CUSIP No. 17252Y104                    13G            Page   1   of  11  Pages
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                           UNITED STATES             OMB Number:       3235-0145
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                                                     ---------------------------

                                  SCHEDULE 13G


                    Under the Securities Exchange Act of 1934

                               (Amendment No.      2 )*
                                             ---------

                           CIPHERGEN BIOSYSTEMS, INC.
--------------------------------------------------------------------------------
                           (Name of Issuer)

                          COMMON STOCK, $.001 par value
--------------------------------------------------------------------------------
                         (Title of Class of Securities)

                                          17252Y104
                            -------------------------
                                 (CUSIP Number)


--------------------------------------------------------------------------------
             (Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule
is filed:

            [_] Rule 13d-1(b)
            [_] Rule 13d-1(c)
            [X] Rule 13d-1(d)

*The remainder of this cover page shall be filled out for a reporting person's
initial filing on this form with respect to the subject class of securities, and
for any subsequent amendment containing information which would alter the
disclosures provided in a prior cover page.

The information required in the remainder of this cover page shall not be deemed
to be "filed" for the purpose of Section 18 of the Securities Exchange Act of
1934 ("Act") or otherwise subject to the liabilities of that section of the Act
but shall be subject to all other provisions of the Act (however, see the
Notes).



CUSIP No. 17252Y104                    13G            Page   2   of  11  Pages
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                                  Schedule 13G

Item 1.

               (a)  Name of Issuer: Ciphergen Biosystems, Inc.

               (b)  Address of Issuer's Principal Executive Offices: 6611
                    Dumbarton Circle, Fremont, CA 94555


Item 2.        (a)  Name of Persons Filing:

               Atlas Venture Fund V, L.P., Atlas Venture Entrepreneurs' Fund V,
               L.P., Atlas Venture Parallel Fund V-A, C.V., Atlas Venture
               Parallel Fund V-B, C.V., Atlas Venture Associates V, L.P., Atlas
               Venture Associates V, Inc., Christopher J. Spray, Jean-Francois
               Formela, Ronald Nordin and Axel Bichara.

               Atlas Venture Associates V, Inc. is the sole general partner of
               Atlas Venture Associates V, L.P. Atlas Venture Associates V, L.P.
               is the sole general partner of Atlas Venture Fund V, L.P., Atlas
               Venture Entrepreneurs' Fund V, L.P., Atlas Venture Parallel Fund
               V-A, C.V. and Atlas Venture Parallel Fund V-B, C.V. Messrs.
               Spray, Formela and Bichara are directors of Atlas Venture
               Associates V, Inc.

               (b)  Address of Principal Business Office or, if none, Residence:

               The address of the principal business office of Atlas Venture
               Fund V, L.P., Atlas Venture Entrepreneurs' Fund V, L.P., Atlas
               Venture Parallel Fund V-A, C.V., Atlas Venture Parallel Fund V-B,
               C.V., Atlas Venture Associates V, L.P., Atlas Venture Associates
               V, Inc. and Messrs. Spray, Formela, Nordin and Bichara is Atlas
               Venture, 890 Winter Street, Suite 320, Waltham, Massachusetts
               02451.

               (c)  Citizenship: Atlas Venture Fund V, L.P., Atlas Venture
               Entrepreneurs' Fund V, L.P. and Atlas Venture Associates V, L.P.
               is each a limited partnership organized under the laws of the
               State of Delaware. Atlas Venture Associates V, Inc. is a
               corporation organized under the laws of the State of Delaware.
               Atlas Venture Parallel Fund V-A, C.V. and Atlas Venture Parallel
               Fund V-B, C.V. is each a Limited Partnership organized under the
               laws of The Netherlands. Mr. Spray is a citizen of the United
               Kingdom. Mr. Formela is a citizen of France. Mr. Nordin is a
               citizen of the United States. Mr. Bichara is a citizen of
               Germany.

               (d)  Title of Class of Securities: Common Stock, $.001 par value.

               (e)  CUSIP Number: 17252Y104.

Item 3.        If this statement is filed pursuant to (S)(S)240.13d-1(b) or
               240.13d-2(b) or (c), check whether the person filing is a:

               Not Applicable.

Item 4.        Ownership.

Provide the following information regarding the aggregate number and percentage
of the class of securities of the issuer identified in Item 1.
               Not Applicable.



