DCT

4:23-cv-40027

MSTM LLC v. Waters Corp

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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 4:23-cv-40027, D. Mass., 04/29/2026
  • Venue Allegations: Venue is alleged to be proper in the District of Massachusetts because Defendant Waters Corporation has a principal place of business in the district, is registered to conduct business there, and engages in the allegedly infringing activities within the district.
  • Core Dispute: Plaintiffs allege that Defendant's mass spectrometry devices and related products infringe eight U.S. patents concerning various methods of sample ionization for mass spectrometry analysis.
  • Technical Context: The dispute centers on ionization technology, a fundamental component of mass spectrometry that enables the chemical analysis of substances at minute concentrations, a critical process in fields like drug development, proteomics, and forensic analysis.
  • Key Procedural History: The complaint details a long and complex history between the parties, beginning before the issuance of the patents-in-suit. Plaintiffs allege that Defendant Waters Corporation entered into a non-exclusive license for the '629 Patent in 2008 (the "ASAP Agreement"), which Plaintiffs claim Waters later breached, leading to its termination. The complaint also alleges that over many years, Waters engaged in licensing discussions and executed non-disclosure agreements (NDAs) to evaluate Plaintiffs' technologies, but ultimately declined to license them. A central allegation is that Waters used confidential information obtained under these NDAs to file its own patents, improperly naming its own employees as inventors and creating a basis for Plaintiffs' claims of willful infringement and unfair business practices.

Case Timeline

Date Event
2006-07-01 Plaintiff M&M is co-founded
2007-09-26 '629 Patent Priority Date
2008-06-01 Waters subsidiary Micromass obtains non-exclusive license to '629 Patent
2010-07-14 Waters executes an NDA with Wayne State
2010-09-02 '973, '096, and '894 Patents Priority Date
2011-07-12 '629 Patent Issues
2011-11-01 Waters executes NDA with USciences
2012-05-21 '458, '838, and '648 Patents Priority Date
2013-11-01 Plaintiff MSTM is founded
2013-11-20 Waters submits 2013 NSF Letter supporting Plaintiffs' technology
2014-06-13 '909 Patent Priority Date
2015-08-11 '458 Patent Issues
2017-01-24 '973 Patent Issues
2018-01-16 '909 Patent Issues
2018-11-13 '096 Patent Issues
2020-01-01 Waters introduces RADIAN ASAP System (approx. date)
2020-06-09 '838 Patent Issues
2020-10-06 '894 Patent Issues
2022-08-30 '648 Patent Issues
2023-03-08 Plaintiffs' initial complaint filed
2026-04-29 Second 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"

  • Patent Identification: U.S. Patent No. 7,977,629, "Atmospheric Pressure Ion Source Probe for a Mass Spectrometer," issued July 12, 2011 Compl. ¶28

The Invention Explained

  • Problem Addressed: The complaint describes the patented technology as an improvement for the "rapid direct analysis of volatile and semi-volatile solid and liquid samples using atmospheric pressure ionization" Compl. ¶42 Conventional mass spectrometry often requires complex sample preparation and introduction into a vacuum, which can be time-consuming.
  • The Patented Solution: The patent discloses an Atmospheric Solids Analysis Probe ("ASAP") that can be "readily fitted to an atmospheric pressure ionization (API) source" of a mass spectrometer Compl. ¶43 The probe facilitates the ionization of compounds from both liquid and solid sources by applying heat from a gas stream, allowing for direct analysis at atmospheric pressure Compl. ¶40 This simplifies the process by replacing other, more complex probes Compl. ¶43
  • Technical Importance: The ASAP technology provided a "low cost alternative" for direct sample analysis, streamlining workflows and making mass spectrometry more accessible for a broad range of samples, including food, pharmaceuticals, and bodily fluids (Compl. ¶¶42; ¶50).

