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Case 1:04-cv-01230—G|\/IS Document 59-23 Filed 11/18/2005 Page 1 0f4
m.m-z4a94s9-1

Case 1:04-cv-01230—G|\/IS Document 59-23 Filed 11/18/2005 Page 2 of 4
In The Matter Of:
APPLERA CORE 22.
MI CROIILFSS
DONALD DOUGLAS
August 24, 2001
AFINK G CARNE Y __
REPORTING VIDEO SERVICES
S 39 WEST.37TH STREET
E NEW/YORRQ NY USA 10018
(212) 869-1500 OT (800) 692——_5’465
OrigfnalF1’l'•2 010824012 TX]; 250 Pages
Mm-Uismpze File IDr196626G379
.
Word Index included with this Min·U~Se1·ipt®
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APL 015475

Case 1 :O4—cv—O1230-GI\/IS Document 59-23 Filed 11/18/2005 Page 3 of 4
-t CONFIDENTIAL I
I MPM °°'“’- tt piliiiilttsptsttctivt ¤<>~A¤> ¤¤¤¤w
MZICROMASS ORDER August 24, 2.001
Page 396 W Page 399
·_ in next sentence: [1; Q: In traps. ,
to “Wi*¤ =¤ i¤¤ ¤”=P· *0**5 °l”=
.s or sclcctcd rangc of mass to charge ratios ei 0: Aim we have a5o`itoii`H tlte`Y diiééttéii. Correct? "I ‘ `
at are trapped or time rm ¤ pcimd ¤t
[S} time (which can be quite lengthy) duo to ts} Q: And titcn, the thrccmliutensional aspect, is that
ts; electric fields generated with [is; from the motion in the Z or Z direction?
3 tn electrodes " {fj Correct?
‘ ia: oc you =g¤=¤ with ghmmrcmcntt
ts; POP0él§;G;Ob]ect1on.Vaguc. g 3: Okay.A.nd in the lmear quadrupole we have motion
{to] Wl IN : es. not in IC X direction. Correct?
r··= MR-» S¤H¤=§¤= _ _
#4 [12} Q: Okay Do you agree that that disungutshcs an ion [1;; ` _ Q: rr1otign'in`tl1erYAdirection. Correct? _ q ` _, M q
r¤=·¤ mtv f¤¤¤’¤ ¤=·¤ ¤w¤=¤¤¤ wt vw <¤it<¤¤<>¤¤¤ in ¤·¤
et tw] 756 patent? [ta] Q: And we have no Z or Z direction. Right?
"" QM; P2,P°"S‘f" °"l°°“°"· "“g“" @**5 ’°' "*’°““'”“°“·
i ‘ tml im ¤ ¤H °°¤¤ **$i°¤i
S tm THE WITNESS: It was two parts to the sentence. lt says [17] Q: Okay. So, it's —- MatI1c::s:»:ttica1ly,wI1en people are
:7 {ta] ions are trapped and stored for a period of time, {ta; discussing motion -—— ion motion in a linear
T [to] which ctn he quitelengt11y:'i`hat’s very different [lll] quztdrupole, they ignore the motion in the Z
j 3 [zo] Rom the ion guicIc.tBut both ion guides and tmps [zo; direction. lsn't that right? ` _
“ " gat] have electric fields gencmted with electrodes. tan MFI. PDPOVSKI: Objeetion.Vague,:utd calls for speculation.
L_ [22] MR- SCHUI-ER: [22} THE WITNESS: No Wei], wh:tt’s the simple B.l'l!iVv‘ClCT}\C1'C is
{za] 0: So, the fact that an RF Held is generated with an [za; no simple answer, because the Z motion determines,
[241 eIc<:trodc,as opposed to a rod set, is not a [24; for example, how long the ions spend in the linear
·--5 tas] distinguishing feature between on ion img and the [as) guadrugole, and that's an irogortam variable. So,
ogo 397 Pago 400
. I1} 736 invention? {:3 the Zmotion is still important, so people do
I {2} MR. POPOVSKI: Objection. Mischaracterizes. Calls for {2] think about its So, it“s not quite correct to say
.. I my legal conclusions. [:1] that nobody is concerned about the Z motion.
