Ownership Submission
FORM 4
Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).
UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP OF SECURITIES

Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940
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(Print or Type Responses)
1. Name and Address of Reporting Person *
Fort Mason Capital, LLC
   2. Issuer Name and Ticker or Trading Symbol
NANOGEN INC [NGEN] 		5. Relationship of Reporting Person(s) to Issuer
(Check all applicable)
_____ Director __X__ 10% Owner
_____ Officer (give title below) _____ Other (specify below)
(Last)
(First)
(Middle)
456 MONTGOMERY STREET, 22ND FLOOR		 3. Date of Earliest Transaction (Month/Day/Year)
09/28/2005
(Street)

SAN FRANCISCO, CA 94104		 4. If Amendment, Date Original Filed(Month/Day/Year)
10/12/2005		 6. Individual or Joint/Group Filing(Check Applicable Line)
_X_ Form filed by One Reporting Person
___ Form filed by More than One Reporting Person
(City)
(State)
(Zip)
Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1.Title of Security
(Instr. 3)		 2. Transaction Date (Month/Day/Year) 2A. Deemed Execution Date, if any (Month/Day/Year) 3. Transaction Code
(Instr. 8)		 4. Securities Acquired (A) or Disposed of (D)
(Instr. 3, 4 and 5)		 5. Amount of Securities Beneficially Owned Following Reported Transaction(s)
(Instr. 3 and 4)		 6. Ownership Form: Direct (D) or Indirect (I)
(Instr. 4)		 7. Nature of Indirect Beneficial Ownership
(Instr. 4)
Code V Amount (A) or (D) Price
Common Stock, par value $0.001 per share 09/28/2005   S   8,119 D $ 3.07 5,093,922 I By Limited Partnerships
Common Stock, par value $0.001 per share 09/28/2005   S   3,308 D $ 3.08 5,090,614 I By Limited Partnerships
Common Stock, par value $0.001 per share 09/28/2005   S   9,917 D $ 3.21 5,080,697 I By Limited Partnerships
Common Stock, par value $0.001 per share 09/28/2005   S   299 D $ 3.24 5,080,398 I By Limited Partnerships
Common Stock, par value $0.001 per share 09/28/2005   S   2,937 D $ 3.25 5,077,461 I By Limited Partnerships
Common Stock, par value $0.001 per share 09/29/2005   S   11,226 D $ 3.07 5,066,235 I By Limited Partnerships
Common Stock, par value $0.001 per share 09/29/2005   S   837 D $ 3.08 5,065,398 I By Limited Partnerships
Common Stock, par value $0.001 per share 09/29/2005   S   5,742 D $ 3.09 5,059,656 I By Limited Partnerships
Common Stock, par value $0.001 per share 09/29/2005   S   1,931 D $ 3.1 5,057,725 I By Limited Partnerships
Common Stock, par value $0.001 per share 09/29/2005   S   400 D $ 3.12 5,057,325 I By Limited Partnerships
Common Stock, par value $0.001 per share 10/04/2005   S   1,131 D $ 3.1 5,056,194 I By Limited Partnerships
Common Stock, par value $0.001 per share 10/04/2005   S   1,307 D $ 3.12 5,054,887 I By Limited Partnerships
Common Stock, par value $0.001 per share 10/04/2005   S   477 D $ 3.13 5,054,410 I By Limited Partnerships
Common Stock, par value $0.001 per share 10/05/2005   S   937 D $ 2.99 5,053,473 I By Limited Partnerships
Common Stock, par value $0.001 per share 10/05/2005   S   1,913 D $ 3 5,051,560 I By Limited Partnerships
Common Stock, par value $0.001 per share 10/06/2005   S   3,313 D $ 2.95 5,048,247 I By Limited Partnerships
Common Stock, par value $0.001 per share 10/06/2005   S   2,048 D $ 2.96 5,046,199 I By Limited Partnerships
Common Stock, par value $0.001 per share 10/07/2005   S   937 D $ 2.94 5,045,262 I By Limited Partnerships
Common Stock, par value $0.001 per share 10/07/2005   S   731 D $ 2.95 5,044,531 I By Limited Partnerships
Common Stock, par value $0.001 per share 10/07/2005   S   100 D $ 2.96 5,044,431 I (1) (2) By Limited Partnerships (1) (2)

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Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned
(e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security
(Instr. 3)		 2. Conversion or Exercise Price of Derivative Security 3. Transaction Date (Month/Day/Year) 3A. Deemed Execution Date, if any (Month/Day/Year) 4. Transaction Code
(Instr. 8)		 5. Number of Derivative Securities Acquired (A) or Disposed of (D)
(Instr. 3, 4, and 5)		 6. Date Exercisable and Expiration Date
(Month/Day/Year)		 7. Title and Amount of Underlying Securities
(Instr. 3 and 4)		 8. Price of Derivative Security
(Instr. 5)		 9. Number of Derivative Securities Beneficially Owned Following Reported Transaction(s)
(Instr. 4)		 10. Ownership Form of Derivative Security: Direct (D) or Indirect (I)
(Instr. 4)		 11. Nature of Indirect Beneficial Ownership
(Instr. 4)
Code V (A) (D) Date Exercisable Expiration Date Title Amount or Number of Shares

Reporting Owners

Reporting Owner Name / Address Relationships
 Director  10% Owner  Officer  Other
Fort Mason Capital, LLC
456 MONTGOMERY STREET
22ND FLOOR
SAN FRANCISCO, CA 94104		     X    

Signatures

 /s/ Dan German, Managing Member   10/31/2005
**Signature of Reporting Person Date

Explanation of Responses:

* If the form is filed by more than one reporting person, see Instruction 4(b)(v).
** Intentional misstatements or omissions of facts constitute Federal Criminal Violations. See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
(1) Fort Mason Master, LP, a Cayman Islands limited partnership ("Master"), and Fort Mason Partners, LP, a Delaware limited partnership ("Partners" and, together with Master, the "Funds"), are the holders of, in the aggregate, 5,044,431 shares of the common stock, par value $0.001 per share (the "Shares"), of Nanogen, Inc., a Delaware corporation (the "Company"). In addition, the Funds are the holders of warrants that entitle the Funds to purchase up to an aggregate of 765,306 additional Shares. The Funds acquired such Shares and warrants in a registered direct offering of up to 6,802,721 units at $2.94 per unit, with each unit consisting of (i) one (1) Share and (ii) one (1) warrant to purchase 0.15 Shares. Fort Mason Capital, LLC, a Delaware limited liability company ("Capital"), serves as the investment manager of the Funds and possesses sole power to vote and direct the disposition of all securities of the Company held by the Funds.
(2) Thus, as of October 7, 2005, for the purposes of Reg. Section 240.13d-3, Capital is deemed to beneficially own 5,809,737 Shares. Capital's interest in the securities reported herein is limited to the extent of its pecuniary interest in the Funds, if any.

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