SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 ---------------------------------------------------- FORM 10-K (mark one) [ X ] Annual Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 for the fiscal year ended January 2, 1999 [ ] Transition Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Commission file number 1-14262 THERMOQUEST CORPORATION (Exact name of Registrant as specified in its charter) Delaware 77-0407461 (State or other jurisdiction (I.R.S. Employer Identification No.) of incorporation or organization) 2215 Grand Avenue Parkway Austin, Texas 78728-3812 (Address of principal executive offices) (Zip Code) Registrant's telephone number, including area code: (781) 622-1000 Securities registered pursuant to Section 12(b) of the Act: Title of each class Name of each exchange on which registered Common Stock, $.01 par value American Stock Exchange Securities registered pursuant to Section 12(g) of the Act: None Indicate by check mark whether the Registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the Registrant was required to file such reports), and (2) has been subject to the filing requirements for at least the past 90 days. Yes [ X ] No [ ] Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of the Registrant's knowledge, in definitive proxy or information statements incorporated by reference into Part III of this Form 10-K or any amendment to this Form 10-K. [ ] The aggregate market value of the voting stock held by nonaffiliates of the Registrant as of January 29, 1999, was approximately $59,136,000. As of January 29, 1999, the Registrant had 50,970,580 shares of Common Stock outstanding. DOCUMENTS INCORPORATED BY REFERENCE Portions of the Registrant's Annual Report to Shareholders for the year ended January 2, 1999, are incorporated by reference into Parts I and II. Portions of the Registrant's definitive Proxy Statement for the Annual Meeting of Shareholders to be held on May 27, 1999, are incorporated by reference into Part III. PART I Item 1. Business (a) General Development of Business The businesses of ThermoQuest Corporation (the Company or the Registrant) are reported in two segments: Analytical Instruments and Scientific Equipment. The Analytical Instruments segment develops, manufactures, sells, and services mass spectrometers, liquid chromatographs, and gas chromatographs used in the quantitative and qualitative analysis of chemical compounds at ultratrace levels of detection. The Analytical Instruments segment also supplies consumables for the chromatography industry. The Company's Scientific Equipment segment develops, manufactures, sells, and services scientific equipment for the preparation and preservation of chemical samples. The Company's products are used primarily by pharmaceutical companies for drug research, testing, and quality control; by biotechnology researchers to study proteins and other biological samples to gain knowledge about diseases and possible treatments; by environmental laboratories for testing water, air, and soil samples for compliance with environmental regulations; by chemical companies for research and quality control; by manufacturers for testing in certain industrial applications, such as the manufacture of silicon chips, and for quality control; by food and beverage companies for quality control and to test for product contamination; and in forensic applications. The Company was incorporated in June 1995 as a wholly owned subsidiary of Thermo Instrument Systems Inc. Thermo Instrument is a publicly traded, majority-owned subsidiary of Thermo Electron Corporation. Where the context requires, references herein to the Company refer to ThermoQuest Corporation and its subsidiaries and to its predecessor businesses as conducted by Thermo Instrument, the Company's parent, including acquired businesses from their dates of acquisition. The Company is a leading manufacturer of mass spectrometers, liquid chromatographs, and gas chromatographs. Many of the major developments in modern mass spectrometry were pioneered by the Company. The ion-trap mass spectrometer, which utilizes the latest mass spectrometer technology, was first commercialized by the Company. In 1995, the Company introduced two instruments that integrate a highly sensitive yet affordable ion-trap mass spectrometer with a liquid chromatograph or a gas chromatograph to form the industry's most powerful benchtop liquid chromatograph/mass spectrometer (LC/MS) and gas chromatograph/mass spectrometer (GC/MS) instruments. An element of the Company's strategy is to combine its internal growth with the acquisition of complementary products and technologies. Effective March 12, 1997, the Company acquired three business units within the Laboratory Products Group of Thermo Instrument's Life Sciences International PLC subsidiary, as well as Life Sciences' Hypersil operation, for approximately $156.9 million. The Laboratory Products businesses develop, manufacture, sell, and service scientific equipment for the preparation and preservation of chemical samples. Hypersil develops, manufactures, and sells liquid chromatography media and columns used in high-performance liquid chromatography. In March and April 1996, the Company sold 3,450,000 shares of its common stock in an initial public offering at $15.00 per share for net proceeds of $47.8 million. In March 1997, the Company sold 1,768,500 shares of its common stock for net proceeds of $24.8 million. As of January 2, 1999, Thermo Instrument owned 45,521,405 shares of the Company's common stock, representing 89% of such stock outstanding. During 1998*, Thermo Instrument purchased 525,200 shares of the Company's common stock on the open market for $3,824,000. Thermo Instrument develops, manufactures, markets, and services instruments and software used for the identification and quantification of complex molecular compounds and elements in gases, liquids, and solids. Uses include pharmaceutical research and clinical diagnostics, monitoring and measuring environmental pollutants, industrial inspection, and test and control for quality assurance and productivity improvement. In addition, Thermo Instrument develops, manufactures, markets, and services equipment for the measurement, preparation, storage, and automation of sample materials and photonics and vacuum components for original equipment manufacturers (OEMs). Thermo Instrument is an 85%-owned subsidiary of Thermo Electron. As of January 2, 1999, Thermo Electron owned 159,880 shares of the Company's common stock, - -------------------- * References to 1998, 1997, and 1996 herein are for the fiscal years ended January 2, 1999, January 3, 1998, and December 28, 1996, respectively. 