CIPHERGEN BIOSYSTEMS, INC. STOCK PURCHASE AGREEMENT

Company, at 650 Page Mill Road, Palo Alto, California 94304 at 9:00 a.m. local time on July 22, 2005 or such other time and date as may be agreed by the parties (the “ Closing Date ”).

3.2                                  Issuance and Delivery .  At the Closing, the Company shall authorize (i) its transfer agent to issue to the Purchaser one or more stock certificates registered in the name of the Purchaser, or in such nominee name(s) as designated by the Purchaser in writing, representing the number of Shares set forth in Section 1.1 above, and (ii) the issuance of a Warrant registered in the name of the Purchaser, or in such nominee name(s) as designated by the Purchaser in writing, for the purchase of the number of shares of Common Stock set forth in Section 1.2 above.  The stock certificates representing the Shares (the “ Certificates ”), and the stock certificates issued upon the Purchaser’s exercise of the Warrant, shall each bear the following legend referring to the fact that the Securities were sold in reliance upon the exemption from registration provided by Section 4(2) of the Securities Act of 1933, as amended (the “ Securities Act ”), and Rule 506 under the Securities Act:

THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), AND HAVE BEEN ISSUED AND SOLD IN RELIANCE UPON THE EXEMPTION FROM REGISTRATION PROVIDED BY SECTION 4(2) OF THE ACT AND RULE 506 PROMULGATED UNDER THE ACT.  THESE SECURITIES HAVE BEEN ACQUIRED FOR INVESTMENT AND NOT WITH A VIEW TO DISTRIBUTION OR RESALE, AND MAY NOT BE TRANSFERRED WITHOUT AN EFFECTIVE REGISTRATION STATEMENT FOR SUCH SECURITIES UNDER THE SECURITIES ACE OF 1933, AS AMENDED, OR PURSUANT TO RULE 144 UNDER SUCH ACT OR AN OPINION OF COUNSEL SATISFACTORY TO THE COMPANY THAT REGISTRATION IS NOT REQUIRED UNDER THE ACT.

The Company will deliver the Certificates in such denominations as requested by the Purchaser against delivery of payment for the Shares by the Purchaser.

3.3                                  Company’s Obligation to Close .  The Company’s obligation to complete the purchase and sale of the Securities shall be subject to the following conditions, any one or more of which may be waived by the Company:

(a)                                   receipt by the Company of same-day funds in the full amount of the purchase price for the Securities being purchased under this Agreement; and

(b)                                  the accuracy in all material respects of the representations and warranties made by the Purchaser and the fulfillment in all material respects of those undertakings of the Purchaser to be fulfilled before the Closing.

3.4                                  Purchaser’s Obligation to Close .  The Purchaser’s obligations to accept delivery of such stock certificates and Warrant, and to pay for the Securities, shall be subject to the

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following conditions, any one or more of which may be waived in writing by the Purchaser with respect to the Purchaser’s obligation:

(a)                                   the representations and warranties made by the Company in this Agreement shall be accurate in all material respects and the undertakings of the Company shall have been fulfilled in all material respects on or before the Closing;

(b)                                  there shall have been no suspension of trading or listing of the Company’s shares of Common Stock on the NASDAQ National Market;

(c)                                   the Company’s board of directors having passed resolutions exempting the purchase of the Securities from (i) the Company’s rights plan; and (ii) the application of Section 203 of the Delaware General Corporation Law; and

(d)                                  the Company shall have delivered to the Purchaser a certificate executed by its Chief Executive Officer and Chief Financial Officer, dated as of the Closing Date, in substantially the form attached hereto as Exhibit B , to the effect that the representations and warranties of the Company set forth in Section 5 hereof are true and correct in all material respects as of the date of this Agreement and as of the Closing Date, and that the Company has complied in all material respects with all the agreements and satisfied all the conditions in this Agreement on its part to be performed or satisfied on or before the Closing Date.