Key Claims at a Glance

The complaint asserts infringement of "one or more claims of the '629 Patent" but does not identify any specific independent or dependent claims Compl. ¶207

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

  • Patent Identification: U.S. Patent No. 9,105,458, "System and Methods for Ionizing Compounds Using Matrix-Assistance for Mass Spectrometry and Ion Mobility Spectrometry," issued August 11, 2015 Compl. ¶29

The Invention Explained

  • Problem Addressed: Conventional ionization techniques like electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) have limitations U.S. Patent 10,679,838, background, col. 1:24-2:65 ESI is not well-suited for direct surface analysis, and MALDI requires expensive lasers, is limited to producing mostly singly charged ions, and can be harsh on fragile molecules U.S. Patent 10,679,838, background, col. 1:24-2:65
  • The Patented Solution: The patent family describes a method termed "matrix-assisted ionization vacuum" (MAIV) Compl. ¶70 This technique uses a specific small molecule compound as a "matrix" which, when mixed with a sample and placed in a vacuum, sublimes or evaporates and produces gas-phase ions of the analyte without requiring a laser, high voltage, or a heated transfer region U.S. Patent 10,679,838, abstract
  • Technical Importance: This approach combines benefits of different methods, producing multiply charged ions similar to ESI (useful for analyzing large molecules on common instruments) while operating from a solid sample in a vacuum, potentially simplifying the instrumentation and enabling new analytical applications '838 Patent, abstract

Key Claims at a Glance

The complaint asserts infringement of "one or more claims of the '458 Patent" but does not identify any specific independent or dependent claims Compl. ¶253

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

  • Patent Identification: U.S. Patent No. 10,679,838, "System and Methods for Ionizing Compounds Using Matrix-Assistance for Mass Spectrometry and Ion Mobility Spectrometry," issued June 9, 2020 Compl. ¶30
  • Technology Synopsis: This patent, a continuation of the '458 patent family, relates to "matrix-assisted ionization vacuum" (MAIV), a method for producing ions from samples mixed with a specific matrix that sublimes or evaporates when placed in a vacuum, generating analyte ions without a laser or high voltage Compl. ¶70 '838 Patent, abstract
  • Asserted Claims: The complaint alleges infringement of one or more unspecified claims Compl. ¶275
  • Accused Features: Various Waters mass spectrometer devices are accused of infringement Compl. ¶273

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

  • Patent Identification: U.S. Patent No. 11,430,648, "System and Methods for Ionizing Compounds Using Matrix-Assistance for Mass Spectrometry and Ion Mobility Spectrometry," issued August 30, 2022 Compl. ¶31
  • Technology Synopsis: This patent is also in the '458 patent family and relates to MAIV technology, where a sample is mixed with a matrix that produces ions upon exposure to vacuum Compl. ¶70 '648 Patent, abstract
  • Asserted Claims: The complaint alleges infringement of one or more unspecified claims Compl. ¶286
  • Accused Features: Various Waters mass spectrometer devices are accused of infringement Compl. ¶284

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

  • Patent Identification: U.S. Patent No. 9,870,909, "Compositions and Methods for Mass Spectrometry," issued January 16, 2018 Compl. ¶32
  • Technology Synopsis: This patent relates to specific "ionizing matrices" that facilitate the transfer of analyte compounds into gas-phase ions when the matrix-analyte mixture is exposed to vacuum conditions, without the need for high voltage or a laser Compl. ¶72 The invention is based on the discovery that certain matrix compounds can produce analyte ions when they sublime or evaporate in a vacuum Compl. ¶72
  • Asserted Claims: The complaint alleges infringement of one or more unspecified claims Compl. ¶264
  • Accused Features: Various Waters mass spectrometer devices are accused of infringement Compl. ¶262

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

  • Patent Identification: U.S. Patent No. 9,552,973, "System and Method for Ionization of Molecules for Mass Spectrometry and Ion Mobility Spectrometry," issued January 24, 2017 Compl. ¶33
  • Technology Synopsis: This patent relates to ionizing systems that include a channel with an inlet in a first, higher-pressure region and an outlet in a second, lower-pressure region Compl. ¶67 A heater is coupled to the channel, and the system is configured to introduce and ionize an analyte within this heated, pressure-differentiated channel Compl. ¶67
  • Asserted Claims: The complaint alleges infringement of one or more unspecified claims Compl. ¶220
  • Accused Features: Various Waters mass spectrometer devices, including those with DESI XS, ionKey, Acquity QDa II, and Radian ASAP systems, are accused of infringement Compl. ¶¶218-219