2 representing 0.31% of such stock outstanding. During 1998, Thermo Electron purchased 101,600 shares of the Company's common stock on the open market for $981,000. Thermo Electron is a world leader in monitoring, analytical, and biomedical instrumentation; biomedical products including heart-assist devices, respiratory-care equipment, and mammography systems; and paper recycling and papermaking equipment. Thermo Electron also develops alternative-energy systems and clean fuels, provides a range of services, including industrial outsourcing and environmental-liability management, and conducts research and development in advanced imaging, laser, and electronic information-management technologies. Forward-looking Statements Forward-looking statements, within the meaning of Section 21E of the Securities Exchange Act of 1934, are made throughout this Annual Report on Form 10-K. For this purpose, any statements contained herein that are not statements of historical fact may be deemed to be forward-looking statements. Without limiting the foregoing, the words "believes," "anticipates," "plans," "expects," "seeks," "estimates," and similar expressions are intended to identify forward-looking statements. There are a number of important factors that could cause the results of the Company to differ materially from those indicated by such forward-looking statements, including those detailed under the heading "Forward-looking Statements" in the Registrant's 1998 Annual Report to Shareholders, which statements are incorporated herein by reference. (b) Financial Information About Segments Financial information concerning the Company's segments is summarized in Note 11 to Consolidated Financial Statements in the Registrant's 1998 Annual Report to Shareholders, which information is incorporated herein by reference. (c) Description of Business The Company develops, manufactures, sells, and services mass spectrometers, liquid chromatographs, and gas chromatographs used in the quantitative and qualitative analysis of chemical compounds at ultratrace levels of detection, as well as supplies for the chromatography industry. The Company also develops, manufactures, sells, and services scientific equipment for the preparation and preservation of chemical samples. (i) Principal Products and Services MARKETS The markets for the Company's products are highly specialized as a result of the differing needs of the industries in which they are used. The Company actively seeks to cross-sell its products among the various industries it serves, particularly by adding its liquid chromatograph or gas chromatograph input devices to its mass spectrometer products, and by introducing customers to the sample preparation and preservation equipment and chromatography consumables produced by the businesses acquired by the Company in 1997. The major markets in which the Company sells its products are: Pharmaceutical. In the pharmaceutical industry, the Company's products are used in the identification of newly synthesized or discovered drug candidates, to measure drugs and metabolites in clinical studies, and for quality assurance of drugs in production. Biotechnology. Researchers are using the Company's products to study genomes, proteins, and peptides in animals, plants, and humans to determine the factors influencing disease, as well as good health, and to develop possible treatments or even cures. 3 Environmental. A second major market for the Company's products is environmental analysis. This market is driven to a great degree by federal, state, local, and foreign environmental regulations, which provide specific methods with respect to the testing of air, water, and soil for contaminants. Industrial/Chemical. Industrial and chemical customers typically utilize the Company's products for quality control and to test for contaminants in substances used in a particular manufacturing application. Food and Beverage. Customers in the food and beverage industry primarily use the Company's products for quality control. In addition to assuring the correct balance of ingredients, customers in these industries must respond both to environmental and health regulations and to societal concerns regarding product contamination. Forensic Sciences. The Company's products are used in a variety of forensic applications, including testing for illicit drug use by employees or athletes, testing body fluids to determine causes of death, testing to determine the identity of substances suspected to be illegal, and testing for the presence of substances of evidentiary significance for use in criminal investigations. TECHNOLOGY Analytical Instruments Mass Spectrometers. A mass spectrometer is an instrument in which the chemical compound to be analyzed is broken down into electrically charged fragments (ions), and then sorted according to their mass-to-charge ratios. All mass spectrometers consist of a device to introduce samples, an ionization source, a mass analyzer that separates ions according to mass ratios, a detector that converts the ions into an electrical signal, a signal processor that amplifies the electrical signal, and a computer that organizes and displays