(e)                                   Wilson Sonsini Goodrich & Rosati, PC, counsel to the Company, shall have delivered a legal opinion to the Purchaser reasonably satisfactory to the Purchaer and counsel to the Purchaser.

4.                                        Registration Rights .

4.1                                  Demand Registration .

(a)                                   Subject to subsection (c) hereof, if the Company receives a written request from the Purchaser that the Company effect any registration with respect to all or a part of the Shares or the Common Stock resulting from the exercise of the Warrant (the Shares and Common Stock resulting from the exercise of the Warrant are collectively referred to as the “ Registrable Securities ”), the Company shall:

(i)                                      As soon as practicable, but in no event later than ninety (90) days following the receipt of such request, prepare and file with the Securities and Exchange Commission (the “SEC”) a registration statement on Form S-3 (the “ Registration Statement ”) relating to the resale of the Registrable Securities by the Purchaser from time to time through the automated quotation system of NASDAQ or the facilities of any national securities exchange on which the Common Stock of the Company is then traded or in privately negotiated transactions;

(ii)                                   Subject to receipt of necessary information from the Purchaser, used its commercially reasonable efforts to cause the SEC to notify the Company of its willingness to declare the Registration Statement effective within ninety (90) days after the Registration

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Statement is filed by the Company, and notify the Purchaser of such notification from the SEC within three (3) business days of receipt;

(iii)                                Promptly prepare and file with the SEC such amendments and supplements to the Registration Statement and the prospectus used in connection therewith as may be necessary to keep each Registration Statement effective until the earlier of (i) 120 days following the date on which the registration first became effective, or (ii) such time as all Registrable Securities held by the Purchaser have been sold pursuant to a registration statement (the “ Registration Period ”);

(iv)                               So long as the Registration Statement is effective covering the resale of Registrable Securities owned by the Purchaser, furnish to the Purchaser with respect to the Common Stock registered under the Registration Statement such reasonable number of copies of prospectuses and such other documents as the Purchaser may reasonably request, in order to facilitate the public sale or other disposition of all or any of the Registrable Securities by the Purchaser;

(v)                                  File documents required of the Company for normal blue sky clearance in states specified in writing by the Purchaser; provided, however, that the company shall not be required to qualify to do business in any jurisdiction in which it is not now so qualified;

(vi)                               Bear all expenses in connection with the procedures in subsection (a) of this section 4.1 and the registration of the Registrable Securities pursuant to the Registration Statement, other than fees and expenses, if any, of counsel or other advisers to the Purchaser or brokerage fees and commissions incurred by the Purchaser, if any.  Notwithstanding anything to the contrary herein, the Company shall not be required to pay for any expenses of any registration proceeding if the registration request is subsequently withdrawn at the request of the Purchaser unless the Purchaser agrees to forfeit their right to a demand registration pursuant to hereto; and

(vii)                            Notwithstanding the foregoing, (i) the Company shall not be obligated to effect a registration pursuant to this Section 4.1 during the period starting with the date sixty (60) days prior to the Company’s estimated date of filing of, and ending on a date sixty (60) days following the effective date of, a registration statement pertaining to an underwritten public offering of the Company’s securities, provided that the Company is actively employing in good faith all reasonable efforts to cause such registration statement to become effective and that the Company’s estimate of the date of filing such registration statement is made in good faith, and (ii) if the Company shall furnish to such Holders a certificate signed by the President of the Company stating that in the good faith judgment of the Board of Directors it would be seriously detrimental to the Company or its shareholders for a registration statement to be filed in the near future, then the Company’s obligation to use its best efforts to file a registration statement shall be deferred for a period not to exceed one hundred twenty (120) days.

(viii)                         If the Purchaser intends to distribute the Registrable Securities covered by their demand by means of an underwriting, they shall so advise the Company as part of their demand made pursuant to this Section 4.1, and the Company shall include such information in

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the notice referred to in Section 4.1(a) above.  The Company shall, together with the Purchaser, enter into an underwriting agreement in customary form with the underwriter or underwriters selected by the Purchaser and reasonably satisfactory to the Company.  If the underwriter has not limited the number of Registrable Securities to be underwritten, the Company may include securities for its own account (or for the account of other shareholders) in such registration if the underwriter so agrees and if the number of Registrable Securities that would otherwise have been included in such registration and underwriting will not thereby be limited.