ps] THE lNiT`N§SS: Yes, it’s a very different devicer lt's a {4] MR. SCHULER:
-·; ts} three dimensional —— It stores tons in three , [sj O: But as far as performing its function, the Z
t [ta} dimensions, or conlines ions in three dimensions; {ts] direction is important in the quadrupole ion trap
g rn whereas, asion guide only confines ions in two pq because you're confining them within the trap.
ta) dimensions. .· tu] ls that right?
wr Mit S¤HULEF¤=
tw; G: Do you agree with me that a device that stores {tot"- A "Nilii.`i$6l$ClVS`Kl:'Olj]EctioH`.`Va`jjue; ``'' ` `'`````'`'``` { ```'``````''`'````'-'``A`-` ` `````.
E mj ions in electric tieitls is fundamentally different {11] THE WITNESS: Well,} mean -—··-
__ [sz; from what is claimed in the 736 patent? nz] MRM SCHULEFI:
{st tjé Q,?1Qg’g§g*;gtgih¤bi¤¤¤¤¤; "¤sy¤—- . U 736 tgt ......., .... ...... ,. t»......,....... . ....... . ........,...... . ..r.., t ._..... . ......, , .........
*-*1 = ·= · •=*<='$ tw =¤¤ S ¤¤¤¤<= m *¤ ....
its t>=¤¤¤t-»
; us; MR. SCHULEH: tts] Q: {md it's true that in both ion traps and in
[17] Q: So, an ion guide that has some trapping would not tm quadrupole mass anaiysers, or quadrupole Eeids
- ; uu; be practicing the invention that you disclosed in [tn] that the motion of an ion in any one direction is ` ‘
. [19} the 756 patent? {to] independent ofits motion in the other dire•:t.ion..
g [zu; MH. ROPOV$K}: Ob§ection.C:tIls for a conclusion — Calls rec] Correct? _
‘ {21] for legal conclusions. Speeulationjtnd the [zz] MR. POPOVSKI: Objection. Calls for speculation.
(22] question is vague. [22] THE WITNESS: In on itiml device, yes.
{za; THE WITNESS: Theres nothing in the 736 patent about [zz] MR. SCHULER:
3 {2-1] trapping. ` [24] Q: Okay. Ideal meaning that the lields are properly
ui [25; MR. SCHULEFI: ms] generated?
` _ Pogo 398 Page 401
; M ¤= Md vw wcs with this r¤i—¤¤it>¤¤ ==¤¤<==¤<=¤¤ ¤·=·t
55 to it dittitttnvisttcs thc i¤v¤¤ti¤·¤ fwm ¤¤ i¤¤ Mp
A- pt that ions are stored for some period of time in {2] El: Okay And that is in fact how most mathematical
[4; the trap? {4] modelling was done of quedmpole lields.
P ts; MR. POPDVS} E THEWITNESSN h ' th diff RTI MFIPP I i p
:5 ts; : o,t ere s o er erences, as we . tcre {ts] . D OVSK : Ob'ection..C:.1lls for s ecuIation..The
5 . m are other differences, as well. V m question is vague.
[at ` MFL SCHULEFI: {H] THE WITNESS: °lltat‘s how the simplest models Of tmps are
[5; Q: Okay.! realize there may be other differences, {tt] described.
E not but do you agree that that one differenee,in and {tu] MR. SCHULER:
$i uu ofitsclf,disti¤1guisl1cs the Schaafarticle and {113 0: And it’s t.rue,is it not, that ifi know the
’ (12; ion tmp from the invention disclosed in the 736 {121 direction -—· the effects of collisions on ion
[sa; patent? l [ta; motion in the X andY direction in an ion trap, l
[us; MH. FDPOVSKI: Objection Calls for legal conclusions, and {1-1; could then apply those matltematical equations,
il; {ts] the question is vague. {ts; with very simple adjustments for the fact that
tts; THE WITNESS: Yeah. I me:m, you are asking mc to make a [ts; it`s a linear quadrupole, to thebelmviour of ions
*‘ tm legal decision.! ea.n’t comment on tl1at.As a tm under the same conditions in a linear quadrupole.
tw; scientist,l would sayt:appir1gions,a.nd not [tat Correct?
pz nu; trapping ions is a big difference. [ts; MR. POPOVSKI: Objection.
