Thermo Fisher Scientific Inc v. Agilent Tech Inc

I. Executive Summary and Procedural Information

• Parties & Counsel:
  • Plaintiff: Thermo Fisher Scientific Inc. (Delaware) and Thermo Fisher Scientific (Bremen) GmbH (Germany)
  • Defendant: Agilent Technologies, Inc. (Delaware)
  • Plaintiff’s Counsel: Shaw Keller LLP; Durie Tangri LLP
• Case Identification: 1:17-cv-00600, D. Del., 04/24/2018
• Venue Allegations: Venue is alleged to be proper as Defendant is a Delaware corporation that transacts continuous and systematic business within Delaware, and the lawsuit arises from infringing activities within the state.
• Core Dispute: Plaintiff alleges that Defendant’s inductively coupled plasma mass spectrometer products infringe patents related to methods and apparatus for removing unwanted interfering ions to improve analytical accuracy.
• Technical Context: The technology involves high-precision analytical instruments used in scientific research and industrial quality control to determine the elemental composition of samples, a critical capability in fields ranging from environmental testing to semiconductor manufacturing.
• Key Procedural History: The complaint notes extensive pre-suit communications beginning in November 2012, where Thermo Fisher accused Agilent’s products of infringing the predecessors to the two reissue patents-in-suit. Following these communications, Thermo Fisher submitted the original patents for reissue, during which it disclosed to the USPTO the prior art references cited by Agilent. The patents were subsequently reissued as the '386 and '553 patents. The complaint also references Inter Partes Review (IPR) petitions filed by Agilent against the patents-in-suit.

Case Timeline

Date	Event
1998-09-16	Priority Date for '386 and '232 Patents
2002-05-13	Priority Date for '553 Patent
2007-04-10	Issue Date for U.S. Patent No. 7,202,470 (predecessor to '386)
2007-05-01	Issue Date for U.S. Patent No. 7,211,788 (predecessor to '553)
2007-06-12	Issue Date for U.S. Patent No. 7,230,232
2009-01-01	Launch of Accused Agilent 7700 Series
2012-01-01	Launch of Accused Agilent 8800 Product
2012-11-09	Thermo Fisher first notifies Agilent of infringement by 8800 product
2013-09-19	Thermo Fisher submits '470 and '788 patents for reissue
2014-01-01	Launch of Accused Agilent 7900 Product
2015-01-01	Launch of Accused Agilent 7800 Product
2015-02-24	Issue Date for U.S. Reissue Patent No. RE45,386
2015-06-09	Issue Date for U.S. Reissue Patent No. RE45,553
2016-01-01	Launch of Accused Agilent 8900 Product
2017-05-24	Original Complaint Filed
2017-12-26	Thermo Fisher notifies Agilent of '232 infringement by 7700 series
2018-04-24	Second Amended Complaint Filed

II. Technology and Patent(s)-in-Suit Analysis

U.S. Reissue Patent No. RE45,386 - "Means for Removing Unwanted Ions From an Ion Transport System and Mass Spectrometer"

• Patent Identification: U.S. Reissue Patent No. RE45,386, "Means for Removing Unwanted Ions From an Ion Transport System and Mass Spectrometer," issued February 24, 2015.

The Invention Explained

• Problem Addressed: In inductively coupled plasma mass spectrometry (ICP-MS), the high-temperature plasma used to ionize a sample also creates unwanted "artefact ions" (e.g., from the argon plasma gas) that have the same mass-to-charge ratio as the desired analyte ions, causing spectral interference that impairs detection ('386 Patent, col. 5:39-49). Furthermore, when a collision cell is used to remove these primary artefact ions, new interfering ions can be formed within the cell itself from reactions involving the high gas load from the plasma source ('386 Patent, col. 6:30-47).
• The Patented Solution: The invention places a mass-selective ion optical device, such as a quadrupole, before the collision cell. This first device is set to transmit only a narrow mass range including the target analyte ion, rejecting other ions before they can enter the collision cell and cause secondary reactions. A second mass analyzer after the collision cell is set to the same mass-to-charge ratio to detect the purified analyte ions, a configuration that "substantially minimize[s] the formation in the collision cell of interfering ions" ('386 Patent, Claim 28; Abstract).
• Technical Importance: This tandem mass filtering approach (mass filter -> collision cell -> mass analyzer) significantly enhances measurement accuracy by proactively preventing the formation of secondary interferences, a key limitation in conventional collision cell designs.