CUSIP No. 17252Y104                    13G            Page   3   of  11  Pages
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Item 5.     Ownership of Five Percent or Less of a Class

If this statement is being filed to report the fact that as of the date hereof
the reporting person has ceased to be the beneficial owner of more than five
percent of the class of securities, check the following [x].

          Atlas Venture Fund V, L.P., Atlas Venture Entrepreneurs' Fund V, L.P.,
          Atlas Venture Parallel Fund V-A, C.V., Atlas Venture Parallel Fund
          V-B, C.V., Atlas Venture Associates V, L.P., Atlas Venture Associates
          V, Inc., Christopher J. Spray, Jean-Francois Formela, Ronald Nordin
          and Axel Bichara is each deemed to own less than five percent of
          outstanding shares of common stock of Ciphergen as of December 31,
          2002.

Instruction: Dissolution of a group requires a response to this item.

Item 6.     Ownership of More than Five Percent on Behalf of Another Person.
If any other person is known to have the right to receive or the power to direct
the receipt of dividends from, or the proceeds from the sale of, such
securities, a statement to that effect should be included in response to this
item and, if such interest relates to more than five percent of the class, such
person should be identified. A listing of the shareholders of an investment
company registered under the Investment Company Act of 1940 or the beneficiaries
of employee benefit plan, pension fund or endowment fund is not required.

            Not Applicable.

Item 7.     Identification and Classification of the Subsidiary Which Acquired
the Security Being Reported on By the Parent Holding Company or Control Person.
If a parent holding company or Control person has filed this schedule, pursuant
to Rule 13d-1(b)(1)(ii)(G), so indicate under Item 3(g) and attach an exhibit
stating the identity and the Item 3 classification of the relevant subsidiary.
If a parent holding company or control person has filed this schedule pursuant
to Rule 13d-1(c) or Rule 13d-1(d), attach an exhibit stating the identification
of the relevant subsidiary.

            Not Applicable.

Item 8.     Identification and Classification of Members of the Group
If a group has filed this schedule pursuant to (S)240.13d-1(b)(1)(ii)(J), so
indicate under Item 3(j) and attach an exhibit stating the identity and Item 3
classification of each member of the group. If a group has filed this schedule
pursuant to (S)240.13d-1(c) or (S)240.13d-1(d), attach an exhibit stating the
identity of each member of the group.

            Not Applicable. The reporting persons expressly disclaim membership
            in a "group" as defined in Rule 13d-1(b)(1)(ii)(J).


Item 9.     Notice of Dissolution of Group
Notice of dissolution of a group may be furnished as an exhibit stating the date
of the dissolution and that all further filings with respect to transactions in
the security reported on will be filed, if required, by members of the group, in
their individual capacity. See Item 5.

            Not Applicable.

Item 10.    Certification

            Not Applicable.



CUSIP No. 17252Y104                    13G            Page   4   of  11  Pages
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SIGNATURE
After reasonable inquiry and to the best of my knowledge and belief, I certify
that the information set forth in this statement is true, complete and correct.
We also hereby agree to file this statement jointly pursuant to the Agreement
listed on Exhibit 1 hereto.

Dated:  February 12, 2003
ATLAS VENTURE FUND V, L.P.                 ATLAS VENTURE PARALLEL FUND V-B, C.V.

By: Atlas Venture Associates V, L.P.       By: Atlas Venture Associates V, L.P.
    General Partner                            General Partner

       By: Atlas Venture Associates V, Inc.       By: Atlas Venture Associates
                                                      V, Inc.

                  By:           *                         By:          *
                     ----------------------                  -------------------
                     Christopher Spray                       Christopher Spray
                     President                               President

ATLAS VENTURE ENTREPRENEURS' FUND V, L.P.  ATLAS VENTURE ASSOCIATES V, L.P.

By: Atlas Venture Associates V, L.P.       By: Atlas Venture Associates V, Inc.
    General Partner
                                                  By:               *
                                                     ---------------------------
       By: Atlas Venture Associates V, Inc.          Christopher Spray
                                                     President

               By:         *
                  -----------------------
                  Christopher Spray
                  President                ATLAS VENTURE ASSOCIATES V, INC.

