<PAGE>

                                                                   EXHIBIT 10.40

                         CONSULTING SERVICES AGREEMENT

     THIS AGREEMENT is entered into this 30th day of January, 1997, by and
between Sequenom, Inc. (the "Company") of San Diego, CA/USA and Sequenom
Instruments GmbH of Hamburg/Germany (the "Company") and Prof.  Dr. Peter
Roepstorff ("Consultant").

     NOW, THEREFORE, it is agreed as follows:

     1.   Definitions
          As used herein:

          (a) The term "Products" shall mean the devices and reagents proposed
to be developed by, or with the assistance of, Consultant hereunder as defined,
and with the specifications set forth in Exhibit A hereto.

          (b) The term "Technology" shall mean the results and product (interim
and/or final) of the consulting services performed by Consultant hereunder,
whether tangible or intangible, including, without limitation, each and every
invention, formula, trade secret, software program (including without
limitation, object code, source code, flow charts, algorithms and related
documentation), listing, routine, manual, specification, technique, product,
concept, know-how, or similar property, whether or not patentable or
copyrightable, and whether or not embodied in any Products that are made,
developed, perfected, designed conceived or first reduced to practice by
Consultant, either solely or jointly with others, in the course and scope of the
consulting services performed hereunder.

     2.   Engagement or Performance of Services

          (a)  Engagement
               ----------
               The Company hereby engages Consultant to be a member of its
Scientific Advisory Board and to perform consulting services in accordance with
the terms and conditions of this Agreement. The specific tasks and services to
be performed by Consultant are set forth in Exhibit A attached hereto. If such
services include the development of specific Products, the specifications of
such Products are set forth in Exhibit A attached hereto.

          (b) Facilities, Equipment and Supplies
              ----------------------------------
              The company will provide to the Consultant the facilities,
equipment and supplies specified in Exhibit A attached hereto. *** It is
understood that milestones cannot be achieved unless funding by either funding
agencies or the Company is available. Consultant shall, at his own cost and
expense, provide all other facilities, equipment and supplies necessary to
perform the consulting services hereunder.

          (c)  Other Services
               --------------
               The Company acknowledges and agrees that, subject to its
obligations hereunder, Consultant shall have the right to engage in researches
and development and

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

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CONSULTING AGREEMENT
Prof. Dr. Peter Roepstorff                                                     2
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consulting activities in all areas other than ***. Such activities in the field
of *** are permissible, provided, however, that Consultant shall not perform any
consulting services for an actual or potential competitor of the Company during
the term of this Agreement and for a period of one (1) year after termination of
this Agreement. It is understood that the consulting activities in all areas
other than ***, are non exclusive.

          (d)  Primary Duty
               ------------
               The Company and the Consultant recognize that Consultant's
primary duty as a member of the faculty of Odense University (the "University")
is to the University. The Company and the Consultant agree that the University's
policies and Consultant's obligations to the University shall be observed in the
event a conflict arises with this Agreement. The same applies to funding
agencies who fund Consultant's research through research contracts with the
University of Odense or by funds administered by the University of Odense.

          (e)  Compensation
               ------------
               As compensation for the consulting services provided by
Consultant hereunder, the Company shall pay to Consultant the amounts specified,
at the time(s) specified, on Exhibit B attached hereto.

          (f)  Expenses
               --------
               In addition to the compensation specified in subsection 2(e), the
Company will pay reasonable out-of-pocket expenses incurred by Consultant and
approved in advance by the Company in the furtherance of or in connection with
the performance of consulting services hereunder.

          (g)  No Violation of Others' Rights
               ------------------------------
               Consultant represents and warrants that in the course of
performing services hereunder Consultant will not infringe or wrongfully
appropriate any patents, copyrights, trade secret rights, or other intellectual
property rights of any person or entity anywhere in the world.

     3.   Protection of Confidential Information
          On or before the date hereof, the Company and the Consultant shall
have entered into a separate agreement regarding Consultant's use of
confidential information (attached as Exhibit C).

     4.   Property Rights
          All rights, title and interest in and to the Products (if any) and the
Technology developed under this Agreement shall at all times be and remain the
sole and exclusive property of the Company, and the Products and the Technology
shall be deemed to be works made for hire.  The parties agree that any patents,
trademarks or copyrights that may issue relating to any of the Products or the
Technology shall be in the name of and assigned to the Company.  Patents and
rights resulting from research and development, the results of which are
disclosed to the Company before or at the time of signature of this Agreement
can be licensed and/or sold by Company only with Consultant's written consent.
In case the Company has an interest in

     *** Portions of this page have been omitted pursuant to a request for
Confidential Treatment and filed separately with the commission.
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CONSULTING AGREEMENT
Prof. Dr. Peter Roepstorff                                                     3
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developing the technology, a license agreement shall be negotiated according to
standard and fair marketing conditions.

