<PAGE>

                                                                 EXHIBIT 10.42


                         CONSULTING SERVICES AGREEMENT

    THIS AGREEMENT is entered into this 1st day of March 1999, by and between
Sequenom, Inc. (the "Company") and Dr. John Cashman ("Consultant").

    NOW, THEREFORE, it is agreed as follows:

    1.   Definitions: As used herein:
         -----------

         (a)  The term "Products" shall mean the devices, if any, proposed to be
              developed by, or with the assistance of, Consultant hereunder as
              defined, and with the specifications set forth in Exhibit 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. Technology will exclude results and or
              products developed in conjunction with co-sponsored Federal or
              other grants.

    2.   Engagement and Performance of Services
         --------------------------------------

         (a)  Engagement.  The Company hereby engages Consultant to perform
              ----------
              consulting services in accordance with the terms and conditions
              of this agreement.  The specific task and services to be
              performed by Consultant are set forth on Exhibit A attached
              hereto.  If such services include the development of specific
              Products, the specifications of such Products are as set forth on
              Exhibit A attached hereto.

         (b)  Facilities, Equipment and Supplies. The Consultant shall provide,
              ----------------------------------
              at his own cost, 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 research and development and consulting
              activities for himself and others during the term of this
              Agreement; provided, however, that Consultant shall not perform
              any consulting services for an actual or potential competitor of
              the Company involved in *** as a primary service or product during
              the term of this agreement.

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

         (d)  Duration of Services.  The Company and the Consultant recognize
              --------------------
              that duration of services will not exceed one (1) year.

         (e)  Compensation.  As compensation for the consulting services
              ------------
              provided by Consultant hereunder, the Company shall pay to
              Consultant *** with the first installment beginning on March 1,
              1999. In addition, the Consultant will receive one thousand five
              hundred (1500) incentive stock options (ISO) on March 1, 2000
              priced at the Fair Market Value.

         (f)  Expenses.  In addition to the compensation specified in
              --------
              subsection (e), the Company will pay reasonable 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.  These expenses include but are
              not limited to ***.

         (g)  No Violation of Other's Rights.  Consultant represents and
              ------------------------------
              warrants that in the course of performing services hereunder
              Consultant will not infringe or wrongly 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.

    4.   Property Rights.  All right, title and interest in and to the Products
         ---------------
         (if any) and the Technology 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.

    5.   Term and Termination.  The terms of this agreement may be terminated
         --------------------
         only by written notice at any time.  The provisions of Sections 3 and
         4 hereof shall survive the termination of this Agreement.

    6.   Miscellaneous.
         -------------

         (a)  Relationships of Parties.  Consultant shall at all time 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

                                       2
<PAGE>

              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 with the exception
              of mutually agreed upon Federal and other grants.

         (b)  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.

         (c)  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.

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

         (e)  Governing Law.  The rights and obligations of the parties to this
              -------------
              agreement shall be governed by and construed in accordance with
              the laws of California.

         (f)  Headings.  Section headings are for convenience of reference only
              --------
              and shall not be considered in the interpretation of this
              Agreement.

         (g)  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
              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.

         (h)  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 same day
              by First Class mail, postage prepaid, or by dispatch by an
              internationally recognized express courier service, and in each
              case addressed as follows:

                                       3
<PAGE>

              If to Consultant:  Dr. John Cashman
              ----------------   Director
                                 Human Biomolecular Research Institute
                                 5310 Eastgate Mall
                                 San Diego, CA 92121
              If to the Company: Sequenom, Inc.
              -----------------  11555 Sorrento Valley Road
                                 San Diego, CA 92121
                                 Attn:  Dr. Andi
                                 Vice President, Genomics

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

         (i)  Attorneys' 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.

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

SEQUENOM, INC.                                   CONSULTANT:
By: /s/ A. Braun                                 /s/  John Cashman
    --------------------------                   ---------------------------
    Date: 5-20-99                                May 20, 1999
    Dr. Andi Braun, VP Genomics                  Dr. John Cashman

                                       4
<PAGE>

                                   EXHIBIT A
                                   ---------

The term of the Agreement shall be the period from March 1, 1999 to February 28,
2000, subject to termination in accordance with Section 5.

                       DESCRIPTION OF SERVICES AND TASKS

The consultant will:

1.  Provide advice and technical assistance to Sequenom on ***

2.  Provide ***

3.  Setup of ***

4.  Publish together with Sequenom data from scientists' application of DNA Mass
    Array.

*** Portions of this page have been omitted pursuant to a request for
confidential treatment and filed separately with the commission.