc., 236 F.3d 1363, 1367-70 (Fed. Cir. 2001) (finding a software license file having unique identification data was the corresponding structure).

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between 0.4 torr and 10 torr by pump 71 and chamber 30', which typically has a vacuum of 5 to 8 x 10-3 torr. JA20, 9:3-4, 13-17, 38-39; JA10, Fig. 12. The specification also teaches that a pressure difference will direct ions, along with neutral gas molecules, to flow through the inlet orifice. For example, the specification states that "[i]t was found that with the physical arrangement shown in Fig. 12, the ion to gas ratio entering the AConly rods 32' increased by a factor of about two to four . . . when the appropriate pressures . . . were used in chamber 30' . . . ." Id., 9:34-39 (emphasis added). Thermo's proposed construction states that "the corresponding structures include `curtain gas plate 22,' `orifice plate 28,' and `rod set 32.'" D.I. 49, Ex. A at 11. This construction is incorrect for several reasons. First, curtain gas plate 22 is not even involved in the function of directing ions through the inlet orifice. The specification describes a DC potential between curtain gas plate 22 and orifice plate 28 in the embodiment of Figure 1, but that potential directs ions though orifice 20 into the curtain gas chamber 24, not through the inlet orifice (orifice 26). In the embodiment of Figure 12, the curtain gas plate 22' is even further removed from the inlet orifice (orifice 76) because there is another vacuum chamber 70 between the curtain gas chamber 24 and the "first vacuum chamber." 35 U.S.C. § 112, ¶ 6, does not "permit incorporation of structure from the written description beyond that necessary to perform the claimed function." Asyst Techs., 268 F.3d at 1369-70 (citing Micro Chem., Inc. v. Great Plains Chem. Co., 194 F.3d 1250, 1257-58 (Fed. Cir. 1999)). Second, although orifice plate 28 and rod set 32 are involved in one of the corresponding structures as described in one of the disclosed embodiments, i.e., DC voltages are applied to them in the embodiment of Figure 1 to produce a potential difference to cause ions to drift through the inlet orifice, Thermo excludes the analogous

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elements in the Figure 12 embodiment, specifically skimmer plate 72 (having an orifice 76) and rod set 32'. AB/Sciex's proposed construction (and the Court's in the Micromass litigation) embraces both embodiments in the recitation "the application of appropriate DC potential between the inlet orifice and the rod set in the first vacuum chamber." Third, orifice plate 28 and rod set 32 do not themselves cause ions to enter the first vacuum chamber. DC voltages must be applied to them (or to skimmer plate 72 and rod set 32' in Figure 12) to create the DC potential that does cause ions to enter the first vacuum chamber. The corresponding structure must actually perform the recited function. Asyst Techs., 268 F.3d at 1371. Finally, Thermo omits the alternative corresponding structure identified in the specification: a difference in the pressures on either side of the inlet orifice. The Court concluded in the Micromass litigation that "it is clear from the patent specification that a pressure differential exists between the curtain gas chamber (24) and the first vacuum chamber (30) and that this pressure differential causes the curtain gas to flow through the orifice (26)." Applera, 186 F. Supp. 2d at 516-17 (JA514-15). The Court thus correctly identified "a difference in the pressures on either side of the inlet orifice" as alternative corresponding structure. Id. at 517-18, 530 (JA515-16; JA528). B. "Means for Flowing Gas Through Said Inlet Orifice" Proposed Construction: The function of the element is "to flow gas through said inlet orifice and into said first space." The corresponding structure, material, or acts described in the specification is the existence of gas in a chamber, separated from the first vacuum chamber by the inlet orifice, at a higher pressure than that in the first vacuum chamber. AB/Sciex and Thermo agree that the phrase "means for flowing gas through said inlet orifice into said first space" in element (g) of claim 1 is a means-plus-function 23

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element, and that the recited function is "to flow gas through said inlet orifice and into said first space." However, AB/Sciex and Thermo disagree on the corresponding structure disclosed in the specification. AB/Sciex's proposed construction was adopted by the Court in the Micromass case, and should be given deference. Applera, 186 F. Supp. 2d at 520 (JA518), 530 (JA528); see also Markman, 517 U.S. at 391; KX Indus., 108 F. Supp. 2d at 387. The construction adopted in the Micromass litigation, "the existence of gas in a chamber, separated from the first vacuum chamber by the inlet orifice, at a pressure higher than the pressure in the first chamber," comes directly from the specification. The specification states with reference to the Figure 1 embodiment that the "curtain gas chamber 24 is connected by an orifice 26 in orifice plate 28 to a first vacuum chamber 30 pumped by a vacuum pump 31." JA17, 4:19-21. The specification goes on to state that the "curtain gas flows through orifice 26 into the first vacuum chamber 30 . . . ." Id., 4:32-33. The fact that there is gas in the curtain gas chamber that is at a higher pressure (approximately atmospheric pressure) than the "first vacuum chamber" ("up to between 150 and 200 millitorr") causes gas to flow through the inlet orifice. Id., 4:13-15, 17-19; JA22, 13:65-66. In the Figure 12 embodiment, a vacuum chamber 70 precedes the "first vacuum chamber" 30'. The pressure in vacuum chamber 70 is "between about 0.4 and about 10 torr" and thus higher than the pressure in the "first vacuum chamber" 30'. JA20, 9:14-15. That difference in pressure causes gas to flow through skimmer orifice 76. Thermo's proposed construction states that the corresponding structures include "curtain gas source 42," "duct 44 to the curtain gas chamber 24," "curtain gas chamber 24," "orifice plate 28," "orifice 26," "vacuum pump 31," and "vacuum chamber 30." D.I. 49, Ex. A at 11. Thermo merely identifies elements in the Figure 1 embodiment that can