     5.   Term and Termination
          The term of this Agreement shall be as set forth in Exhibit A attached
hereto.  Unless otherwise specified in Exhibit A, either party may terminate
this Agreement at any time upon thirty days written notice delivered to the
other.  The provision of Sections 3 and 4 hereof shall survive the termination
of this Agreement.

     6.   Miscellaneous

          (a)  Use of University's Name
               ------------------------
               With the limited exception of citing Consultant's faculty title,
the Company and its affiliates will not use the names, likeness, or logos of the
University, any of its schools or divisions in any of their fund raising or in
investment documents, general publications, advertisements, or marketing and
promotional materials without the prior written permission of the University.

          (b)  Relationship of Parties
               -----------------------
               Consultant shall at all times during the performance of his
services hereunder be an independent contractor, maintaining sole and exclusive
control over its business and operations. At no time will either party hold
itself out to be the agent, employee, lessee, sublessee, partner or joint
venturer of the other party. Neither party hereto shall have the express or
implied right or authority to assume or create any obligation on behalf of or in
the name of the other party, or to bind the other party in regard to any
contract, agreement or undertaking with any third party.

          (c)  Entire Agreement
               ----------------
               This Agreement, together with the exhibits attached hereto,
constitutes the entire agreement between the parties relating to the subject
matter hereof and supersedes all prior written or oral negotiations,
representations or agreements.  No modification of this Agreement shall be
binding on either party unless it is in writing and signed by both parties.

          (d)  Severability
               ------------
               The provisions of this Agreement are severable, and if one or
more provisions are judicially determined to be illegal or otherwise
unenforceable, in whole or in part, the remaining provisions or portions of this
Agreement shall nevertheless be binding on and enforceable by and between the
parties hereto.

          (e)  Assignment
               ----------
               This Agreement shall insure to the benefit or and be binding upon
the successors and assigns of the parties hereto; provided, however, that
Consultant shall not transfer or assign this Agreement without the prior written
consent of the Company.

          (f)  Governing Law
               -------------
               The rights and obligations of the parties to this Agreement shall
be governed by and construed in accordance with the laws of the Commonwealth of
Massachusetts.
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CONSULTING AGREEMENT
Prof. Dr. Peter Roepstorff                                                     4
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          (g)  Headings
               --------
               Section headings are for convenience of reference only and shall
not be considered in the interpretation of this Agreement.

          (h)  Unavoidable Delays
               ------------------
               Either party shall be excused for any delays or defaults in the
performance of this Agreement (except the payment of amounts due and payable
hereunder) unavoidably caused by the act of the other, the act of any agent of
the other, the act of any governmental authority, acts of God, the elements,
war, litigation, strikes, walkouts, or any other cause beyond its reasonable
control.  Each party shall use all reasonable diligence to avoid any such delay
or default and to resume performance under this Agreement as soon as practicable
after such delay or default.

          (i)  Notices
               -------
               All notices, requests, demands and other communications to be
given pursuant to this Agreement shall be in writing and shall be deemed to have
been duly given if delivered by hand or mailed by registered or certified mail,
return receipt requested, postage prepaid, or by facsimile transmission if a
true and correct copy is sent the same day by first class mail, postage prepaid,
or by dispatch by in internationally recognized express courier service, and in
each case addressed as follows:

     If to Consultant:   Prof.  Dr. Peter Roepstorff
     ----------------    Kolding Landevej 43
                         DK-7000 Fredericia/Denmark

     If to the Company:  Sequenom, Inc.
     -----------------   c/o Sequenom Instruments GmbH
                         Mendelssohnstrasse 15 D
                         D-22761 Hamburg/Germany
                         Attn.: Prof. Dr. Hubert Koster

     with copy to:       Foley, Hoag & Eliot
                         One Post Office Square
                         Boston, MA  02109/USA
                         Attn.: David Pearson, Esq.

or such other address as either party hereto shall have designated by notice in
writing to the other a party.

          (j)  Attorney's fees and Costs
               -------------------------
               Should litigation arise concerning the enforcement or
interpretation of this Agreement, the prevailing party shall be entitled to
recover its reasonable attorney's fees and costs as determined by the court.
<PAGE>

CONSULTING AGREEMENT
Prof. Dr. Peter Roepstorff                                                     5
--------------------------------------------------------------------------------

     IN WITNESS WHEREOF, the Parties hereto have executed this Agreement on the
date first above written.