Key Claims at a Glance

• The complaint asserts independent claims 13 (method) and 28 (apparatus) ('Compl. ¶¶34, 47).
• Key elements of independent apparatus claim 28 include:
  • An inductively coupled plasma (ICP) ion source generating analyte ions and interfering artefact ions.
  • An "ion optical device" (first mass filter) configured to "mass select" ions at a first mass-to-charge ratio.
  • A "collision cell" disposed to receive the mass-selected ions, with the upstream ion optical device being "configured substantially to minimize the formation in the collision cell of interfering artefact ions."
  • A "mass analyzer" (second mass filter) configured to analyze the ion beam at the "same mass-to-charge ratio as the ion optical device."
• The complaint reserves the right to assert additional claims ('Compl. ¶¶34, 46).

U.S. Patent No. 7,230,232 - "Means for Removing Unwanted Ions From an Ion Transport System and Mass Spectrometer"

• Patent Identification: U.S. Patent No. 7,230,232, "Means for Removing Unwanted Ions From an Ion Transport System and Mass Spectrometer," issued June 12, 2007.

The Invention Explained

• Problem Addressed: The patent addresses the problem of unwanted artefact ions and also the "gas load" from the plasma source, which consists of a directed flow of neutral gas that can enter downstream components and create new interferences ('232 Patent, col. 5:46-54). A separate problem is "unresolved baseline noise" caused by neutral particles and photons from the plasma traveling in a straight line to the detector ('232 Patent, col. 8:18-20).
• The Patented Solution: The invention describes a system with an "ion optical device" placed upstream of a collision cell specifically to "reduce gas loading from the ion source on the collision cell" ('232 Patent, Claim 1). This is achieved by having an evacuated chamber where the neutral gas can diverge and be pumped away before reaching the collision cell ('232 Patent, col. 7:11-19). The invention also describes deflecting the ion beam off its original axis before it reaches the mass analyzer, ensuring that neutral particles, which cannot be deflected, miss the detector and do not contribute to noise ('232 Patent, col. 8:10-20).
• Technical Importance: The use of an off-axis ion path is a foundational technique for improving the signal-to-noise ratio in mass spectrometry by physically blocking non-ionic species from reaching the detector.

Key Claims at a Glance

• The complaint asserts independent claim 1 and dependent claims 11, 12, and 13 (apparatus), as well as independent claim 23 and dependent claims 30 and 32 (method) ('Compl. ¶¶62-63, ¶¶85-86).
• Key elements of independent apparatus claim 1 include:
  • An ion source generating a beam with unwanted gas components and artifact ions.
  • A collision cell within an evacuation chamber, pressurized with a target gas.
  • An "ion optical device configured upstream of the collision cell to reduce gas loading from the ion source on the collision cell."
  • A mass-to-charge ratio analyzer.
• The complaint reserves the right to assert additional claims ('Compl. ¶¶62, 84).

U.S. Reissue Patent No. RE45,553 - "Mass Spectrometer and Mass Filters Therefor"

• Patent Identification: U.S. Reissue Patent No. RE45,553, "Mass Spectrometer and Mass Filters Therefor," issued June 9, 2015.
• Technology Synopsis: The patent addresses the degradation of high-resolution mass filters caused by the deposition of material from rejected ions. The solution is a multi-stage filter system where a first, "sacrificial" mass filter operates as a coarse pre-filter, removing the majority of unwanted ions from the beam. The cleaned, lower-intensity ion beam then enters a second, primary resolving filter, which can operate at high resolution for longer periods because it is shielded from the material deposition that would otherwise distort its electric fields and degrade performance ('553 Patent, Abstract; col. 2:19-28).
• Asserted Claims: The complaint asserts independent method claim 32 ('Compl. ¶¶108, 122).
• Accused Features: The complaint alleges the Agilent 8800 and 8900 products infringe by operating in a mode where the first quadrupole (Q1) acts as an adjustable bandpass filter (a sacrificial, coarse filter) to pre-filter ions before they are transmitted to the second quadrupole (Q2) for primary mass analysis ('Compl. ¶¶111-114).

III. The Accused Instrumentality

Product Identification

• The accused instrumentalities are the Agilent 8800 and 8900 ICP-QQQ Mass Spectrometer series, and the Agilent 7700, 7800, and 7900 ICP-MS Mass Spectrometer series ('Compl. ¶¶16-17, 21-23).

Functionality and Market Context

• The complaint alleges the 8800 and 8900 products are "Triple Quadrupole" (QQQ) systems, comprising an inductively-coupled plasma (ICP) ion source, a first quadrupole (Q1), an octopole collision/reaction cell, and a second quadrupole (Q2) ('Compl. ¶18). The complaint alleges these devices can operate in an "MS/MS mode," where Q1 and Q2 are both used as mass filters, a functionality central to the infringement allegations for the '386 and '553 patents ('Compl. ¶¶38, 113).
• The complaint alleges the 7700, 7800, and 7900 products feature a collision/reaction cell and an "off-axis" ion lens system (referred to as an "Omega Lens") that deflects the ion beam ('Compl. ¶¶70, 75, 78). This off-axis design is central to the infringement allegations for the '232 patent. The complaint provides a diagram from an Agilent poster showing the "Omega Lens" performing two deflections. This diagram depicts a first and second deflection of the ion beam's axis ('Compl. ¶71, p. 25). The complaint also presents images of a "deflector" component in the 7800 and 7900 models ('Compl. ¶77, p. 30).
• The complaint positions these products as significant in the market, noting the 8900 is the "2nd generation" of the 8800 and that the various 7X00 series models are marketed for different applications and performance needs ('Compl. ¶¶19, 21).