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enable gas in curtain gas chamber 24 to have a higher pressure than that of the first vacuum chamber 30. However, it is the fact, not the possibility, of gas at a higher pressure that performs the recited function of flowing gas through the inlet orifice. Thermo's proposed construction should be rejected because it "incorporat[es] structure from the written description beyond that necessary to perform the claimed function." Asyst Techs., 268 F.3d at 1369-70. The elements Thermo identifies are not themselves the cause of gas flow though the inlet orifice. That does not occur unless and until the gas in the curtain gas chamber (or in vacuum chamber 70 in the Figure 12 embodiment) is at a higher pressure than the "first vacuum chamber." C. "Means for Maintaining Kinetic Energies of Ions" Proposed Construction: The function of the element is "maintaining the kinetic energy of ions moving from said inlet orifice to said first rod set at a relatively low level." The corresponding structure, material, or acts described in the specification is the application of two variables: (1) a DC potential voltage between the inlet orifice and the first rod set, and (2) the pressure in the first vacuum chamber. AB/Sciex and Thermo agree that the phrase "means for maintaining the kinetic energies of ions moving from said inlet orifice to said rod set at a relatively low level" in element (k) of claim 1 is a means-plus-function element subject to 35 U.S.C. § 112, ¶ 6, and that the recited function is "maintaining the kinetic energy of ions moving from said inlet orifice to said first rod set at a relatively low level." However, AB/Sciex and Thermo disagree on the corresponding structure disclosed in the specification. AB/Sciex's proposed construction was adopted by the Court in the Micromass case, and should be given deference. Applera, 186 F. Supp. 2d at 520 (JA518), 530 (JA528); see also Markman, 517 U.S. at 391; KX Indus., 108 F. Supp. 2d at 387.

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The construction adopted in the Micromass litigation comes directly from the specification, which makes clear that the function of maintaining the kinetic energies of the ions at a relatively low level is accomplished by the application of the proper voltage for a given pressure in the chamber. In particular, the experiments described in the specification demonstrate that the kinetic energies of the ions are increased by an increased DC voltage, but are decreased by increased pressure in the chamber. With respect to the impact of pressure on kinetic energy, the specification discloses experiments where increasing the pressure of chamber 30 to 5.9 mtorr decreased the kinetic energy of the ions, and where increasing the pressure "to 9.8 millitorr, the . . . maximum energy were reduced even further." JA19, 7:67-8:40. With respect to the impact of the DC voltage, dependent claims 8-10, all of which were present in the original application as filed and thus are part of the specification, require that the means for maintaining "the kinetic energy of said ions" of claim 1 comprises a means for applying a "low DC voltage between said first rod set and said inlet wall." JA23, 15:2038. Finally, the specification makes clear that there is a relationship between voltage and pressure, and that the appropriate voltage depends upon the pressure. See, e.g., JA21, 11:7-12 ("It is found that when the AC-only rod set 32' is operated at a high pressure (e.g. 5 millitorr), with a relatively low DC difference voltage . . . ."). Accordingly, the specification makes clear that applying voltage without regard to the pressure cannot be the structure which corresponds to the recited function, and that the corresponding structure is the application of the proper combination of both voltage and pressure. Thermo's proposed construction states that the corresponding structures include "curtain gas plate 22," "orifice plate 28," and "rod set 32." This construction is incorrect for several reasons. First, curtain gas plate 22 is not even involved in the function of

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maintaining the kinetic energies of ions moving from the inlet orifice to the first rod set at a relatively low level. The specification nowhere associates the curtain gas plate with that function. Indeed, in the embodiment of Figure 12, the curtain gas plate 22' is removed from region between the inlet orifice (orifice 76) and the first rod set by a vacuum chamber 70 between the curtain gas chamber 24 and the first vacuum chamber. 35 U.S.C. § 112, ¶ 6, does not "permit incorporation of structure from the written description beyond that necessary to perform the claim