(b)                                  With a view to making available to Purchaser the benefits of Rule 144 under the Securities Act (“ Rule 144 ”) (or its successor rule) and any other rule or regulation of the SEC that may at any time permit Purchaser to sell the Registrable Securities to the public without registration, the Company covenants and agrees to: (i) make and keep public information available, as those terms are understood and defined in Rule 144, until such date as all of Purchaser’s Registrable Securities shall have been resold; (ii) file with the SEC in a timely manner all reports and other documents required of the Company under the Securities Act and under the Securities Exchange Act of 1934 (the “ Exchange Act ”); and (iii) furnish to Purchaser upon request, as long as Purchaser owns any Securities, (A) a written statement by the Company that it has complied in all material respects with the reporting requirements of the Securities Act and the Exchange Act, and (B) such other information as may be reasonably requested in order to avail Purchaser of any rule or regulation of the SEC that permits the selling of such Registrable Securities without registration;

(c)                                   The Company shall not be obligated to effect, or to take any action to effect, any registration pursuant to this Section 4.1:

(i)                                      During the first twelve (12) months following the Closing Date;

(ii)                                   During the one hundred eighty (180) day period following the effective date of the first Registration Statement filed pursuant to this Section 4.1;

(iii)                                After the Purchaser has made two (2) demands for registration pursuant to this Section 4.1, and such demands have been declared or ordered effective by the SEC;

(iv)                               If Purchaser holds 3% or less of the outstanding Common Stock of the Company, after the date on which the Purchaser is able to immediately sell all Registrable Securities held or entitled to be held by the Purchaser under Rule 144; or

(v)                                  At any time after the tenth anniversary of the date of this Agreement; provided however , should the Company postpone an offering pursuant to Section 4.1(a)(vii), or suspend an offering by the issuance of a Suspension Notice (as such term is defined herein) the expiration date hereof shall be extended by the time of such postponement or suspension (as applicable).

4.2                                  Piggy-Back Registration .

(a)                                   If, at any time prior to the date which is two (2) years from the date hereof, the Company proposes to file with the SEC a registration statement relating to an offering of

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any of its securities for its own account or the account of security holders exercising their demand registration rights (other than on Form S-4 or Form S-8 or their then equivalents relating to securities to be issued solely in connection with an acquisition of any entity or business or equity securities issuable in connection with stock option or other employee benefit plans), the Company shall promptly send to the Purchaser written notice of the Company’s intention to file such a registration statement and of such Purchaser’s rights under this Section 4.2 and, if within fifteen (15) days after receipt of such notice, such Purchaser shall so request in writing, the Company shall include in such registration statement all or any part of the Registrable Securities such Purchaser requests to be registered.  No right to registration of Registrable Securities under this Section 4.2 shall be construed to limit any registration rights granted under Section 4.1.

(b)                                  The Company shall bear and pay all expenses incurred in connection with any registration, filing or qualification of Registrable Securities with respect to the registrations pursuant to Section 4.2, including all registration, filing, and qualification fees, printers and accounting fees relating or apportionable thereto, and the reasonable fees and expenses of counsel for Purchaser.

