Exhibit
10.2


	
     CONFIDENTIAL TREATMENT
  REQUESTED

  	
   

  	
  Bruker
  Confidential

  
	
  UNDER 17 C.F.R. §§ 200.80(b)4, AND 240.24b-2

  	
   

  	
   

  



 


AMENDMENT NO. 1


This Amendment No. 1 (the “Amendment”) amends
the  MANUFACTURING,
COMMERCIALIZATION AND DEVELOPMENT AGREEMENT (the “Agreement”)
entered into as of July 31, 2006 between ISIS
PHARMACEUTICALS, INC., a Delaware corporation, through its IBIS BIOSCIENCES division (“Ibis”), and BRUKER DALTONICS INC., a Delaware
corporation (“Bruker”) and is effective on the date both parties have signed
below.


BACKGROUND


T5000 System: Over the
past several months, Ibis has further refined, developed and replaced the Ibis
T5000 System as described in the Agreement based on customer input and
need.  The instrument described and
outlined in the Agreement was enhanced to include automation systems which
allow the user to more easily run assays on the instrument.  Therefore, this Amendment to the Agreement is
agreed to, as the revenue sharing terms in Article 5 of the Agreement were
based on the non-automated basic T5000 System.


Article 5 of the Agreement is therefore
amended to fairly compensate each party for the enhancements included in this
upgraded version of the Ibis T5000 System with a targeted average list price of
$[***], targeted average selling price of $[***] and a targeted discount price
of $[***].


Ibis Consumables:  Some of the  consumables for the T5000 System presently still require
[***] and logistics.  Ibis and Bruker
agree that it will be a [***] to make all Ibis Consumables available in a [***]
format by [***] or earlier, so that the expense and complexity of [***] and
logistics can be eliminated.


Moreover, as Ibis Consumables are only becoming products over time in
[***], it is clear that a major part of the early European market development
in [***] will require Bruker to demonstrate the Ibis T5000 process and
instrumentation in the applications laboratory in Bremen to potential European
customers and collaborators. This Bruker applications lab itself will therefore
be a significant consumer of Ibis Consumables, and needs access to Ibis
Consumables [***] for potential customer demonstrations.


In consideration of the foregoing premises, the mutual covenants
contained herein and other good and valuable consideration, the receipt and
sufficiency of which are hereby acknowledged, the parties hereto, intending to
be legally bound, hereby agree to amend the Agreement, in accordance with
Article 15.10 of the Agreement, as follows:













AMENDED OR NEW ARTICLES AND DEFINITIONS


Amended Definition: 
Exhibit A of the Agreement is amended as follows:


“T5000 Systems” means the fully integrated, automated system comprising a MicrOTOF, an
Ibis Amplicon Desalting Module, the Ibis Analytical Systems, the Thermo CRS
robot, mircotiter plate ‘hotel’ and related automation accessories, and other
computers and hardware, as more fully described in Schedule 3, as updated from
time to time by written agreement of the parties.  “T5000 Systems” does not include Ibis
Consumables.  “T5000 Systems” includes
new versions of the T5000 System as it exists as of the Effective Date, as well
as successor products designed to perform mass spectrometry analysis of
PCR products, but excluding any systems exclusively used for IVD Use.


The
updated list of components representing the Ibis “T5000 Systems” described
herein is an Attachment A to this Amendment.


Article
5.1 through and including 5.5 of the Agreement are replaced in their entirety
by the following:


5.1                             Sales
of T5000 Systems (Full Bruker Participation).  With respect to each sale of a T5000 System
for which (a) Bruker sells, delivers and Installs, trains End Users on,
services and supports and provides Updates for such T5000 System (all as
contemplated by the Commercialization Plan) and (b) Ibis fulfills its
obligations as contemplated by the Commercialization Plan with respect to such
T5000 System, Bruker will pay Ibis the following amounts, which amounts will be
cumulative and in addition to any other payments to be made to Ibis under this
Agreement:


For Ibis T5000 System Sales in
North America, Europe, and the Middle East:  Bruker will receive the first $[***] of the
total amount received from the sale of a T5000 System, for the manufacture,
delivery, installation and warranty of the Ibis T5000 System. Then, to the
extent available from the remainder of the amount received from such T5000
System sale, Bruker will pay Ibis $[***]. 
Finally, following such payments to Bruker and Ibis, for T5000 System
sales in North America, Ibis and Bruker will [***] ([***]%) any remainder of
the sale price received for such T5000 System, and for T5000 System sales in
Europe and the Middle East, Ibis and Bruker will divide any remainder of the
sale price received for such T5000 System by providing [***]% of such remainder
to Ibis and [***]% of such remainder to Bruker, excluding shipping, taxes and
other ancillary payments of revenue.


However, notwithstanding
the foregoing, Bruker may negotiate sales of the T5000 System at its option
provided Ibis receives the minimum amount of $[***] per system on Bruker
negotiated sales, and Ibis may negotiate sales of the T5000 System at its
option so long as Bruker receives the minimum amount of $[***] per system on
Ibis negotiated sales.