information in a convenient and useful manner. The resulting data creates a "fingerprint" that is then compared to a database for identification. Mass spectrometers are the most powerful tools for the identification and quantification of chemical substances. A gas or liquid chromatograph is used to separate complex mixtures of chemicals into discrete components, which can then be analyzed based on the chromatograph results alone or can be introduced into a mass spectrometer to give additional information and to specifically identify unknown components. The Company has pioneered many of the significant developments in mass spectrometry and holds numerous U.S. and international patents relating to mass spectrometry, with additional patents pending. The Company has a distinguished record of being the first to commercialize new technologies coming from its own laboratories as well as from an extensive worldwide network of university collaborators. Examples include the first computerized GC/MS quadrupole system, the first commercial chemical ionization ion source, the first commercial triple quadrupole MS/MS system, the first commercial ion-trap system, and the first commercial ion-trap MS/MS system. In January 1996, the Company acquired Extrel FTMS, Inc., a leading manufacturer of Fourier transform mass spectrometry (FT/MS) instruments. Extrel introduced the first commercial FT/MS product in 1981 and today offers a unique multisource mass spectrometer with a range of ionization techniques. This research-grade analytical instrument has the advantage of both high resolution and high mass range and is particularly useful in pharmaceutical and polymer research applications where large molecules in complex solutions need to be precisely identified. Effective January 1996, the Company acquired the Automass division of Analytical Technology, Inc., a manufacturer of benchtop mass spectrometers, from Thermo Instrument. Manufactured near Paris, France, these mass spectrometers incorporate a quadrupole design that provides enhanced sensitivity and can accommodate gas chromatographs as well as liquid chromatographs. These products complement the Company's existing GCQ(R) and LCQ(R) line of benchtop ion-trap mass spectrometers. 4 Effective March 1996, the Company acquired MassLab Instruments, a manufacturer of mass spectrometry instruments, from Thermo Instrument. Located near Manchester, U.K., MassLab manufactures a line of mass spectrometers for both gas chromatography and liquid chromatography applications. MassLab was originally part of the Scientific Instruments Division of Fisons plc, a substantial portion of which was acquired by Thermo Instrument in March 1996. The Company currently manufactures three types of mass spectrometers: Magnetic Sector Mass Spectrometers. Magnetic sector mass spectrometers are generally used in high-resolution applications where an accurate analysis of molecular weight is required to determine the elemental composition of unknown samples. Magnetic sector instruments are typically purchased by universities and pharmaceutical and chemical companies for use in research applications. Quadrupole Mass Spectrometers. Single quadrupole mass spectrometers are typically utilized in environmental and forensic laboratories, which require dependable, routine analyses that meet applicable regulatory requirements, such as those promulgated by the U.S. Environmental Protection Agency. Although lacking the resolution of some types of magnetic sector mass spectrometers, these instruments provide reliable performance at a relatively low price. Single quadrupoles are frequently combined to form MS/MS spectrometers for use in more complex analyses such as molecular structure analysis. Together with the Company's triple stage quadrupoles, the most powerful type of quadrupole mass spectrometer, single quadrupoles comprise a complete family of quadrupole mass spectrometers. Ion-trap Mass Spectrometers. The Company developed the first commercial ion-trap mass spectrometer. The ability to trap and integrate the intensities of ions has made the ion trap the most sensitive method of mass analysis for certain applications. Ion traps are smaller, mechanically simpler, and therefore easier to maintain than other types of mass spectrometers. While other types of mass spectrometers separate and analyze a continuous stream of ions, ion-trap mass spectrometers trap ions in a confined space using an electric field, which can be adjusted to eject ions as a function of their mass-to-charge ratio. An advantage of ion-trap mass spectrometers is that, through software, MS/MS analysis can be performed in a single ion-trap mass spectrometer, theoretically to an infinite number of stages (MS(n)). The Company has recently introduced ion traps that incorporate an external ion source, such as those found in quadrupole and magnetic sector mass spectrometers, which use sophisticated ionization techniques to increase the specificity and detection limits of the instrument. Due to their relative mechanical simplicity and small size, ion traps are well suited for coupling with chromatographs to form benchtop LC/MS and GC/MS instruments. Benchtop LC/MS(n) instruments were not commercially available until the Company introduced the first such instrument in June 1995. Through significant advancements in integration techniques and information technology, the Company has developed the benchtop GCQ (GC/MS(n)) and LCQ (LC/MS(n)) instruments, which combine ion-trap mass spectrometers with chromatographs. These instruments allow users to combine GC and LC with MS(n) in a benchtop format, and offer high performance at a competitive price for appropriate applications. Liquid Chromatographs. High performance liquid chromatography (HPLC) is an analytical technique used to separate, identify, and quantify complex mixtures of primarily organic chemicals. In HPLC, the sample is introduced into a solvent stream that is being pumped at a high pressure through a liquid chromatography column. The column, both through physical and chemical properties, separates the complex mixtures into discrete bands, allowing identification. The separated sample is then passed through a detector that measures the sample by various technologies, including ultraviolet and visible light absorption, changes in refractive index, fluorescence, and conductivity. The data produced by the detector is converted to an electronic form and transmitted for display and manipulation on a personal computer. For complex mixtures, the HPLC may be coupled with a mass spectrometer to give additional information and specifically identify unknown components. 