<PAGE>

                                                                   EXHIBIT 10.29

                            Collaboration Agreement

                                by and between


Bruker-Franzen Anajytik GmbH
Fahrenheitstr. 4
28359 Bremen                            hereinafter referred to as `Bruker'

and

Sequenom Instruments GmbH
Mendelssohnstr. 15 D
22761 Hamburg                           hereinafter referred to as `Sequenom'

                                        November 24, 1997


                                   Preamble

(1)  Bruker-Franzen Analytik develops and manufactures mass spectrometers and
     supplies such instruments on a worldwide scale.

     Bruker-Franzen Analytik has exclusive intellectual property rights and
     know-how, covering
     .   MALDI-TOF mass spectrometer technology
     .   Pulsed Ion Extraction
     .   Multi-Target Acquisition
     .   Postprocessing XMASS(TM) software.

     Bruker-Franzen Analytik maintains an organisation appropriate for the
     manufacture, marketing and customer service with regard to such mass
     spectrometers.

(2)  Sequenom has exclusive intellectual property rights and know-how, covering
     Sequenom's DNA MassArray(TM) technology basis and comprising
     .   Sample preparation and sample conditioning of nucleic acids, optimized
         for MS separation and detection
     .   DNA analysis application formats specifically designed for MS analysis
         (BiomassSIZE(TM), BiomassSCAN(TM), BiomassPROBE(TM) BiomassSEQUENCE
         (TM), BiomassINDEX(TM))
     .   Parallel processing features, applying DNA chips (SpectroChip(TM)) and
         multiplexing
     .   Separation and detection of nucleic acids by MS, incl. analytical and
         diagnostic applications.

(3)  The parties intend to establish a broad relationship focusing on Nucleic
     Acid Analysis by Mass Spectrometey subject to the experience within this
     Collaboration.

<PAGE>

Collaboration

(1)  Bruker-Franzen and Sequenom intend to collaborate in the manufacture and
     marketing of and in the provision of customer service for ZD-Array MALDI-
     TOF Mass Spectrometers designed to process Sequenom's SpectroChips(TM) (the
     "Mass Spectrometer") under a joint Bruker-Franzen -- Sequenom logo.

     The Mass Spectrometer will be made available as stand-alone instrument and
     will be integrated by Sequenom in collaboration with highly qualified
     instrument manufacturers in the area of microliter and nanoliter liquid
     handling, mass spectrometry and system integration in modular analytical
     lines (the "Modular System"), comprising automatic liquid handling modules,
     DNA amplification and sequencing modules, sample-to-chip transfer modules
     and controlling and data management units. The Modular System will be
     designed to run applications of Sequenom's DNA MassArray(TM) technology

(2)  Bruker-Franzen will design and manufacture the Mass Spectrometer, meeting
     the specifications required for use in the DNA MassArray(TM) process and
     dedicated and appropriate to process Sequenom's Spectrochips(TM) ,
     including the XY-stage component and signal acquisition software. The
     parties will mutually agree on specifications for the Mass Spectrometer and
     the SpectroChip. Bruker will make available to Sequenom the complete
     details of the interface, including software protocols and time behavior,
     enabling Sequenom to develop the specific application DNA MassArray(TM)
     software.

(3)  The Mass Spectrometer will be available by June 30, 1998.

(4)  Bruker-Franzen and Sequenom will promote the Mass Spectrometer under a
     joint label. The procedure will be defined on a case-by-case basis.

(5)  Bruker-Franzen will market and provide service for the Mass Spectrometer on
     a world-wide scale and under the name of Bruker-Franzen and Sequenom.

(6)  Sequenom will provide nucleic acid analysis services to customers and to
     corporate partners using DNA MassArray(TM)
     Sequenom will provide DNA MassArray(TM) application development, including
     necessary software, to Mass Spectrometry users.
     Sequenom will develop, manufacture and market SepctroChips(TM) for whatever
     applications.

                                       2
<PAGE>

Business Terms

(1)  Bruker-Franzen will supply the Mass Spectrometer to the market at a
     competitive market price (the "Market Price").

(2)  Sequenom maintains the option to purchase from Bruker-Franzen the Mass
     Spectrometer *** (the "Supply Price"). The Supply Price will be calculated
     by ***, referring to the basic instrument, in the respective country of
     instrument delivery.

(3)  Bruker-Franzen Analytik will provide one Mass Spectrometer to Sequenom,
     Hamburg as Beta test site by June 30, 1998 ***. Initially, a
     prototype instrument equipped for handling of a single SpectroChip (TM)
     will be supplied by March 30, 1998. The Modular System in Hamburg will be
     used as demonstration and test site by both parties.

     A second Mass Spectrometer will be supplied to Sequenom, San Diego, the
     price being the Supply Price, by June 30, 1998.

(4)  The Mass Spectrometer will be *** for the exclusive processing of
     Sequenom's SpectroChip(TM).


Timelines

(1)  The Collaboration Agreement will come into force with the date of
     signature.

(2)  The Collaboration agreement may be terminated by either party at 12 months
     notice; such first notice of termination may, however, not be given earlier
     than 30 Dec. 1999.


Date:     December 4, 1997                     Date:    December 4, 1997
     -------------------------                      ------------------------
Bruker-Franzen                                 Sequenom

/s/ Dr. Frazen                                 /s/ Dr. H. Koster
                                               (Dr. H. Koster)

/s/ ppa H.J. [illegible]

*** - Portions of this page have been omitted pursuant to Confidential Treatment
request and filed separately, with the Commission.

                                       3