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.


<PAGE>


                                   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.

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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.


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<PAGE>

      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.

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<PAGE>

    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
<PAGE>

    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.


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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.

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    (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.

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(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.




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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.

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                                  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.

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                                  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
<PAGE>

                                  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
<PAGE>

                                 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
<PAGE>

                  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
<PAGE>
<TABLE>
<CAPTION>

SCHEDULE II

                                         THERMOQUEST CORPORATION
                                    Valuation and Qualifying Accounts
                                              (In thousands)

<S>                                 <C>         <C>          <C>          <C>         <C>         <C>   

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.

</TABLE>


                                       16
<PAGE>

                               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
<PAGE>

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