5 Gas Chromatographs. Like HPLC, gas chromatography is an analytical technique used to separate, identify, and quantify complex mixtures of primarily organic chemicals. Although gas chromatographs are generally easier to use and have higher resolution than liquid chromatographs, only a relatively small percentage of compounds can be converted to gaseous form for analysis in a gas chromatograph. In gas chromatographs, samples are introduced typically by syringe injection and are converted into the gas phase by heating. The sample passes through an analytical column, and the various components of the sample mixture are separated into discrete bands that are suitable for analysis by detectors. Detectors can be assembled in various configurations to facilitate analysis of different chemical and physical properties in a sample mixture. The data produced by the detector is converted to electronic form and transmitted for display and manipulation on a personal computer. For complex mixtures, where compounds cannot be adequately separated and identified by gas chromatography, the gas chromatograph can be coupled with a mass spectrometer to give additional information and specifically identify unknown components. Effective March 1996, the Company acquired CE Instruments, a manufacturer of gas chromatography instruments, from Thermo Instrument. Located near Milan, Italy, CE Instruments has a long history of technological innovation in gas chromatography. In 1956, CE Instruments produced the first commercial gas chromatograph manufactured in Europe, and, in 1976, introduced the first commercially available high-resolution gas chromatograph. In addition to gas chromatography instruments, CE Instruments produces a line of organic elemental analysis, mercury porosimetry, and gas absorption instruments for use in research and quality-control laboratories in a number of application fields. CE Instruments was originally part of the Scientific Instruments Division of Fisons, a substantial portion of which was acquired by Thermo Instrument in March 1996. High-performance Liquid Chromatography Columns. These tubes are packed with materials that have the ability to separate complex mixtures into their individual ingredients. Scientific Equipment Sample Preparation Equipment Biological Safety Cabinet. This cabinet protects the researcher, the sample being examined, and the laboratory environment by providing a partially enclosed work space that uses a combination of fans to circulate air and filters to trap harmful biological substances. Cell Culture Incubator. This device controls temperature, relative humidity, and carbon dioxide and oxygen levels to provide the perfect in-vitro environment for cell growth. Cell culture incubators are used in research and clinical laboratories throughout the world for growing mammalian cells, bacteria, and viruses. Centrifugal Vacuum Concentrator. This equipment uses a rotational spinning concentrator, refrigerated vapor trap, and vacuum source to dry multiple samples for analysis, without losing portions of them, or cross-contaminating them. Centrifuge. This equipment is used to prepare laboratory samples for analysis by spinning them around a central axis to separate materials of different specific gravities. Electrophoresis System. This system prepares a biological sample for analysis by using electricity to separate DNA/RNA and protein molecules based upon electrophoretic mobility. Orbital Shaker. This equipment, used in research and fermentation laboratories, provides a controlled orbital motion for biological cultures in glass flasks. The orbital agitation of the culture provides increased oxygen for optimal cell growth. Combination incubators/orbital shakers provide precise conditions of temperature and orbital agitation. 6 Sample Preservation Equipment Ultra-low Temperature Freezer. This specially designed cascade refrigeration system is designed to store all types of biological material, providing storage temperatures down to -86 degrees Celsius. Cryopreservation System. This vacuum-insulated equipment controls liquid nitrogen to produce extremely low temperatures, as low as -196 degrees Celsius, in order to store biological material, such as bone marrow, cornea, heart valves, spermatozoa, bacteria, and viruses, for very long periods of time. SALES AND MARKETING The Company markets its products in larger international markets through its own worldwide sales force of direct salespeople, and in smaller markets through a network of dealers and distributors. In addition, the Company sells certain of its liquid and gas chromatographs as well as scientific equipment pursuant to OEM arrangements under which third parties purchase and resell the Company's products. The Company's sales force is supported throughout the world by a customer support group which provides training, instrument servicing, and parts replacements. (ii) and (xi) New Products; Research and Development The Company maintains active programs for the development of new technologies and the enhancement of existing products. Research and development expenses for the Company were $31.5 million, $28.2 million, and $21.8 million in 1998, 1997, and 