Q; R01 MR. SCHULEH: [20} MR. SCHLFLER: Yes, in EI.Hl'lC1.[ qtmtirupole. .
tg [21] Q: Now, you are familiar with the mathematics of [2:1 MH. POPDVSKI: l'l1 object to the question as vague, and
to .... i<2xt.t.a¤i2to>=.t1s.ts,:zsat; ......... V ...,.... - ..... , ...,..., . . rw <==~¤¤f¤r¤t>=¤¤t¤¤¤¤»-
.._. jittiifvv mt : c e uauons mt escr' e an motion in
YM`SQZ,,w,...!..QQQQ;...C,jILQYZQ§];g§.f;.`lQ Y;L.`T.Q;JfiQ§Q. "T°;L`.c ,...Q.;[tl;TL.,L.§...LZ. THE WTINESS Th tt ` U d ¤i¤ X dY
li Ejiuh ___, yye lyute ipytiorijrt the; _____ _____ _)___} I __ _____ {24] :1 linear quadrupole -—— in a linear quadrupole are
il tgt.;} rite-ati:-%A:i%¥eali2§S`ogy·" ;g_.g similar to the equations that describe X rmdY
PINK 8: CARNEY (800) NYC·F1NK (21) Page 596 · Page 401
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Case 1 :O4—cv—O1230-GI\/IS Document 59-23 Filed 11/18/2005 Page 4 of 4
1 ' CONFIDENUAL
i APPLERA "°“"· "· £$§$XZ¤T¤pR¤w¤cw¤w nomm DOUGLA5
g MICROMASS P ORDER August 24, 2001
PBQG 429 _ Pago 423
. 5:] concerning Schzmfin the rccmmimtion proceeding? {1] Do you see that?
#21 MR *°¤P¤V5*<*= 0i¤i·=¤¤<>¤ M*<·=<* md =¤=¤w==¤=<* ¤¤¤¤<=¤>=¤$ ¤m<·-S
T5 1:;] uirczdy. . ia; t Q: Dowifbclowg online 34, it says: ` " l H `````````'` ` ' ` ` ` ` ` "
(.1] THE WITNESS: No one consulted with me- {4; “(AltcrmtivcIy this cam be
H {sy MPL SCHULER: qs; accomplished by placing xr higher voltage
i¤1 °= OF-1Y¤.. ... .],,.]... ,.4 A. .... 4... ... ...... . ........ .. .. . ws ¤¤ vim 52 cr orifcc 50. md ¤¤¤i¤i¤s
[ 2 m grid "70—J”
" [ts; O: Okay. Had they comultcd with you,l mice it you {ng Do you sec thm?
wr W¤¤¤<* *·¤v¤ ¤**=¤¤¤¤S=¤ vw r·¤¤~=¤¤ ¤<·¤¢¤¤i¤¤
;e ¤¤¤1 ¤¤vr»i¤s i¤¤S in ¤ '¤1“”d*’“P°I°?
