DCT

4:23-cv-40027

MSTM LLC v. Waters Corp

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Key Events
Amended Complaint

I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 4:23-cv-40027, D. Mass., 05/15/2023
  • Venue Allegations: Venue is alleged to be proper in the District of Massachusetts because Defendant Waters Corporation maintains its principal place of business and corporate headquarters in Milford, Massachusetts, and engages in infringing activities within the district.
  • Core Dispute: Plaintiffs allege that Defendant’s mass spectrometry products infringe eight patents related to atmospheric pressure and vacuum-based ionization technologies for mass spectrometry.
  • Technical Context: The technology at issue involves methods for ionizing chemical samples, a foundational step in mass spectrometry, which is a critical analytical technique used in pharmaceutical development, chemical analysis, and life sciences research.
  • Key Procedural History: The complaint alleges a long history of business dealings, including a 2008 non-exclusive license agreement for the ’629 Patent between Plaintiff M&M and a subsidiary of Defendant, which Plaintiffs allege was breached and subsequently terminated. The complaint also details numerous non-disclosure agreements beginning in 2010 under which Plaintiffs allegedly disclosed confidential information and unpublished patent applications to Defendant for the purpose of evaluating a potential licensing or business partnership that never materialized.

Case Timeline

Date Event
2007-09-26 U.S. Patent 7,977,629 Priority Date
2008-06-01 Waters subsidiary Mircomass obtains non-exclusive license to the '629 Patent
2010-09-02 U.S. Patents 9,552,973, 10,128,096, and 10,796,894 Priority Date
2011-07-12 U.S. Patent 7,977,629 Issued
2012-05-21 U.S. Patents 9,105,458, 10,679,838, and 11,430,648 Priority Date
2014-06-13 U.S. Patent 9,870,909 Priority Date
2015-08-11 U.S. Patent 9,105,458 Issued
2017-01-24 U.S. Patent 9,552,973 Issued
2018-01-16 U.S. Patent 9,870,909 Issued
2018-11-13 U.S. Patent 10,128,096 Issued
2020-01-01 Waters introduces RADIAN ASAP System (approximate date)
2020-06-09 U.S. Patent 10,679,838 Issued
2020-10-06 U.S. Patent 10,796,894 Issued
2022-08-30 U.S. Patent 11,430,648 Issued
2023-03-08 Plaintiffs' initial complaint filed
2023-05-15 Plaintiffs' Amended Complaint Filed

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

U.S. Patent No. 7,977,629 - "Atmospheric Pressure Ion Source Probe for a Mass Spectrometer"

The Invention Explained

  • Problem Addressed: Prior art atmospheric pressure ionization (API) sources for mass spectrometers were primarily designed to analyze liquid samples, making the rapid analysis of solid or neat liquid samples without extensive preparation difficult (Compl. ¶39; ’629 Patent, col. 2:42-51).
  • The Patented Solution: The invention is a probe device that can be inserted into a commercial API source. A solid or liquid sample placed on the probe's tip is introduced into a heated gas stream, which vaporizes the sample. The resulting gas-phase analyte molecules are then ionized by a corona discharge for mass analysis (’629 Patent, Abstract; ’629 Patent, col. 3:1-12). This allows for direct analysis of compounds from both liquid and solid sources (Compl. ¶37).
  • Technical Importance: This technology provided a "low cost alternative" for rapid, direct analysis of volatile and semi-volatile samples, becoming what the complaint alleges was the "single best selling accessory in Waters history" (Compl. ¶¶39, 43).

Key Claims at a Glance

  • The complaint asserts infringement of one or more claims without specifying them (Compl. ¶205). Independent claim 1 is representative:
    • An enclosure having at least one wall and interior at substantially atmospheric pressure.
    • A solid or neat liquid probe means for individually and directly inserting a sample into the enclosure.
    • Flange means for mounting and aligning the probe means through a port in the enclosure wall.
    • Sample holding means on the probe for receiving the sample.
    • Adjusting means on the probe for positioning the sample holding means within an ionization region in the enclosure.
    • Means for ionizing the sample by forming a vaporized analyte in the ionization region.
    • A port in the enclosure for transferring ions into a mass spectrometer.