1996, respectively. (iii) Raw Materials Raw materials, components, and supplies purchased by the Company are either available from a number of different suppliers or from alternative sources that could be developed without a material adverse effect on the Company. To date, the Company has experienced no material difficulties in obtaining these materials. (iv) Patents, Licenses, and Trademarks The Company's policy is to protect its intellectual property rights, including applying for and obtaining patents when appropriate. The Company holds numerous patents expiring at various dates related to its technologies, with additional patents pending. The Company also enters into licensing agreements expiring at various dates with other companies pursuant to which it has obtained rights to specific patents and technical know-how. The Company also considers technical know-how, trade secrets, and trademarks to be important to its business. (v) Seasonal Influences There are no significant seasonal influences on the Company's sales of its products. (vi) Working Capital Requirements There are no special inventory requirements or credit terms extended to customers that would have a material adverse effect on the Company's working capital. (vii) Dependency on a Single Customer No single customer accounted for 10% or more of the Company's total revenues in any of the past three years. 7 (viii) Backlog The Company's backlog of firm orders was: (In thousands) 1998 1997 - -------------------------------------------------- ---------- ---------- Analytical Instruments $ 48,719 $ 45,083 Scientific Equipment 8,512 7,498 -------- -------- $ 57,231 $ 52,581 ======== ======== The Company includes in its backlog only orders confirmed with a purchase order for products and related services scheduled to be shipped or rendered within one year. Certain of such firm orders are cancelable by the customer upon payment of a cancellation charge. The Company believes that substantially all of the backlog at January 2, 1999, will be shipped or completed during 1999. The Company does not believe that the level of, or changes in the level of, its backlog is necessarily a meaningful indicator of future results of operations. (ix) Government Contracts Not applicable. (x) Competition The Company competes in each of its markets primarily on technical performance, customer service and support, and price. Analytical Instruments The Company's principal competitors in the mass spectrometry market include the Chemical Analysis Group of Hewlett-Packard Company, the MicroMass Group of Waters Corporation, Shimadzu Corporation, and Perkin-Elmer Corporation. The Company's principal competitors in the liquid chromatography market include Waters, Hewlett-Packard, Shimadzu, and Perkin-Elmer. In the gas chromatography market, the Company competes with numerous companies including Hewlett-Packard, Varian Associates, Inc., Perkin-Elmer, and Shimadzu. The Company's principal competitors in the chromatography consumables market include Waters, Hewlett-Packard, Merck Corporation, Phenomenex Inc., and numerous regional suppliers. Scientific Equipment The Company's principal competitors in the scientific equipment market include Jouan S.A., NuAire Inc., Sanyo Electric Co. Ltd., and Labconco Corporation. (xii) Environmental Protection Regulations The Company believes that compliance by the Company with federal, state, and local environmental protection regulations will not have a material adverse effect on its capital expenditures, earnings, or competitive position. (xiii) Number of Employees As of January 2, 1999, the Company employed approximately 2,010 people. 8 (d) Financial Information About Exports by Domestic Operations and About Geographic Areas Financial information about exports by domestic operations and about geographic areas is summarized in Note 11 to Consolidated Financial Statements in the Registrant's 1998 Annual Report to Shareholders, which information is incorporated herein by reference. (e) Executive Officers of the Registrant Name Age Present Title (Fiscal Year First Became Executive Officer) ----------------------------------------------------------------- Dr. Richard W.K. Chapman 54 Chief Executive Officer and President (1995) Theo Melas-Kyriazi 39 Chief Financial Officer (1998) Paul F. Kelleher 56 Chief Accounting Officer (1995) Each executive officer serves until his successor is chosen or appointed by the Board of Directors and qualified or until his earlier resignation, death, or removal. Dr. Chapman has been Chief Executive Officer and President of the Company since its inception in June 1995. Dr. Chapman served as President of Finnigan Corporation, a subsidiary of the Company, from 1992 to 1995. Mr. Melas-Kyriazi was appointed Chief Financial Officer of the Company and Thermo Electron on January 1, 1999. He joined Thermo Electron in 1986 as Assistant Treasurer, and became Treasurer in 1988. He was named President and Chief Executive Officer of ThermoSpectra Corporation, a public subsidiary of Thermo Instrument, in 1994, a position he held until becoming Vice President of Corporate Strategy for Thermo Electron in 1998. Mr. Melas-Kyriazi remains a Vice President of Thermo Electron. Messrs. Melas-Kyriazi and Kelleher are full-time employees of Thermo Electron, but devote such time to the affairs of the Company as the Company's needs reasonably require. Item 2. Properties The location and general character of the Company's principal properties by segment as of January 2, 1999, are: Analytical Instruments The Company owns approximately 609,000 square feet of office, engineering, laboratory, and production space, principally in California, Texas, Florida, Germany, and Italy; and leases approximately 218,000 square feet of office space under leases expiring from 1999 through 2006, principally in New York, England, Germany, France, Japan, and the Netherlands. As of January 2, 1999, the Company had a $7.3 million mortgage loan that is secured by 200,000 square feet of property in California with a net book value of $14.9 million. Scientific Equipment The Company owns approximately 363,000 square feet of office, engineering, laboratory, and production space in Ohio and Massachusetts; and leases approximately 81,000 square feet of office space under leases expiring from 1999 through 2001, principally in New York and England. The Company believes that its facilities are in good condition and are suitable and adequate for its present operations and that suitable space is readily available if any of such leases are not extended. With respect to leases expiring in the near future, in the event the Company does not renew such leases, the Company believes suitable alternate space is available for lease on acceptable terms. 