vv MFL F‘¤*’°V$*<*= <>*¤>i¤¤¤i¤¤~ CMS M sv¤¤¤*¤¤¤¤ Md ¥<‘=s=¤¤
ii ata} conciusions. {123 Q: Ok:1y,And then, {inc 51 —- it"s`tough to sag
{ia] THE WITNESS: I do have il patent for napping ions in :1 [ts] bcc:1useit's in between 50 and 51 — it says:
L gm] linmr quadrupole, but I don*t know when that ·- gm] “An advmumgc of using
{ts} what year that is. _ {15] quadrupole RF only rods as il pre-tmp
j us; (iixhibit 16 for identiiimtionc United States Patent gw] for an ion tmp is that the RF only rods
{sn 5179,278 dntcdjanuzry 12, 1993.) R nv; can store more ions than on ion trap and
_ isa; NIFL SCHULE : {18] cm be used to store ions while the ion
{mg Q: Doctor Douglas,} hzmded you wh:1t's been marked as {to] tmp is performing its zmolysisi"
[20] Douglas Exhibit I6, which, for the record, is {go] D0 you 54;;; {mt? _
‘ r·==¤ U¤i=¤¤ SMS ¥‘=·*¤·=¤ N¤¤¤b==¢ $-179278- ·*¤¤<=¢
m; jmuary 12th, 1983, issued to Donald _|.. Douglas., [zz; CI: And you agree with me that it might be pertinent
Fi pa] it’s entitled Muhipolc Inlet System for Ion [za; to cvaiunting the veracity of Lhesc smtements
[.24] Tmps. gz-1] about the differences between an ion Trap and :m
rr ps] I mke it that you recognize Exhibit ps) A(I·onlg ion guide that :1nAC·o¤1[ion guide
P¤¤¤ **21 Page 424
' isr1..§w%sx..i.§tR9s.t:=2;R92sl&2? .s..,.a.......s..... _ ....................................,....... , _ ...,..... w ==¤¤¤¤¤y ==<¤¤ mp mm i<>¤s ¤¤¤¤ = ¤===fi¤¤¤=·¤
z :21 ¤1¤¤¤¤<1¤ i¤n mp-t
. · gy Q: ls Lhis the patent to which you wcic referring in 2 [sy Correct?
gt] your prrgzvious answer? [4] MR. POPOVSKI; Objcction.C:11ls for speculation, legal
»-7 gs] MR. OPOVSKI: 'Tnke your Limb, and read through it. is] conclusions. "
; is) THE WITNESS: Ok;1y,W”h¤t was the question again? [sj THE WITNESS: Yeah. idon't know how relevant this would be
{7] MR. SCHULEFI: {71 in n {ego! sense.
{ny Q: Very simply, is this the patent to which you were [sy MR. SCHULER:
J?%!.E$*I‘?‘IiT¥!Ti¥i?¥¥.Y9T~?¥ P£$£i9H%.t4€z€EK¢£Z ,... . ....................i.,.. R ....i.., ..,.. ,, M ¤= *~¤ = 5¤i·=¤¤*¤¤ ¤·=¤===· d¤ ww =·s¢=== i= W¤¤*¢ *¤·¤
um r=!==v¤¤¤? _
:111... .... 1.3%% 12232 ..... . ............... , v ¤ MFL ¥’¤*’¤V5*<•= sms ¤¤i¤¤¤¤¤ - ws f¤r ¤1><>¤¤k·¤¤¤» ¤¤s=¤
tm ¤¤¤¤¤¤Si<>¤5-
gas] Q: And do you see that the date ~·» lf you look with E res} THE WITNESS: No,.Scicntilic:sJiy,it‘s differengbecmse
: 514; me on page I of Exhibit 10, it’s dated {ua; in the BD tmp you confine ions in the Z direction
: us} September 30:11 —·~—· the next page -— September BGU1, {11] mdio fre uen tieid, but here :I1ere‘s no RF
fl CY
w$t.1.??Zi ...,.....,.` ...... . .... . .... A ....... , .._. W, ..., , e. .. ...... . ,.... .,, ...........`......,. vo ¤·=¤¤ i¤ ¤»*=<= Z <¤r<=<=¤i¤¤t 5·¤· ¤h== ¤¤=¤m¤i¤s
im m¤¤¤¤·¤i¤¤¤ is ¤iff¤r<=¤¤ —
UPI ...95 HTS: .. . . . . .... . , .. ..... ¤=¤¤ —- in ms Z ¤¤¤=<=¤<>¤» Sm ¤h<= ¤=·:¤n¤¤s
sw r¤<=¤¤¤=¤¤i==¤¤ in mc Z <¤i:¤¤¤¤¤ hw: is ¤¤iff=r=¤¤-
5 ren] Q: Okay So, approximately four years prior to the {zo] MR. SCHULEH:
’·*’ ' {21] submission of Exhibit Number 10 to the Potent gzq Q: You agree with me that it would bc relevant
{22] 0{Ecc, you had patented the idea of utilizing a gu] scientihcaiiy to know thm: zm ion guide can ~
52:1) qtmdrupole ion guide as zm iron tmpl. {zz] function ns :1 trapping mechanism. _
=5_ 524] Correct? , {E4] Correct? -· 1
E5 gas] - MR. PDPOVSKI: Ob`gccti0n.C:1£ls for lcgui conclusions, cmd $25] MR. POPOVSKI: Ob'[CC[i0{I.I*:fiSC[12lfZlCI£1`i.2€$ his [§¥j.,l1}0I1X.