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

  • Patent Identification: U.S. Patent No. 10,128,096, "System and Method for Ionization of Molecules for Mass Spectrometry and Ion Mobility Spectrometry," issued November 13, 2018 Compl. ¶34
  • Technology Synopsis: As a continuation of the '973 patent, this patent also relates to ionization systems using a heated channel that spans a pressure differential to ionize an analyte (Compl. ¶67; Compl. ¶68, Compl. ¶abstract).
  • Asserted Claims: The complaint alleges infringement of one or more unspecified claims Compl. ¶231
  • Accused Features: Various Waters mass spectrometer devices are accused of infringement Compl. ¶¶229-230

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

  • Patent Identification: U.S. Patent No. 10,796,894, "System and Method for Ionization of Molecules for Mass Spectrometry and Ion Mobility Spectrometry," issued October 6, 2020 Compl. ¶35
  • Technology Synopsis: Also in the '973 patent family, this patent relates to methods and systems for ionizing molecules using a heated channel positioned between two different pressure regions (Compl. ¶67; Compl. ¶68, Compl. ¶abstract).
  • Asserted Claims: The complaint alleges infringement of one or more unspecified claims Compl. ¶242
  • Accused Features: Various Waters mass spectrometer devices are accused of infringement Compl. ¶¶240-241

III. The Accused Instrumentality

Product Identification

The complaint names a wide range of Waters Corporation's mass spectrometry products. The primary accused products for the '629 Patent are the RADIAN ASAP system and the Waters ASAP System (probe accessory) (Compl. ¶207; Compl. ¶208). For the remaining seven patents, the accused instrumentalities include, but are not limited to, the SELECT SERIES Cyclic IMS, SYNAPT XS, Vion IMS, Xevo TQ-MQ, Xevo TQ-S, Acquity QDa, REIMS, and UniSpray source, among others (Compl. ¶¶218; ¶229; ¶240; ¶251; ¶262; ¶273; ¶284).

Functionality and Market Context

The accused products are analytical instruments and accessories used for mass spectrometry (Compl. ¶3). The complaint alleges that the ASAP Probe accessory became the "single best-selling accessory in Waters' history" due to its utility in enabling rapid, direct analysis of samples (Compl. ¶¶46; ¶61). The RADIAN ASAP is described as a "standalone system" that incorporates this ASAP technology (Compl. ¶56). A diagram in the complaint shows the Synapt G2 instrument, which incorporates a secondary "glow discharge source" in addition to a standard ESI source, illustrating the multi-source capability of some accused platforms Compl. ¶444 The other accused systems are alleged to incorporate various patented ionization technologies, including matrix-assisted and channel-based methods, to generate ions for analysis (Compl. ¶¶67; ¶70).

IV. Analysis of Infringement Allegations

The complaint references infringement claim charts attached as exhibits but does not provide them in the body of the document (Compl. ¶¶207; ¶218; ¶251). Therefore, a detailed claim-chart-based analysis is not possible.

Narrative Infringement Theory ('629 Patent)

The complaint alleges that Waters' RADIAN ASAP and ASAP System products directly infringe the '629 Patent (Compl. ¶207; Compl. ¶208). The central allegation is that after years of selling a licensed version of the ASAP probe, Waters developed and launched its own "redesigned" RADIAN ASAP system in 2020 without notifying or paying royalties to the Plaintiffs (Compl. ¶¶56-57; ¶140). The complaint cites a Waters webinar in which a product manager allegedly admits that for the RADIAN instrument, "[Waters] redesigned the ASAP source" originally developed by the inventor Dr. McEwen (Compl. ¶59). This narrative suggests that the infringement dispute will center on whether Waters' "redesigned" source is merely a copy or colorable imitation of the patented technology.