                                           By:          *
                                              -------------------------
                                              Christopher Spray
                                              President

ATLAS VENTURE PARALLEL FUND V-A, C.V.
                                                        *
                                           ----------------------------
By: Atlas Venture Associates V, L.P.       Christopher J. Spray
    General Partner
                                                        *
                                           ----------------------------
      By: Atlas Venture Associates V, Inc. Jean-Francois Formela

              By          *                             *
                ------------------------   ----------------------------
                Christopher Spray          Ronald Nordin
                President

                                                        *
                                           ----------------------------
                                           Axel Bichara

*   The undersigned attorney-in-fact, by signing her name below, does hereby
    sign this statement on behalf of the above indicated filers pursuant to
    Powers of Attorney filed hereto as Exhibit 2.

     /s/Jeanne Larkin Henry
     ----------------------
     Jeanne Larkin Henry
     Attorney-in-fact



CUSIP No. 17252Y104                    13G            Page   5   of  11  Pages
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                                                                       Exhibit 1

                                    AGREEMENT

     Pursuant to Rule 13d-1(k)(1) under the Securities Exchange Act of 1934, the
undersigned hereby agree that only one statement containing the information
required by Schedule 13G need be filed with respect to the ownership by each of
the undersigned of shares of Common Stock of Ciphergen Biosystems, Inc. This
agreement may be executed in any number of counterparts, each of which shall be
deemed an original.

     EXECUTED this 12 day of February, 2003.

ATLAS VENTURE FUND V, L.P.                 ATLAS VENTURE PARALLEL FUND V-B, C.V.

By: Atlas Venture Associates V, L.P.       By: Atlas Venture Associates V, L.P.
    General Partner                            General Partner

       By: Atlas Venture Associates V, Inc.       By: Atlas Venture Associates
                                                      V, Inc.

                By:         *                              By:        *
                   ----------------------                     ------------------
                   Christopher Spray                          Christopher Spray
                   President                                  President

ATLAS VENTURE ENTREPRENEURS' FUND V, L.P.  ATLAS VENTURE ASSOCIATES V, L.P.

By: Atlas Venture Associates V, L.P.       By: Atlas Venture Associates V, Inc.
    General Partner
                                                   By:         *
                                                      -------------------
      By: Atlas Venture Associates V, Inc.            Christopher Spray
                                                      President

              By:        *
                 ----------------
                 Christopher Spray         ATLAS VENTURE ASSOCIATES V, INC.
                 President
                                           By:           *
                                              -------------------------
                                              Christopher Spray
                                              President

ATLAS VENTURE PARALLEL FUND V-A, C.V.
                                                         *
                                           ----------------------------
By: Atlas Venture Associates V, L.P.       Christopher J. Spray
    General Partner
                                                         *
                                           ----------------------------
      By: Atlas Venture Associates V, Inc. Jean-Francois Formela

             By               *                          *
               --------------------------  ----------------------------
               Christopher Spray           Ronald Nordin
               President

                                                         *
                                           ----------------------------
                                           Axel Bichara

*   The undersigned attorney-in-fact, by signing her name below, does hereby
    sign this statement on behalf of the above indicated filers pursuant to
    Powers of Attorney filed hereto as Exhibit 2.

     /s/Jeanne Larkin Henry
     ----------------------
     Jeanne Larkin Henry
     Attorney-in-fact



CUSIP No. 17252Y104                 13G              Page  6  of  11  Pages
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The original statement shall be signed by each person on whose behalf the
statement is filed or his authorized representative. If the statement is signed
on behalf of a person by his authorized representative other than an executive
officer or general partner of the filing person, evidence of the
representative's authority to sign on behalf of such person shall be filed with
the statement, provided, however, that a power of attorney for this purpose
which is already on file with the Commission may be incorporated by reference.
The name and any title of each person who signs the statement shall be typed or
printed beneath his signature.

NOTE: Schedules filed in paper format shall include a signed original and five
copies of the schedule, including all exhibits. See (S)240.13d-7 for other
parties for whom copies are to be sent.