SEQUENOM, Inc.                        CONSULTANT:

By: /s/   illegible                   /s/ illegible
    -------------------------         ----------------------------

Title: CTO
       ----------------------


                            SEQUENOM Instruments GmbH:

                            By:  /s/ illegible
                                 -------------------------

                            Title:  illegible
                                    ----------------------
<PAGE>

CONSULTING AGREEMENT
Prof. Dr. Peter Roepstorff                                                     6
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                                   EXHIBIT A
                                   ---------

                                     TERM

The term of the Agreement shall be the period from March 1, 1997 to February 28,
2000, subject to termination in accordance with Section 5.

                       DESCRIPTION OF SERVICES AND TASKS

The Consultant will:

(1)  be a member of the Sequenom Scientific Advisory Board;

(2)  provide advice and technical assistance to Sequenom on all aspects of ***
     and proteins, including applications in the area of ***.

(3)  provide technical advice, in particular also with reference to ***

(4)  assist Sequenom in *** and related technologies, with appropriate expertise
     in applications of ***

(5)  make every reasonable effort to attend all meetings of the Scientific
     Advisory Board and participate in all discussions and decisions related to
     strategies, technical approaches and technical progress for the overall
     project;

and, in addition to regular communication with Sequenom personnel via telephone,
fax, courier or normal mail, spend up to one day per month at Sequenom
Instruments GmbH, Hamburg/Germany, or the location of Sequenom, Inc. in the USA.

*** Portions of this page have been omitted pursuant to a request for
Confidential Treatment and filed separately with the commission.
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CONSULTING AGREEMENT
Prof. Dr. Peter Roepstorff                                                     7
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                                   EXHIBIT B
                                   ---------

                       COMPENSATION AND PAYMENT SCHEDULE

In return, Sequenom will provide to the Consultant:

(1)  ***

(2)  ***

(3)  ***

(4)  ***

(5)  options to purchase 9,000 shares of the common stock of Sequenom, with
     3,000 of such options to vest on March 31, 1998, 3,000 to vest on March 31,
     1999, and the remaining 3,000 shares to vest on March 31, 2000; such
     options shall have an exercise price per share equal to the fair market
     value of the common stock on the date of grant as determined by the Board
     of Directors;

(6)  options to purchase 15,000 shares of the common stock of Sequenom, with
     such options to be portioned in number in accordance with the priorities
     set for the three milestones below, and such options to vest in full on
     March 31, 2005, provided, however, that the vesting of the defined portions
     of such shares shall be accelerated upon completion of each of the
     following milestones:

     (a)
     (b)  to be defined
     (c)

(7)  the options shall have an exercise price per share equal to the fair market
     value of the common stock on the date of grant as determined by the Board
     of Directors.

*** Portions of this page have been omitted pursuant to a request for
Confidential Treatment and filed separately with the commission.
<PAGE>

CONSULTING AGREEMENT
Prof. Dr. Peter Roepstorff                                                     8
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                                   EXHIBIT C
                                   ---------

                           CONFIDENTIALITY AGREEMENT

Under the terms of the Consulting Agreement, the Consultant is under obligation
not to disclose any business information or company secrets to unauthorized
parties and/or to persons outside the Company.

Maintaining confidentiality is a constituent part of the Consultant's loyalty to
the Company and protects business and company secrets.  Company secrets are data
and materials identified as confidential or those which, upon careful
consideration, a Consultant can recognize as being confidential (e.g. technical
expertise, even if not patentable, supply sources for goods, customer lists,
price schedules, calculations, investment plans, etc., including also the
Consultant's own inventions made in the performance of the Consulting Agreement.
This agreement to confidentiality is deemed to extend and apply also to any co-
workers involved in the execution of the collaboration project with the Company.

Details of any production or analytical methods of which the Consultant may gain
knowledge and regarding which the Company as license holder is committed to
maintain strictest confidentiality are also classified as secret.  This applies
to details of production processes to which the Company has gained access in the
course of an exchange of know-how with another company or which are classified
secret by the Company under its commitment to confidentiality with another
company.

The Consultant further undertakes to maintain strictest confidentiality
regarding all matters of the Company's business also after termination of the
Consulting Agreement.  In this context the Consultant is obliged, if so
required, to sign a respective personal commitment to confidentiality vis-a-vis
third parties.

In the event of any violation of this agreement to confidentiality, the Company
is entitled to impose a penalty for each violation, without prejudice to the
Company's right to claim for higher damages, or the Company's right to
termination of the Consulting Agreement.

Consultant:                                    /s/ Prof. Dr. Peter Reopstorff
                                               ------------------------------
                                                   Prof. Dr. Peter Roepstorff

SEQUENOM, Inc.                                 /s/  Dr. Hubert Koster
                                               ------------------------------
                                                   Name:  Dr. Hubert Koster
                                                   Title:  CTO

SEQUENOM Instruments GmbH:                     /s/ illegilbe
                                               ------------------------------
                                                   Name:  illegible
                                                   Title: illegible