SUPPORTING INFORMATION
Electron transfer followed by collision-induced dissociation (NET-CID)
for generating sequence information from backbone modified
oligonucleotide anions
Yang Gao and Scott A. McLuckey*
Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA
*Correspondence to: S. A. McLuckey, Department of Chemistry, Purdue University, 560
Oval Drive, West Lafayette, IN 47907-2084, USA.
E-mail: mcluckey@purdue.edu
Figure S1. (a) Summary of the total contributions from a-, d-, w-, and z-ions to the
product ion spectrum of Fig. 1(b) of the main text. (b) Breakdown of contributions of the
various ion types according to linkage site.
1
a
d
0.5
w
z
0
1
0.2
a
d
0.1
w
z
0
1
2
3
4
5
6
7
8
9
10
11
fA dA dC fC dC fC dG fG dA fA dG fG
Figure S2. (a) Summary of the total contributions from a-, d-, w-, and z-ions to the
product ion spectrum of Fig. 2(b) of the main text. (b) Breakdown of contributions of the
various backbone ion types according to linkage site.
1
a
d
0.5
w
z
0
1
0.25
a
d
0.125
w
z
0
1
2
3
4
5
6
7
8
9
dA mC dG dT dC fC dG mA dT dG
Figure S3. Isotopic distribution of base loss peaks from ion trap CID of [M–4H]3–• of 2'-
[M-4H-CH]3-•
[M-4H-C•]3-
[M-4H-AH]3-•
[M-4H-A•]3-
150
[M-4H-GH]3-•
Intensity (Arb. Unit)
300
[M-4H-G•]3-
(F, H,OMe) mix-mer.
0
982
984
986
988
990
m/z
992
994
996
998
Figure S4. MS/MS product ion spectrum of 2'-(F, H) mix-mer. Ion trap CID of
d113-
w3d103w10
w52-
w73- d73-
-GH
-CH -AH
4-∙
d3- [M-5H]
z62a72--B
w933d62-
a62-
d42- d2
w32-
a2--B
150
a3--B
d52-
w42a52--B
fA dA dC fC dC fC dG fG dA fA dG fG
d1w1-
Intensity (Arb. Unit)
300
w83-
a93--B
[M–5H]4–•, excitation amplitude was set to 450 mV.
0
300
400
500
600
700
800
m/z
900
1000
1100
1200
Figure S5. MS3 product ion spectrum of a3-ions (A*CC) from generated from ion/ion
a3-
reaction between [M–3H]3– of PS 6-mer (A*CC*GA*G) and [CuII(phen)2] 2+.
a3--B
90
d2-
*CC-
Intensity (Arb. Unit)
180
0
500
550
600
650
700
m/z
750
800
850
Figure S6. Ion trap CID of the PS 2'-OMe 6-mer (mA*mCmC*mGmA*mG) of different
charge states: (a) 3- charge state, 120.45 kHz, 180mV; (b) 4- charge state, 161.85kHz,
180 mV. Excitation amplitude was set at the level at which 80% of the precursor ions
were fragmented.
c32-
a.
d533-AH x5
2y4
[M-3H]3-
mA * mC mC * mG mA * mG
[M-4H]4-
650
x32-
800
850
x3-
y3-
b3-A
b53-
c2x2a5 -B c42-
z42-
b32y32-
450
c32-
b.
b32-
0
1600 250
xw1- 1
c1y1-
Intensity (Arb. Unit)
1250
x32-
y32-
2500
1050
1250
mA * mC mC * mG mA * mG
0
250
450
650
850
m/z
1050
1250
Figure S7. MS/MS product ion spectrum of PS 2'-OMe 6-mer ([M–3H]3–) reacting with
[CuII(phen)]2+. Δ represents the triply deprotonated anion with the plasticizer adduct that
[M-3H]2-∙
+Cu
is commonly seen in an ion trap.
[M-3H]3-
x2 ~
w3-
w1-
d52-
w52-
200
~ X1.7
+O2
~
mA * mC mC * mG mA * mG X1.2
d1-
Intensity (Arb. Unit)
400
Δ
0
300
400
500
600
700
m/z
800
900
1000
1100
1200
Figure S8. MS/MS product ion spectra of 2'-OMe 6-mer. (a) ion trap CID of [M–3H]2–•,
excitation amplitude was set to 550 mV; (b) product ion spectrum of [M–3H]3– reacting
with [CuII(phen)]2+. (c) and (d) are the zoomed-in spectra at the [M–3H]2–• peak showing
[M-3H]2-∙
400
350
300
c.
250
200
200
150
100
0
50
0
988
989
988 989
990
990
991
992
991 992
[M-3H][M-3H+Cu]-
400
- +O
2
w3- d3
w52-
a3-
w2- d2
d52-
a2-
d1-
w1-
150
0
[M-3H]2-∙
b.
250
400
[M-3H]2-∙
d.
200
150
200
[M-3H]3-
150
150
100
50
00
988
989
988 989
990
1300
1500
990
991
992
991 992
[M-3H+Cu]-
300
300
[M-3H]-
Intensity (Arb. Unit)
~
a.
[M-3H]3x2
300
-32 [M-3H]2-∙
that the fragments come from the radical anion species.
0
300
500
700
900
1100
m/z
1700
1900
2100