9 Item 3. Legal Proceedings On January 23, 1997, the Company's Finnigan subsidiary filed complaints against Bruker-Franzen Analytik GmbH and its U.S. affiliate, and Hewlett-Packard, for alleged violation of two U.S. patents owned by Finnigan. The patents pertain to methods used in ion-trap mass spectrometers. One of Finnigan's complaints was filed in the United States District Court for the District of Massachusetts, and the other was filed with the United States International Trade Commission (ITC) in Washington, DC. Finnigan has asked for damages to compensate for the infringements, for injunctions against further infringement, and for an order excluding further imports into the U.S. of ion-trap mass spectrometers that use the patented methods. The District Court action has, at the request of Hewlett-Packard and Bruker, been stayed pending completion of an investigation by the ITC. In April 1998, the ITC determined that the defendants did not engage in unfair practices in U.S. import trade with respect to the Finnigan patents, and that the Finnigan patents are invalid and/or not infringed. Finnigan has appealed the ITC's determination with respect to one of its patents to the United States Court of Appeals for the Federal Circuit (CAFC). The CAFC heard arguments in the appeal on March 4, 1999. Bruker presented counterclaims in the ITC investigation. The counterclaims, which have been removed to the District Court in Massachusetts, allege that the Finnigan patents are invalid and unenforceable and are not infringed by the mass spectrometers co-marketed by Bruker. They also allege that Finnigan has violated U.S. and Massachusetts antitrust laws and engaged in unfair competition by attempting to maintain a monopoly position and restrain trade through enforcement of allegedly fraudulently obtained patents. Bruker has asked for judgment consistent with its counterclaims, and for three times the antitrust damages (including attorneys' fees) it has sustained. There can be no assurance as to the outcome of these matters or that an unfavorable resolution would not have a material adverse effect on the Company's future results of operations and financial position. Item 4. Submission of Matters to a Vote of Security Holders Not applicable. 10 PART II Item 5. Market for Registrant's Common Equity and Related Stockholder Matters Information concerning the market and market price for the Registrant's common stock, $.01 par value, and dividend policy is included under the sections labeled "Common Stock Market Information" and "Dividend Policy" in the Registrant's 1998 Annual Report to Shareholders and is incorporated herein by reference. Item 6. Selected Financial Data The information required under this item is included under the sections labeled "Selected Financial Information" and "Dividend Policy" in the Registrant's 1998 Annual Report to Shareholders and is incorporated herein by reference. Item 7. Management's Discussion and Analysis of Financial Condition and Results of Operations The information required under this item is included under the heading "Management's Discussion and Analysis of Financial Condition and Results of Operations" in the Registrant's 1998 Annual Report to Shareholders and is incorporated herein by reference. Item 7A. Quantitative and Qualitative Disclosures About Market Risk The information required under this item is included under the heading "Management's Discussion and Analysis of Financial Condition and Results of Operations" in the Registrant's 1998 Annual Report to Shareholders and is incorporated herein by reference. Item 8. Financial Statements and Supplementary Data The Registrant's Consolidated Financial Statements as of January 2, 1999, and Supplementary Data are included in the Registrant's 1998 Annual Report to Shareholders and are incorporated herein by reference. Item 9. Changes in and Disagreements with Accountants on Accounting and Financial Disclosure Not applicable. 11 PART III Item 10. Directors and Executive Officers of the Registrant The information concerning directors required under this item is incorporated herein by reference from the material contained under the caption "Election of Directors" in the Registrant's definitive proxy statement to be filed with the Securities and Exchange Commission pursuant to Regulation 14A, not later than 120 days after the close of the fiscal year. The information concerning delinquent filers pursuant to Item 405 of Regulation S-K is incorporated herein by reference from the material contained under the caption "Section 16(a) Beneficial Ownership Reporting Compliance" under the caption "Stock Ownership" in the Registrant's definitive proxy statement to be filed with the Securities and Exchange Commission pursuant to Regulation 14A, not later than 120 days after the close of the fiscal year. Item 11. Executive Compensation The information required under this item is incorporated herein by reference from the material contained under the caption "Executive Compensation" in the Registrant's definitive proxy statement to be filed with the Securities and Exchange Commission