Narrative Infringement Theory ('458 Patent)

The complaint alleges that a range of Waters' mass spectrometer devices infringe the '458 Patent by practicing the claimed methods of "matrix-assisted ionization vacuum" (Compl. ¶70; Compl. ¶71; Compl. ¶72; Compl. ¶73; Compl. ¶74; Compl. ¶75; Compl. ¶76; Compl. ¶77; Compl. ¶78; Compl. ¶79; Compl. ¶80; Compl. ¶81; Compl. ¶82; Compl. ¶83; Compl. ¶84; Compl. ¶85; Compl. ¶86; Compl. ¶87; Compl. ¶88; Compl. ¶89; Compl. ¶90; Compl. ¶91; Compl. ¶92; Compl. ¶93; Compl. ¶94; Compl. ¶95; Compl. ¶96; Compl. ¶97; Compl. ¶98; Compl. ¶99; Compl. ¶100; Compl. ¶101; Compl. ¶102; Compl. ¶103; Compl. ¶104; Compl. ¶105; Compl. ¶106; Compl. ¶107; Compl. ¶108; Compl. ¶109; Compl. ¶110; Compl. ¶111; Compl. ¶112; Compl. ¶113; Compl. ¶114; Compl. ¶115; Compl. ¶116; Compl. ¶117; Compl. ¶118; Compl. ¶119; Compl. ¶120; Compl. ¶121; Compl. ¶122; Compl. ¶123; Compl. ¶124; Compl. ¶125; Compl. ¶126; Compl. ¶127; Compl. ¶128; Compl. ¶129; Compl. ¶130; Compl. ¶131; Compl. ¶132; Compl. ¶133; Compl. ¶134; Compl. ¶135; Compl. ¶136; Compl. ¶137; Compl. ¶138; Compl. ¶139; Compl. ¶140; Compl. ¶141; Compl. ¶142; Compl. ¶143; Compl. ¶144; Compl. ¶145; Compl. ¶146; Compl. ¶147; Compl. ¶148; Compl. ¶149; Compl. ¶150; Compl. ¶151; Compl. ¶152; Compl. ¶153; Compl. ¶154; Compl. ¶155; Compl. ¶156; Compl. ¶157; Compl. ¶158; Compl. ¶159; Compl. ¶160; Compl. ¶161; Compl. ¶162; Compl. ¶163; Compl. ¶164; Compl. ¶165; Compl. ¶166; Compl. ¶167; Compl. ¶168; Compl. ¶169; Compl. ¶170; Compl. ¶171; Compl. ¶172; Compl. ¶173; Compl. ¶174; Compl. ¶175; Compl. ¶176; Compl. ¶177; Compl. ¶178; Compl. ¶179; Compl. ¶180; Compl. ¶181; Compl. ¶182; Compl. ¶183; Compl. ¶184; Compl. ¶185; Compl. ¶186; Compl. ¶187; Compl. ¶188; Compl. ¶189; Compl. ¶190; Compl. ¶191; Compl. ¶192; Compl. ¶193; Compl. ¶194; Compl. ¶195; Compl. ¶196; Compl. ¶197; Compl. ¶198; Compl. ¶199; Compl. ¶200; Compl. ¶201; Compl. ¶202; Compl. ¶203; Compl. ¶204; Compl. ¶205; Compl. ¶206; Compl. ¶207; Compl. ¶208; Compl. ¶209; Compl. ¶210; Compl. ¶211; Compl. ¶212; Compl. ¶213; Compl. ¶214; Compl. ¶215; Compl. ¶216; Compl. ¶217; Compl. ¶218; Compl. ¶219; Compl. ¶220; Compl. ¶221; Compl. ¶222; Compl. ¶223; Compl. ¶224; Compl. ¶225; Compl. ¶226; Compl. ¶227; Compl. ¶228; Compl. ¶229; Compl. ¶230; Compl. ¶231; Compl. ¶232; Compl. ¶233; Compl. ¶234; Compl. ¶235; Compl. ¶236; Compl. ¶237; Compl. ¶238; Compl. ¶239; Compl. ¶240; Compl. ¶241; Compl. ¶242; Compl. ¶243; Compl. ¶244; Compl. ¶245; Compl. ¶246; Compl. ¶247; Compl. ¶248; Compl. ¶249; Compl. ¶250; Compl. ¶251; Compl. ¶252). The infringement theory appears to be that the functionality of these accused devices, which are used to analyze various compounds, inherently performs the patented method of using a matrix that sublimes or evaporates under vacuum to generate ions (Compl. ¶254). The complaint cites a Waters-authored publication referring to "Matrix Assisted Ionization Vacuum (MAIV)" as a "New Ionization Method," which may be used to suggest Waters' awareness and adoption of the technology (Compl. ¶196).