IV. Analysis of Infringement Allegations

RE45,386 Infringement Allegations

Claim Element (from Independent Claim 28)	Alleged Infringing Functionality	Complaint Citation	Patent Citation
an inductively coupled plasma ion source for generating ions from a sample, the generated ions including first atomic ions having a first mass-to-charge ratio and artefact ions having a mass-to-charge ratio that interferes with the first mass-to-charge ratio	The accused 8800 and 8900 products comprise an ICP ion source that generates both desired analyte ions and artefact ions that cause "spectral interference."	¶¶36-37	col. 5:26-31
an ion optical device disposed to receive at least a portion of an ion beam generated by the ion source, the ion optical device being configured to mass select at least a portion of the ion beam generated by the ion source at the first mass-to-charge ratio, thereby removing, from the ion beam, ions not having the first mass- to-charge ratio	The first quadrupole, "Q1," is placed after the ion source and, in MS/MS mode, "is driven as mass filter with unit mass resolving power" to select only ions with the same mass as the targeted analyte ion.	¶38	col. 8:56-60
a collision cell disposed to receive at least a portion of a mass selected ion beam from the ion optical device and configured to remove... artefact ions... the ion optical device being configured substantially to minimize the formation in the collision cell of interfering artefact ions having the first mass-to-charge ratio	The octopole resides in a gas-filled collision cell. By pre-selecting ions with Q1, the system prevents other ions from entering the cell and reacting to form new interfering products, thereby minimizing their formation.	¶39	col. 8:46-51
a mass analyzer disposed to receive at least a portion of the mass selected ion beam from the collision cell, the mass analyzer being configured to mass analyze the received ion beam at the same mass-to-charge ratio as the ion optical device, wherein the mass analyzer is configured to detect the first atomic ions when the same mass-to-charge ratio is the first mass-to-charge ratio	The second quadrupole, "Q2," is a mass analyzer located after the collision cell. The complaint alleges that in MS/MS mode, both Q1 and Q2 are set to the same mass-to-charge ratio (e.g., m/z=103 in an example) to detect the target atomic ions. A diagram shows this principle of operation.	¶¶39-40	col. 8:10-15

• Identified Points of Contention:
  • Scope Questions: A central question may be the interpretation of "configured substantially to minimize the formation." Defendant may argue that this requires more than the inherent result of pre-filtering ions with Q1 and that the reduction in new interfering ions is not "substantial." Plaintiff alleges that placing Q1 before the cell is the specific configuration that achieves this claimed function ('Compl. ¶39).
  • Technical Questions: The analysis will depend on evidence showing how the MS/MS mode of the 8800/8900 operates and whether the pre-selection by Q1 demonstrably prevents the formation of new interfering species within the collision cell to a "substantial" degree, as required by the claim.

7,230,232 Infringement Allegations

Claim Element (from Independent Claim 1)	Alleged Infringing Functionality	Complaint Citation	Patent Citation
A mass spectrometer, comprising: an ion source for generating an ion beam from a sample introduced into a plasma, the beam containing unwanted gas components and artifact ions	The accused 8800/8900 and 7X00 series products all use an ICP ion source that generates an ion beam, which the complaint alleges contains "contamination and spectral interference" (unwanted gas and artifact ions).	¶¶64-65, 72-73	col. 8:35-39
a collision cell within an evacuation chamber, the collision cell being disposed to receive at least a portion of the ion beam from the ion source and arranged to be pressurized with a target gas for removing unwanted artifact ions from the ion beam in the collision cell	All accused products are alleged to have a "collision/reaction cell" located within an evacuated chamber that is pressurized with gas to remove interferences.	¶¶66, 74	col. 8:40-45
an ion optical device configured upstream of the collision cell to reduce gas loading from the ion source on the collision cell	For the 8800/8900, "Q1" is identified as this device. For the 7X00 series, the complaint identifies an "off-axis ion lens" or "double deflector" as this device, which focuses ions while rejecting neutral species that contribute to gas load.	¶¶67, 75	col. 8:46-49
and a mass-to-charge ratio analyzer disposed within an analyzing chamber and arranged to receive at least a portion of the ion beam from the collision cell and to mass analyze the received ion beam to produce a mass spectrum of the received ion beam.	For the 8800/8900, "Q2" is the mass analyzer. For the 7X00 series, a "quadrupole mass analyzer" is located after the collision cell. The complaint alleges these components are in a separate analyzing chamber and produce a mass spectrum.	¶¶68, 76	col. 8:50-55