pursuant to Regulation 14A, not later than 120 days after the close of the fiscal year. Item 12. Security Ownership of Certain Beneficial Owners and Management The information required under this item is incorporated herein by reference from the material contained under the caption "Stock Ownership" in the Registrant's definitive proxy statement to be filed with the Securities and Exchange Commission pursuant to Regulation 14A, not later than 120 days after the close of the fiscal year. Item 13. Certain Relationships and Related Transactions The information required under this item is incorporated herein by reference from the material contained under the caption "Relationship with Affiliates" in the Registrant's definitive proxy statement to be filed with the Securities and Exchange Commission pursuant to Regulation 14A, not later than 120 days after the close of the fiscal year. 12 PART IV Item 14. Exhibits, Financial Statement Schedules, and Reports on Form 8-K (a,d) Financial Statements and Schedules (1)The consolidated financial statements set forth in the list below are filed as part of this Report. (2)The consolidated financial statement schedule set forth in the list below is filed as part of this Report. (3)Exhibits filed herewith or incorporated herein by reference are set forth in Item 14(c) below. List of Financial Statements and Schedules Referenced in this Item 14 Information incorporated by reference from Exhibit 13 filed herewith: Consolidated Statement of Income Consolidated Balance Sheet Consolidated Statement of Cash Flows Consolidated Statement of Comprehensive Income and Shareholders' Investment Notes to Consolidated Financial Statements Report of Independent Public Accountants Financial Statement Schedules filed herewith: Schedule II: Valuation and Qualifying Accounts All other schedules are omitted because they are not applicable or not required, or because the required information is shown either in the financial statements or in the notes thereto. (b) Reports on Form 8-K None. (c) Exhibits See Exhibit Index on the page immediately preceding exhibits. 13 SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. Date: March 16, 1999 THERMOQUEST CORPORATION By: /s/ Richard W.K. Chapman Richard W.K. Chapman President and Chief Executive Officer Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the Registrant and in the capacities indicated below, as of March 16, 1999. Signature Title By: /s/ Richard W.K. Chapman President, Chief Executive Officer, Richard W.K. Chapman and Director By: /s/ Theo Melas-Kyriazi Chief Financial Officer Theo Melas-Kyriazi By: /s/ Paul F. Kelleher Chief Accounting Officer Paul F. Kelleher By: /s/ George N. Hatsopoulos Director George N. Hatsopoulos By: /s/ Frank Jungers Director Frank Jungers By: /s/ Earl R. Lewis Chairman of the Board and Director Earl R. Lewis By: /s/ Anthony J. Pellegrino Director Anthony J. Pellegrino By: /s/ Michael E. Porter Director Michael E. Porter 14 Report of Independent Public Accountants To the Shareholders and Board of Directors of ThermoQuest Corporation: We have audited, in accordance with generally accepted auditing standards, the consolidated financial statements included in ThermoQuest Corporation's Annual Report to Shareholders incorporated by reference in this Form 10-K, and have issued our report thereon dated February 16, 1999. Our audits were made for the purpose of forming an opinion on those statements taken as a whole. The schedule listed in Item 14 on page 13 is the responsibility of the Company's management and is presented for purposes of complying with the Securities and Exchange Commission's rules and is not part of the basic consolidated financial statements. This schedule has been subjected to the auditing procedures applied in the audits of the basic consolidated financial statements and, in our opinion, fairly states in all material respects the consolidated financial data required to be set forth therein in relation to the basic consolidated financial statements taken as a whole. Arthur Andersen LLP Boston, Massachusetts February 16, 1999 15 SCHEDULE II THERMOQUEST CORPORATION Valuation and Qualifying Accounts (In thousands) Description Balance at Provision Accounts Accounts Other (a) Balance Beginning Charged to Recovered Written at End of Expense Off of Year Year - ----------------------------------- ----------- ------------ ------------ ----------- ----------- ----------- Allowance for Doubtful Accounts Year Ended January 2, 1999 $4,361 $ 825 $ 90 $(1,357) $ 146 $4,065 Year Ended January 3, 1998 $4,459 $ 549 $ 33 $ (760) $ 80 $4,361 Year Ended December 28, 1996 $2,341 $ 220 $ 43 $ (351) $2,206 $4,459 Description Balance at Established Activity Other (c) Balance Beginning as Cost of Charged to at End of Acquisitions Reserve of Year Year - ----------------------------------- ----------- ------------ ------------ ----------- ----------- Accrued Acquisition Expenses (b) Year Ended January 2, 1999 $1,048 $ 331 $ (369) $ (679) $ 331 Year Ended January 3, 1998 $ 357 $1,571 $ (789) $ (91) $1,048 Year Ended December 28, 1996 $ 129 $1,493 $(1,303) $ 38 $ 357 Description Balance at Provision Activity Other (f) Balance Beginning Charged to Charged to at End of Expense (e) Reserve of Year Year - ----------------------------------- ----------- ------------- ----------- ----------- ----------- Restructuring Reserves (d) Year Ended January 2, 1999 $ - $3,660 $(2,010) $ (16) $1,634 (a) Includes allowance of businesses acquired during the year as described in Note 2 to Consolidated Financial Statements in the Registrant's 1998 Annual Report to Shareholders and the effect of foreign currency translation. (b) The nature of activity in this account is described in Note 2 to Consolidated Financial Statements in the Registrant's 1998 Annual Report to Shareholders. (c) Represents reversal of accrued acquisition expenses and corresponding reduction of cost in excess of net assets of acquired companies resulting from finalization of restructuring plans and the effect of foreign currency translation. (d) The nature of activity in this account is described in Note 9 to Consolidated Financial Statements in the Registrant's 1998 Annual Report to Shareholders. (e) Excludes provision of $0.9 million for an asset write-down. (f) Represents the effect of foreign currency translation. 