V. Key Claim Terms for Construction

The complaint does not identify specific asserted claims, making a definitive analysis of key terms speculative. However, based on the technology descriptions, the following terms may be central to the dispute.

For the '629 Patent:

The complaint does not provide sufficient detail for analysis of key claim terms.

For the '458 Patent and related patents ('838, '648):

  • The Term: "ionizing matrix" (or a similar term defining the active compound).
  • Context and Importance: The core of the MAIV invention is the use of a specific type of chemical matrix that, unlike traditional MALDI matrices, can produce ions by subliming or evaporating in a vacuum without a laser '838 Patent, abstract Practitioners may focus on the definition of this term to determine whether the materials and processes used in Waters' accused devices fall within the scope of the patent's claims, or if they rely on a different, non-infringing physical phenomenon.
  • Intrinsic Evidence for Interpretation (from U.S. Patent 10,679,838, a continuation of the '458 Patent):
    • Evidence for a Broader Interpretation: The specification provides a functional definition: "The term 'matrix' or 'matrix compound' refers to any one or more compounds that facilitate the ionization of an analyte" '838 Patent, col. 5:48-50 This language could support an argument that any compound performing this function is covered.
    • Evidence for a Narrower Interpretation: The patent claims and describes specific chemical compounds that act as ionizing matrices, such as "3-nitrobenzonitrile" '838 Patent, claim 1 A defendant could argue that the claims are limited to the disclosed chemical classes or compounds that share their specific property of subliming/evaporating at or near room temperature in a vacuum '838 Patent, abstract

VI. Other Allegations

Indirect Infringement

Plaintiffs allege both induced and contributory infringement for all eight patents-in-suit. The allegations for inducement are based on Waters providing customers with instructions, manuals, videos, and technical support that allegedly encourage and facilitate direct infringement by end-users (e.g., Compl. ¶211; ¶222). The allegations for contributory infringement are based on Waters selling devices that are not staple articles of commerce and were specially made and adapted for use in an infringing manner (e.g., Compl. ¶212; ¶223).

Willful Infringement

Willfulness is a central theme, with extensive allegations of both pre- and post-suit knowledge for all asserted patents. Plaintiffs allege Waters had pre-suit knowledge through years of licensing negotiations, NDAs, internal evaluations, and public praise for the patented technologies (Compl. ¶¶11-12; ¶99; ¶177-178). The complaint further alleges that Waters' own patent prosecution files cite the Plaintiffs' patents as prior art, demonstrating actual knowledge (Compl. ¶¶185; ¶190). For the '629 Patent specifically, willfulness is also predicated on the alleged breach of the ASAP license agreement and continued sales after the agreement was allegedly terminated (Compl. ¶¶199-200; ¶213).

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

This case presents a complex interplay of contract law, patent infringement, and allegations of business torts. The resolution will likely depend on the court's determination of three central questions:

  1. A question of contract and license scope: For the '629 Patent, did Waters' development of the "redesigned" RADIAN ASAP constitute a breach of the 2008 ASAP Agreement? The answer will depend on whether the redesigned product is an unlicensed infringement or a permissible, non-covered product, which will also influence the willfulness analysis.

  2. A question of inventorship and trade secrets: Can Plaintiffs prove that Waters misappropriated confidential information, disclosed under NDA, to conceive of the inventions in its own patents? While these Waters patents are not asserted for infringement, this allegation underpins the claims of unfair competition and bad faith, and if proven, would substantially strengthen the overarching willfulness narrative across all infringement counts.

  3. A question of technical and functional scope: Do Waters' various accused mass spectrometry systems infringe the claims of the seven non-'629 patents? This will require a highly technical, fact-intensive inquiry into how the accused devices operate and whether their functions meet the specific limitations of the claims, particularly the definitions of "matrix-assisted ionization vacuum" (for the '458 patent family) and the heated, pressure-differentiated "channel" (for the '973 patent family).

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