U.S. Patent No. 9,105,458 - "System and Methods for Ionizing Compounds Using Matrix-Assistance for Mass Spectrometry and Ion Mobility Spectrometry"

The Invention Explained

  • Problem Addressed: Conventional methods for ionizing nonvolatile compounds, such as matrix-assisted laser desorption/ionization (MALDI), required expensive and complex equipment like high-power lasers and high-voltage sources, and often produced primarily singly charged ions, which limited their utility on certain types of mass spectrometers (’458 Patent, col. 2:1-19).
  • The Patented Solution: The invention uses specific small-molecule matrix compounds that have the property of sublimating or evaporating when placed in a vacuum. When an analyte is mixed with such a matrix, this sublimation process carries the analyte into the gas phase and produces both singly and multiply charged ions without requiring a laser, high voltage, or heated ion transfer region (’458 Patent, Abstract; Compl. ¶¶67, 69).
  • Technical Importance: This "matrix assisted ionization vacuum" (MAIV) approach simplifies the ion source, reduces cost and pumping requirements, and allows for the analysis of a wider range of molecules, including large proteins, on various types of mass spectrometers (Compl. ¶¶67, 111).

Key Claims at a Glance

  • The complaint asserts infringement of one or more claims without specifying them (Compl. ¶245). Independent claim 1 is representative:
    • A method of ionizing an analyte for analysis by ion mobility or mass spectrometry.
    • Providing a sample comprising an analyte and a matrix.
    • Producing gas phase positive or negative ions of the analyte without irradiating the sample with a laser, without exposing it to an electrical potential, and without exposing it to high velocity particles.
    • The step of producing ions does not include passing the sample through a heated ion transfer region or a heated ion skimmer.

U.S. Patent No. 10,679,838 - "System and Methods for Ionizing Compounds Using Matrix-Assistance for Mass Spectrometry and Ion Mobility Spectrometry"

  • Technology Synopsis: This patent is a continuation of the family that includes the ’458 Patent. It relates to systems and methods for "matrix-assisted ionization vacuum," where specific matrix compounds facilitate the transfer of analyte molecules into gas-phase ions when exposed to sub-atmospheric pressure, without requiring a laser or high voltage (Compl. ¶¶67-69; ’838 Patent, Abstract).
  • Asserted Claims: At least one claim is asserted (Compl. ¶265).
  • Accused Features: The accused features are embodied in "Waters’ MS Devices," which include but are not limited to the SYNAPT XS, SYNAPT G2, and SELECT SERIES Cyclic IMS, among others (Compl. ¶264).

U.S. Patent No. 11,430,648 - "System and Methods for Ionizing Compounds Using Matrix-Assistance for Mass Spectrometry and Ion Mobility Spectrometry"

  • Technology Synopsis: This patent is also a continuation of the family that includes the ’458 Patent. It discloses systems and methods for "matrix-assisted ionization vacuum" technology (Compl. ¶¶67-69; ’648 Patent, Abstract).
  • Asserted Claims: At least one claim is asserted (Compl. ¶275).
  • Accused Features: The accused features are embodied in various "Waters’ MS Devices," including but not limited to the SYNAPT XS, SYNAPT G2, and SELECT SERIES Cyclic IMS (Compl. ¶274).

U.S. Patent No. 9,870,909 - "Compositions and Methods for Mass Spectrometry"

  • Technology Synopsis: This patent is directed to specific compositions of ionizing matrix compounds that facilitate the transfer of analyte compounds into gas-phase ions when the mixture is exposed to vacuum conditions, without requiring a high voltage or laser. This is a key component of the "matrix-assisted ionization vacuum" technology (Compl. ¶69; ’909 Patent, Abstract).
  • Asserted Claims: At least one claim is asserted (Compl. ¶255).
  • Accused Features: The accused features are embodied in "Waters’ MS Devices," which include but are not limited to the SYNAPT XS, SYNAPT G2, and SELECT SERIES Cyclic IMS (Compl. ¶254).

U.S. Patent No. 9,552,973 - "System and Method for Ionization of Molecules for Mass Spectrometry and Ion Mobility Spectrometry"

  • Technology Synopsis: This patent relates to ionizing systems that use a pressure differential across a heated channel to ionize an analyte. An inlet is disposed in a first, higher-pressure region (e.g., atmospheric pressure) and an outlet is in a second, lower-pressure region, with a heater coupled to the channel (Compl. ¶64; ’973 Patent, Abstract).
  • Asserted Claims: At least one claim is asserted (Compl. ¶215).
  • Accused Features: The accused features are embodied in "Waters’ MS Devices," which include but are not limited to the SELECT SERIES Cyclic IMS, SYNAPT XS, and Vion IMS (Compl. ¶214).