• Identified Points of Contention:
  • Scope Questions: The dispute may turn on the construction of "double deflector" (from dependent claim 13). Defendant might argue its "Omega Lens" is a single component that creates a continuous bend, not two discrete deflections as the term might imply. The interpretation of "to reduce gas loading" will also be critical—is this the primary designed-for purpose of the accused upstream optics, or an inherent, unclaimed side effect?
  • Technical Questions: Evidence will be needed to establish whether the accused "Omega Lens" in the 7X00 series and the Q1/lens combination in the 8800/8900 are, in fact, "configured to" reduce gas load from the source, as opposed to performing other primary functions like ion focusing or mass filtering.

V. Key Claim Terms for Construction

• Term ('386 Patent, Claim 28): "configured substantially to minimize the formation in the collision cell of interfering artefact ions"

  • Context and Importance: This functional language is the core of the invention claimed in the '386 patent. The infringement analysis will hinge on whether placing a mass filter (Q1) before the collision cell is itself the claimed "configuration," and what quantum of reduction qualifies as "substantially to minimize."
  • Intrinsic Evidence for a Broader Interpretation: The specification states an objective is to provide a means "whereby the formation, or re-formation, of unwanted artefact ions...may be minimised" ('386 Patent, col. 4:13-16). This broad objective could support an interpretation where any configuration that achieves this goal, such as pre-filtering, meets the limitation.
  • Intrinsic Evidence for a Narrower Interpretation: The term "substantially" implies a high degree of minimization. A defendant may argue that this requires more than just the baseline effect of pre-filtering and points toward a specific, optimized operational mode. The patent’s focus on preventing the formation of new ions inside the cell might be argued to require a showing that this specific problem is solved to a substantial degree, not just that overall interference is reduced.

• Term ('232 Patent, Claim 13): "double deflector"

  • Context and Importance: Infringement of asserted claim 13 depends entirely on this term. Practitioners may focus on this term because the complaint alleges a single component, the "Omega Lens," meets this limitation, which could be a point of dispute.
  • Intrinsic Evidence for a Broader Interpretation: The patent describes the deflector as "advantageously in the form of two small cylindrical electrostatic sectors, cross-coupled and in series" ('232 Patent, col. 8:15-18). This could be read to describe the functional character of a single device rather than mandating two physically separate structures. The complaint provides a diagram, allegedly from Agilent's own materials, showing a single lens structure causing two distinct deflections ('Compl. ¶71, p. 25).
  • Intrinsic Evidence for a Narrower Interpretation: The plain meaning of "double" could be argued to require two distinct and separate components. A defendant may argue that the "Omega Lens" is a unitary lens element that creates a single, continuous ion trajectory, not two discrete deflections.

VI. Other Allegations

• Indirect Infringement: The complaint alleges induced infringement for all three patents. The allegations are based on Defendant’s affirmative acts of publishing marketing materials, such as the "Agilent 8800 Posters," and other instructions that allegedly encourage and teach end-users to operate the accused products in a manner that directly infringes the method claims (e.g., using MS/MS mode) ('Compl. ¶¶46-47, 84-85, 122).
• Willful Infringement: Willfulness is alleged for all patents. The complaint alleges pre-suit knowledge based on a series of notification letters sent to Agilent beginning on November 9, 2012, regarding the patents that were later reissued as the '386 and '553 patents ('Compl. ¶¶56, 116, 130). Post-suit knowledge is alleged from the service of the original complaint in August 2017 ('Compl. ¶¶42, 81, 117). The complaint alleges that despite this knowledge, Agilent has taken no steps to design around the patents ('Compl. ¶¶43, 81, 118).

VII. Analyst’s Conclusion: Key Questions for the Case

• A core issue will be one of claim construction and function: can the functional limitation "configured substantially to minimize the formation" of new ions be met simply by the architecture of placing a mass filter before a collision cell, or does it require a higher, specific showing of optimized performance? Similarly, can a single optical component like the "Omega Lens" be construed as a "double deflector"?
• A key strategic question will revolve around the impact of the reissue proceedings: how will the fact that the USPTO reissued the '386 and '553 patents after considering prior art submitted by Agilent affect the strength of Agilent's invalidity defenses and, conversely, bolster Thermo Fisher's arguments for willful infringement based on extensive pre-suit knowledge?
• A central evidentiary question will be one of operational reality versus capability: does the infringement analysis turn on the default operation of the accused systems, or does the mere capability to operate in an infringing mode (e.g., the user-selectable "MS/MS mode"), combined with instructions on how to do so, suffice to prove direct and induced infringement?