16 EXHIBIT INDEX Exhibit Number Description of Exhibit 2.1 Stock Purchase Agreement dated as of November 4, 1996, between SID Instruments Inc. and the Registrant (filed as Exhibit 2.1 to the Registrant's Quarterly Report on Form 10-Q for the quarter ended September 28, 1996 [File No. 1-14262] and incorporated herein by reference). 2.2 Stock Purchase Agreement dated as of November 4, 1996, among SID Instruments Inc., Thermo Instrument, and Finnigan MAT (Nevada) Inc. (filed as Exhibit 2.2 to the Registrant's Quarterly Report on Form 10-Q for the quarter ended September 28, 1996 [File No. 1-14262] and incorporated herein by reference). 2.3 Asset and Share Purchase Agreement dated as of July 30, 1997, between the Registrant and Thermo Instrument (filed as Exhibit 2 to the Registrant's Quarterly Report on Form 10-Q for the quarter ended June 28, 1997 [File No. 1-14262] and incorporated herein by reference). 3.1 Certificate of Incorporation, as amended, of the Registrant (filed as Exhibit 3.1 to the Registrant's Registration Statement on Form S-1 [Reg. No. 333-00276] and incorporated herein by reference). 3.2 By-laws of the Registrant (filed as Exhibit 3.2 to the Registrant's Registration Statement on Form S-1 [Reg. No. 333-00276] and incorporated herein by reference). 10.1 Corporate Services Agreement dated as of June 30, 1995, between Thermo Electron and the Registrant (filed as Exhibit 10.1 to the Registrant's Registration Statement on Form S-1 [Reg. No. 333-00276] and incorporated herein by reference). 10.2 Thermo Electron Corporate Charter, as amended and restated effective January 3, 1993 (filed as Exhibit 10.1 to Thermo Electron's Annual Report on Form 10-K for the fiscal year ended January 2, 1993 [File No. 1-8002] and incorporated herein by reference). 10.3 Tax Allocation Agreement dated as of June 30, 1995, between Thermo Electron and the Registrant (filed as Exhibit 10.3 to the Registrant's Registration Statement on Form S-1 [Reg. No. 333-00276] and incorporated herein by reference). 10.4 Amended and Restated Master Repurchase Agreement dated as of June 30, 1995, between Thermo Electron and the Registrant (filed as Exhibit 10.4 to the Registrant's Annual Report to Form 10-K for the fiscal year ended January 3, 1998 [File No. 1-14262] and incorporated herein by reference). 10.5 Amended and Restated Master Guarantee Reimbursement and Loan Agreement dated December 2, 1997, by and among Thermo Electron and the Registrant (filed as Exhibit 10.7 to Thermo Instrument's Annual Report on Form 10-K for the fiscal year ended January 3, 1998 [File No. 1-9786] and incorporated herein by reference). 10.6 Amended and Restated Master Guarantee Reimbursement and Loan Agreement dated December 2, 1997, by and among Thermo Instrument and the Registrant (filed as Exhibit 10.6 to the Registrant's Annual Report to Shareholders for the fiscal year ended January 3, 1998 [File No. 1-14262] and incorporated herein by reference). 10.7 Equity Incentive Plan of the Registrant (filed as Exhibit 10.7 to the Company's Registration Statement on Form S-1 [Reg. No. 333-00276] and incorporated herein by reference). 17 Exhibit Number Description of Exhibit 10.8 Deferred Compensation Plan for Directors of the Registrant (filed as Exhibit 10.8 to the Registrant's Registration Statement on Form S-1 [Reg. No. 333-00276] and incorporated herein by reference). 10.9 Directors Stock Option Plan of the Registrant (filed as Exhibit 10.9 to the Registrant's Registration Statement on Form S-1 [Reg. No. 333-00276] and incorporated herein by reference). 10.10 Form of Indemnification Agreement for Officers and Directors (filed as Exhibit 10.10 to the Registrant's Registration Statement on Form S-1 [Reg. No. 333-00276] and incorporated herein by reference). In addition to the stock-based compensation plans of the Registrant, the executive officers of the Registrant may be granted awards under stock-based compensation plans of Thermo Electron and Thermo Instrument for services rendered to the Registrant or to such affiliated corporations. The terms of such plans are substantially the same as those of the Registrant's Equity Incentive Plan. 10.11 Fiscal Agency Agreement dated as of August 3, 1995, among the Registrant, Thermo Electron, and The Chase Manhattan Bank (formerly Chemical Bank) (filed as Exhibit 10.12 to the Registrant's Registration Statement on Form S-1 [Reg. No. 333-00276] and incorporated herein by reference). 10.12 Deed of Trust and Security Agreement dated February 22, 1989, between the Company (as successor-in-interest to Finnigan Properties, Inc.) and the Northwestern Mutual Life Insurance Company (filed as Exhibit 10.13 to the Registrant's Registration Statement on Form S-1 [Reg. No. 333-00276] and incorporated herein by reference). 10.13 Indemnification Agreement dated as of November 4, 1996, between Thermo Instrument and the Registrant (filed as Exhibit 10.1 to the Registrant's Quarterly Report on Form 10-Q for the quarter ended September 28, 1996 [File No. 1-14262] and incorporated herein by reference). 10.14 Amended and Restated Stock Holdings Assistance Plan and Form of Promissory Note (filed as Exhibit 10.14 to the Registrant's Annual Report to Shareholders for the fiscal year ended January 3, 1998 [File No. 1-14262] and incorporated herein by reference). 13 Annual Report to Shareholders for the Year Ended January 2, 1999 (only those portions incorporated herein by reference). 21 Subsidiaries of the Registrant. 23 Consent of Arthur Andersen LLP. 27 Financial Data Schedule. 18