U.S. Patent No. 10,128,096 - "System and Method for Ionization of Molecules for Mass Spectrometry and Ion Mobility Spectrometry"

  • Technology Synopsis: This patent is a continuation of the family including the ’973 Patent and is directed to the same "inlet ionization" technology. It describes an ionizing system comprising a heated channel with an inlet and outlet in different pressure regions, which generates charged particles from a sample introduced into the channel (Compl. ¶64; ’096 Patent, Abstract).
  • Asserted Claims: At least one claim is asserted (Compl. ¶225).
  • Accused Features: The accused features are embodied in "Waters’ MS Devices," such as the SELECT SERIES Cyclic IMS and SYNAPT XS (Compl. ¶224).

U.S. Patent No. 10,796,894 - "System and Method for Ionization of Molecules for Mass Spectrometry and Ion Mobility Spectrometry"

  • Technology Synopsis: This patent is also a continuation of the family including the ’973 Patent and is directed to the same "inlet ionization" technology using a heated channel across a pressure differential (Compl. ¶64; ’894 Patent, Abstract).
  • Asserted Claims: At least one claim is asserted (Compl. ¶235).
  • Accused Features: The accused features are embodied in "Waters’ MS Devices," such as the SELECT SERIES Cyclic IMS and SYNAPT XS (Compl. ¶234).

III. The Accused Instrumentality

  • Product Identification: The complaint accuses two categories of products:

    1. The "ASAP Probe" and "RADIAN ASAP" system, which are accused of infringing the ’629 Patent (Compl. ¶¶53, 206).
    2. A broad range of "Waters’ MS Devices" are accused of infringing the other seven patents. These include, but are not limited to, the SELECT SERIES Cyclic IMS, SYNAPT XS, Vion IMS, Xevo TQ-MQ, Xevo TQ-S, Acquity QDa, REIMS, REIMS with iKnife, and UniSpray source (Compl. ¶¶214, 224, 234, 244, 254, 264, 274).

  • Functionality and Market Context:

    • The RADIAN ASAP is described as a "novel direct mass detector" for fast analysis of solids and liquids, which the complaint alleges "solely uses the ASAP technology embodied in the '629 Patent" (Compl. ¶53). The complaint quotes Waters as stating that for the RADIAN instrument, it "redesigned the ASAP source to incorporate horizontal sample loader" (Compl. ¶56).
    • The other accused "Waters’ MS Devices" are advanced mass spectrometers. The infringement allegations center on their use of ionization technologies which Plaintiffs allege were patented by and disclosed to Waters under NDAs (Compl. ¶¶71, 125). For example, the complaint alleges Waters directs customers to use a "Matrix Assisted Ionization Vacuum (MAIV)" method, developed by the inventors, with these devices (Compl. ¶193).
    • The complaint alleges the original ASAP Probe was the "single best-selling accessory in Waters' history" (Compl. ¶128).

IV. Analysis of Infringement Allegations

No probative visual evidence provided in complaint.

The complaint references claim chart exhibits (Exhibits M, N, O, P, Q, R, S, T) for each asserted patent but these exhibits were not provided in the submitted documents (Compl. ¶¶204, 214, 224, 234, 244, 254, 264, 274). Therefore, a claim chart summary cannot be constructed. The narrative infringement theories are summarized below.

  • ’629 Patent Infringement Allegations

    • The complaint alleges that Waters' RADIAN ASAP device practices one or more claims of the ’629 Patent (Compl. ¶137). The theory is based on Waters' own alleged admissions that the technology was "developed by Chuck McEwen and his group" and that Waters "redesigned the ASAP source" for its RADIAN instrument (Compl. ¶¶56, 209). This suggests an infringement theory based on direct adoption and modification of the patented technology.
    • Identified Points of Contention:
      • Scope Questions: A central question may be whether the "redesigned" features of the RADIAN ASAP, such as the "horizontal sample loader" (Compl. ¶56), take the device outside the literal scope or doctrine of equivalents of the ’629 Patent’s claims.
      • Technical Questions: What specific structural and functional elements of the RADIAN ASAP correspond to the claimed elements of the probe means, sample holding means, and adjusting means as recited in the asserted claims?