Attention: Intentional misstatements or omissions of fact constitute Federal
           criminal violations (See 18 U.S.C. 1001)



CUSIP No. 17252Y104                        13G       Page  7  of  11  Pages
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                                                                       Exhibit 2
                                                                       ---------

                                POWER OF ATTORNEY

     KNOW ALL MEN BY THESE PRESENTS, that each person whose signature appears
below hereby constitutes and appoints each and any of Christopher J. Spray and
Jeanne Larkin Henry his true and lawful attorney-in-fact and agent, with full
power of substitution and resubstitution, for him and in his name, place and
stead, in any and all capacities (until revoked in writing) to sign any and all
instruments, certificates and documents required to be executed on behalf of
himself individually or on behalf of each or any of Atlas Venture Fund, L.P.,
Atlas Venture Associates, L.P., Atlas Venture Partners III, B.V., Atlas Venture
Fund II, L.P., Atlas Venture Associates II, L.P., Atlas Venture Europe Fund
B.V., Atlas InvesteringsGroep N.V., Atlas Venture Beheer II B.V., Partno
Deelmingen B.V., Atlas Venture Fund III, L.P., Atlas Venture Entrepreneurs' Fund
III, L.P., Atlas Venture Associates III, L.P., Atlas Venture Associates III,
Inc., Atlas Venture Fund V, L.P., Atlas Venture Entrepreneurs' Fund V, L.P.,
Atlas Venture Parallel Fund V-A, C.V., Atlas Venture Parallel Fund V-B, C.V.,
Atlas Venture Associates V, L.P., and Atlas Venture Associates V, Inc. pursuant
to sections 13 and 16 of the Securities Exchange Act of 1934, as amended (the
"Exchange Act"), and any and all regulations promulgated thereunder, and to file
the same, with all exhibits thereto, and any other documents in connection
therewith, with the Securities and Exchange Commission, and with any other
entity when and if such is mandated by the Exchange Act or by the By-laws of the
National Association of Securities Dealers, granting unto said attorney-in-fact
and agent full power and authority to do and perform each and every act and
thing requisite and necessary fully to all intents and purposes as he might or
could do in person thereby ratifying and confirming all that said
attorney-in-fact and agent, or his substitute or substitutes, may lawfully do or
cause to be done by virtue hereof.

                  [REMAINDER OF PAGE LEFT BLANK INTENTIONALLY]

                      [SIGNATURE PAGE FOLLOWS IMMEDIATELY]



CUSIP No. 17252Y104               13G                Page  8  of  11  Pages
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      IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 13th
day of February, 2001.

                                               /s/ Christopher J. Spray
                                               ------------------------------
                                               Christopher J. Spray

Commonwealth of Massachusetts)
                               ) ss:
County of Suffolk              )

      On this 13th day of February, 2001, before me personally came Christopher
J. Spray, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.

[Notary Seal]                                  /s/ Kyle Walkden
                                               ----------------
                                               Notary Public

                                               My commission expires: 9/9/05



CUSIP No. 17252Y104                13G               Page  9  of  11  Pages
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      IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 13th
day of February, 2001.

                                               /s/ Jean Francois Formela
                                               ------------------------------
                                               Jean Francois Formela

Commonwealth of Massachusetts)
                               ) ss:
County of Suffolk              )

      On this 13th day of February, 2001, before me personally came
Jean-Francois Formela, known to me to be the person described and who executed
the foregoing instrument that he acknowledged that he executed the same.

[Notary Seal]                                  /s/Kyle Walkden
                                               ---------------
                                               Notary Public

                                               My commission expires: 9/9/05



CUSIP No. 17252Y104                  13G             Page  10  of  11  Pages
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      IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 13th
day of February, 2001.

                                               /s/ Ronald Nordin
                                               ------------------------------
                                               Ronald Nordin

Commonwealth of Massachusetts)
                                ) ss:
County of Suffolk               )

      On this 13th day of February, 2001, before me personally came Ronald
Nordin, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.

[Notary Seal]                                  /s/ Kyle Walkden
                                               ----------------
                                               Notary Public

                                               My commission expires: 9/9/05



CUSIP No. 17252Y104              13G                 Page  11  of  11  Pages
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      IN WITNESS WHEREOF, this Power of Attorney has been signed as of the 1st
day of February, 2002.

                                               /s/ Axel Bichara
                                               ------------------------------
                                               Axel Bichara

Commonwealth of Massachusetts)
                               ) ss:
County of Suffolk              )

      On this 1/st/ day of February, 2002, before me personally came Axel
Bichara, known to me to be the person described and who executed the foregoing
instrument that he acknowledged that he executed the same.

[Notary Seal]                                  /s/ Stephen TenBarge
                                               --------------------
                                               Notary Public

                                               My commission expires: 10/9/03