For
clarification, for purposes of Section 5.1(b), Ibis’ obligations under the
Commercialization Plan are not specific to particular sales or deployments of
T5000 



 2
 









Systems,
but rather require Ibis to provide Bruker generally with the Ibis Analytical
Systems installed on a computer that will be integrated with each particular
sale and deployment of a T5000 System.


5.2                               Sales
of T5000 Systems (Other than Full Bruker Participation).  For each sale of a T5000 System for
which  Bruker does not perform all of the
tasks assumable by Bruker as set forth in the Commercialization Plan, Ibis and
Bruker, in accordance with Section 15.10, will determine an equitable
allocation of System Revenues based on obligations assumed by Ibis (either
directly or through a Third Party, including an Ibis Partner).


5.3                               Bruker
Purchase of Ibis Consumables.  Solely
in connection with satisfying its obligations under the Commercialization Plan,
beginning on the Effective Date Bruker may purchase, and Ibis will sell, Ibis
Consumables at [***]% of Ibis’ then current list price for such Ibis
Consumables in the United States. 
However, if Ibis discounts particular Ibis Consumables by more than
[***]% from its current list price in the United States for purchases of the
same or equivalent Ibis Consumables in the same or similar volume, then Bruker
may purchase, and Ibis will sell, Ibis Consumables at [***]% of Ibis average
selling price in the United States for purchases of the same or similar Ibis
Consumables in the same or similar volume. 
Notwithstanding the foregoing, the parties understand and agree that
Ibis may, from time to time, provide discounted Ibis Consumables to customers
who will be supplying data to Ibis for marketing, regulatory or other valuable
purposes or in connection with a significant relationship.  Such discounted Ibis Consumables will not be
included in calculating such average price; provided, however, that in any case
not more than [***]% of Ibis Consumables sales will be excluded from the
calculation of such average price.


During
the start-up phase of the Ibis Consumables business, while the Ibis Consumables
still require [***] and logistics, Ibis will replace consumables which are
damaged due to loss of [***] during shipping. 
This replacement will be limited to a maximum of [***] kits for any
customer or shipment.  Bruker will use
reasonable care in assuring shipments of consumbles requiring [***] are
appropriately packaged and shipped.  Any
reimbursement to Bruker from the carrier for loss of consumables during
shipment of [***] products will be remitted to Ibis.


Ibis will make Ibis
Consumables available to the Bruker demonstration and applications laboratory
for Bruker-internal use only as follows:


i)             For customer
demonstrations: at [***]% of Ibis’ then current list price for such Ibis
Consumables in the United States, limited to a maximum of [***] kit per
demonstration.


5.4                               Extended Warranty.  (a) For each Extended Warranty sold to an End
User located in the North American Territory, Bruker will pay Ibis [***]% of
Extended Warranty Revenues, but in no event less than $[***] for each year of
coverage under such Extended Warranty (unless specifically authorized in
writing by the Ibis President for any particular End User or any particular
defined business incentive) and (b) for each Extended Warranty sold to an End User
located outside the North American Territory, Bruker will pay Ibis [***]% 



 3
 









                                                of
Extended Warranty Revenues, but in no event less than $[***] for each year of
coverage under such Extended Warranty (unless specifically authorized in
writing by the Ibis President for any particular End User or any particular
defined business incentive).  Bruker
acknowledges and agrees that these payments are tied to each Extended Warranty
sold to an End User for each T5000 System purchased by such End User for each
year of coverage under such Extended Warranty. 
For clarification, (c) for purposes of Section 5.4(a), Ibis’ obligations
under the Commercialization Plan with respect to providing Bruker with Renewal
Updates are not specific to particular sales of Extended Warranties, but rather
require Ibis to provide Bruker generally with Renewal Updates that will be
integrated with each particular sale of an Extended Warranty and (d) Bruker has
no obligation to compensate Ibis for providing Renewal Updates other than as
set forth in Section 5.4(a) and (b).


 


# # #




IN WITNESS WHEREOF, the parties have caused
this Amendment to be executed by their duly authorized representatives.


 


	
  Isis Pharmaceuticals, Inc.

  	
  Bruker Daltonics, inc.

  
	
  By: 

  	
  /s/ Michael J. Treble

  	
   

  	
  By: 

  	
  /s/ Gary Kruppa, Ph.D.

  	
   

  
	
  Name: 

  	
  Michael J. Treble

  	
   

  	
  Name: 

  	
  Gary Kruppa, Ph.D.

  	
   

  
	
  Title: 

  	
  President, Ibis Biosciences, Inc.

  	
   

  	
  Title: 

  	
  Vice President, Bruker
  Daltonics,Inc.

  	
   

  
	
  Date: 

  	
  May 15, 2007

  	
   

  	
  Date: 

  	
  May 22, 2007

  	
   

  



 



 4
 









Attachment A


List of Ibis T5000 System Components


Item


 


[***]


[***]


[***]


[***]


[***] 


[***]


[***]


[***]


[***]


[***]


 



 5