  • ’458 Patent Infringement Allegations

    • The complaint alleges that various Waters’ MS Devices practice one or more claims of the ’458 Patent (Compl. ¶246). The infringement theory is grounded in a long history of alleged technical disclosures by the inventors to Waters under NDAs, followed by Waters' incorporation of the disclosed "matrix-assisted ionization vacuum" technology into its products (Compl. ¶¶71, 125). The complaint points to Waters' promotion of publications authored by the inventors describing the "Matrix Assisted Ionization Vacuum (MAIV)" method for use with its devices as evidence of infringement (Compl. ¶193).
    • Identified Points of Contention:
      • Scope Questions: Does the term "ionizing matrix" as used in the patent, which produces ions upon exposure to vacuum without a laser or high voltage, read on the specific chemical matrices and protocols recommended or used by Waters' customers with the accused devices?
      • Technical Questions: What evidence demonstrates that the accused Waters' MS Devices, when operated as instructed, generate ions through the specific mechanism claimed in the patent (i.e., spontaneous ionization from a matrix in a sub-atmospheric pressure region without a heated transfer tube)?

V. Key Claim Terms for Construction

  • For the ’629 Patent

    • The Term: "probe means for individually and directly inserting a solid or neat liquid sample into said enclosure" (from claim 1).
    • Context and Importance: The definition of this "means-plus-function" term will be critical for determining whether the RADIAN ASAP's sample introduction mechanism infringes. Practitioners may focus on this term because the complaint alleges Waters "redesigned the ASAP source to incorporate horizontal sample loader" (Compl. ¶56), suggesting a potential structural difference from the embodiments disclosed in the patent.
    • Intrinsic Evidence for Interpretation:
      • Evidence for a Broader Interpretation: The specification describes the function broadly as a way to place a sample into a heated gas stream inside the source, which may support construing the term to cover various mechanical arrangements that achieve this result (’629 Patent, col. 3:1-12).
      • Evidence for a Narrower Interpretation: The figures and detailed description show specific embodiments of a manually inserted probe with a sample on its tip, which may support a narrower construction limited to structures corresponding to those disclosed embodiments (’629 Patent, Fig. 1-3).

  • For the ’458 Patent

    • The Term: "producing gas phase positive or negative ions of the analyte without irradiating the sample with a laser, without exposing the sample to an electrical potential, and without exposing the sample to high velocity particles" (from claim 1).
    • Context and Importance: This negative limitation defines the core of the MAIV invention: spontaneous ionization in a vacuum. The infringement analysis will depend on whether the accused Waters' MS Devices, when used as directed by Waters, generate ions through this specific passive mechanism or through other active means.
    • Intrinsic Evidence for Interpretation:
      • Evidence for a Broader Interpretation: The specification describes the invention broadly as a process where placing a sample with a suitable matrix into a sub-atmospheric region is sufficient to initiate ionization, which may support a construction covering any method that relies on this fundamental principle (’458 Patent, col. 5:57-67).
      • Evidence for a Narrower Interpretation: The specification discusses specific attributes of the matrices, such as their ability to sublime or evaporate at or near room temperature in a vacuum, which could be argued to narrow the scope of the process to matrices exhibiting these specific properties (’458 Patent, Abstract; col. 6:1-5).

VI. Other Allegations

  • Indirect Infringement: The complaint alleges inducement of infringement across all asserted patents, stating that Waters provides "instructions, videos, demonstrations, operating manuals, educational materials, website materials, and technical support" that encourage and instruct customers to use the accused products in an infringing manner (Compl. ¶¶207, 217). Contributory infringement is also alleged, on the basis that the accused devices embody a material part of the inventions, are specifically adapted for infringing use, and are not staple articles of commerce (Compl. ¶¶208, 218).
  • Willful Infringement: Willfulness is alleged for all asserted patents. The complaint provides a detailed narrative of Waters' alleged pre-suit knowledge, beginning as early as 2011. The allegations are based on: (i) a prior license to the ’629 Patent; (ii) numerous NDAs and extensive licensing discussions where patent applications and technical data were allegedly disclosed (Compl. ¶¶174-175); (iii) Waters' own patent applications citing the patents-in-suit as prior art (Compl. ¶¶182, 187); and (iv) Waters' alleged promotion of the inventors' own scientific publications describing the patented technology (Compl. ¶193).

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

  • A core issue will be one of contract and conduct: what was the scope of the 2008 license for the ’629 Patent, was it breached, and to what extent did information disclosed under subsequent NDAs for the other patents inform the development of the accused Waters' MS Devices? The extensive history of interactions alleged in the complaint will be central to the claims of willful infringement.
  • A key technical question will be one of operative mechanism: do the accused Waters' MS Devices, when used with certain chemical matrices as directed by Waters, actually generate ions through the novel, passive "vacuum ionization" and "inlet ionization" methods described and claimed in the patents, or do they operate via conventional, non-infringing principles?