. Page 422 Page 425
{g [1} specuI:1tio1nNE W [1] Besides the fact that it’s i1“rc!cv:1nt,it's vague,
[2} 'FHE Wi SS: c!1,wc did have I1 patent in 19 ····~ rz; and calls for legal conclusions, ’
tj ra} apparently, in 1993 on trapping ions in a linen: [sy THE WITNESS: All I can soy is maybe. i
[43 ion guide. {43 MR. SCHULER:
[51 MR. SCHULER: [5] G: Now,i.f you would tum back with me to -·~ We put
E [s1 Q: And had someone consumed with you about whether [6; it aside awhile ago, and 1 a olo ' c,but it's
, P B12
-. m an ion transmission rod set was fundamentmliy rr] the —·· it’s your articio with Doctor French,
` my different Ijrcm :111 ion tmp prior to making ns] Exhibit 8.
rg! 5¤=¤·=¤¤¤¤¤ ¤¤ ¤1<= *’==¤=¤¤ ¤¥¤¤= in 1997-I ¤k·= it or .. ,.*119 m<¤ass.ha=v= [email protected]¤@ ¤f.x9¤3.. .......A . ... . ...... ., .. ..... . .. .... . ............
{ ¤·¤r You wvuld Mts =¤=·<¤<= um ¤w=¤¤ <>f ¤1¤ f¤<== ¤·—·¤¤ =¤·
3 gu} ion guide can be used as zm ion tmp., gu] Q: Okay. Now, in the Hrst cohurm —·»W<:|1, in the`
ig {12} Correct? E12] obstmct —-~
pcs; MFL POPOVSKI: Ob`ection..Ca1Is for legal conclusions, and ps] Did ou write the absuuct?
M P cum F ..,.,.... W .... ...e...,e.. ¥..5iE5§Bw.ma, ..,,... . ....e.e.e.,.~.e.. .e.e.e..,., { .... s ...Je`..,,...e\....,....`. . W. .,.` .,,...``. . .
5 ~‘= 0*1- 4...d ....... ;i&.;a% ..._.......e.. on ....,.
E ns; THE WHNESS: { might have said that I don't know what this {xs] Q: Ok.:1y_ Do you scc, about midway down in the
? gis; means legally, but maybe you should consider ps; abstract, it says:
{tn this — Imve il look at this, gm "This 'ccilisionai focusing
sts} MR. SCHULEH: {wg appears to be analogous to effects seen ..
is " vm ¤= if you w¤¤1¤ mm ¤¤ ¤¤i¤¤¤¤ 4.1i¤¤ 35 ¤¤ You .. .....,. , ....s...........s....s......,.,..................
`* . im! M if ¤¤¥S=
Eg on "W"h<=n thc quadrupole rods 44 [2.11 __._.`. 9i,.4!1¢.X9!5,E*;£9£%,h£*s%LL ..`. . . ,,., . ...... , ...... .. .. .. ...........»....`... V ........... ..
ml =¤¤ r·¤==¤·=¤ in uw mth ¤f ¤¤¤¤ iw s=¤==¤¤
mg 46 between the ion source 12 and the ion [23} Q: Then, at the bottom of the lirst column on the ·
, {24} tmp 58, the rods 44 cm be used as a (za; left-{umd side, the inst line, there’s :1 sentence
Q, {Z5! lng to store ions"? {as; that begins: .
gg
FINK 8c CARNEY (800) NYGFINK (25) P c 420 ·— P c 425
38
APL 015498