(c)                                   If the registration of which the Company gives notice is for a registered public offering involving an underwriting, the Company shall so indicate in the notice given pursuant to this Section 4.2.  In such event the right of any Purchaser to registration pursuant to this Section 4.2 shall be conditioned upon Purchaser’s agreeing to participate in such underwriting and in the inclusion of such Purchaser’s Registrable Securities in the underwriting to the extent provided herein.  The Purchaser shall (together with the Company and the other holders distributing their securities through such underwriting) enter into an underwriting agreement in customary form with the underwriter or underwriters selected for such underwriting by the Company or by other holders exercising any demand registration rights.  Notwithstanding any other provision of this Section 4.2, if the underwriter determines that marketing factors require a limitation of the number of shares to be underwritten, the underwriter may exclude some or all Registrable Securities or other securities from such registration and underwriting (hereinafter an “ Underwriter Cutback ”).  In the event of an Underwriter Cutback, the Company shall so advise the Purchaser and the other holders distributing their securities through such underwriting, and the number of Registrable Securities that may be included in the registration and underwriting shall be allocated in proportion, as nearly as practicable, to the respective amounts of Registrable Securities held by the Purchaser and those certain Holders having piggy-back registration rights set forth in the Fourth Amended and Restated Investors Rights Agreement dated as of March 3, 2000 at the time of filing the registration statement.  If the Purchaser disapproves of the terms of any such underwriting, the Purchaser may elect to withdraw therefrom by written notice to the Company and the underwriter.  Any securities excluded or withdrawn from such underwriting shall be withdrawn from such registration.

4.3                                  Indemnification .  In the event any Registrable Securities are included in a Registration Statement under this Section 4:

(a)                                   To the extent permitted by law, the Company will indemnify and hold harmless the Purchaser, each of the Purchaser’s officers, directors and agents, each person who participates in the offering of the Registrable Securities, including underwriters (as defined in the Securities Act) and each person, if any, who controls the Purchaser (or other participating person)

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within the meaning of the Securities Act, or the Exchange Act, against any losses, claims, damages, or liabilities (joint or several) to which they may become subject under the Securities Act, the Exchange Act, or other federal or state law, insofar as such losses, claims, damages, or liabilities (or actions in respect thereof) arise out of or are based upon any of the following statements, omissions or violations (collectively a “ Violation ”): (i) any untrue statement or alleged untrue statement of a material fact contained in such registration statement, including any preliminary prospectus or final prospectus contained therein or any amendments or supplements thereto, including any information deemed to be a part thereof as of the time of effectiveness pursuant to paragraph (b) of Rule 430A, or pursuant to Rule 434, of the Rules and Regulations, or the prospectus, in the form first filed with the SEC pursuant to Rule 424(b) of the Regulations, or filed as part of the Registration Statement at the time of effectiveness if no Rule 424(b) filing is required (the “ Prospectus ”), or any amendment or supplement thereto (ii) the omission or alleged omission to state therein a material fact required to be stated therein, or necessary to make the statements therein not misleading, or (iii) any violation or alleged violation by the Company of the Securities Act, the Exchange Act, any state securities law or any rule or regulation promulgated under the Securities Act, or the Exchange Act, or any state securities law; and the Company will pay to the Purchaser or controlling person, any legal or other expenses reasonably incurred by them in connection with investigating or defending any such loss, claim, damage, liability, or action; provided, however, that the indemnity agreement contained in this subsection 4.3(a) shall not apply to amounts paid in settlement of any such loss, claim, damage, liability, or action if such settlement is effected without the consent of the Company (which consent shall not be unreasonably withheld), nor shall the Company be liable in any such case for any such loss, claim, damage, liability, or action to the extent that it arises out of or is based upon the Company’s reliance upon written information furnished expressly for use in connection with such registration by the Purchaser or an officer, director or agent thereof,

(b)                                  To the extent permitted by law, of the Purchaser will, if Registrable Securities held by such Purchaser are included in the registration, indemnify and hold harmless the Company, each of its directors, each of its officers who has signed the registration statement, each person, if any, who controls the Company within the meaning of the Act, against any losses, claims, damages, or liabilities (joint or several) to which any of the foregoing persons may become subject, under the Securities Act, the Exchange Act, or other federal, state law, insofar as such losses, claims, damages, or liabilities (or actions in respect thereto) arise out of or are based upon the Company’s reliance upon written information furnished by the Purchaser expressly for use in connection with such registration; and the Purchaser will pay, as incurred, any legal or other expenses re