1. Separation and Sequencing of Isomeric Oligonucleotide Adducts using Ion-pair Reversed Phase LC-ESI-MS/MS
and GenoMass Software
Vaneet Sharma,1 James Glick,1 Qing Liao,2 and Paul Vouros 1
1Barnett Institute & Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA; 2Shenitech LLC, Woburn, MA
An efficient high resolution reversed phase - ion pairing- liquid chromatography electrospray ionization tandem mass spectrometry (RP-IP-LC-MS/MS) method for separation of oligonucleotides adducted
with N-acetoxy-N-acetyl-2-aminofluorene (AAAF) or (±)-anti-7r,8t-dihydroxy-9t,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(±)-anti-BPDE] using a polymeric (styrene-divinylbenzene) monolithic capillary
column is presented. The method presents itself as a tool for the identification, characterization and mapping of sites of base modification of isomeric oligonucleotide adducts using GenoMass software.
Overview
A key advantage of LC-ESI-MS/MS lies in its ability to identify, characterize and thus locate the exact position of the genotoxic adduct on the oligonucleotide. The effects of different ion pairing reagents (IPR), their
concentration, mobile phase conditions and mobile phase additives were evaluated towards chromatographic separation of isomeric oligonucleotides adducts. Following optimization this on-line PS-DVB monolith-IP-RP-
LC-ESI-MS/MS method was further evaluated for the direct detection and mapping of genotoxic adducted oligonucleotides fragments individually or in mixtures.
Method: Negative ionization LC-ESI-MS/MS was performed using an Agilent series binary pump, a ESI source equipped LCQ Deca quadrupole ion trap mass spectrometer (Finnigan MAT, San Jose, CA) and monolithic
PS-DVB column. Total ion chromatograms and mass spectra were recorded on a personal computer using Xcalibur software version 1.4 (Thermo Finnigan, San Jose, CA). The LC-MS/MS experiments were conducted for
the scan range m/z 700-2000 and data dependent MS/MS spectra were acquired at a collision width of 2 Da and relative collision energy of 30%.
polymeric (styrene-divinylbenzene) monolithic capillary column Effect of ion pairing reagent on RP-IP-LC-ESI-MS/MS separation of AAF adducted oligonucleotide Structural identification of positional isomers of AAF adducted
(CCC CGA GCA ATC TCA AT)2 oligonucleotide by tandem mass spectrometry/ GenoMass
PS-DVB Monolithic capillary columns1,2 are fabricated by following a two-step procedure (i) Pre- D:01_2012...data05_111103193140
D:01_2012...data05_111103193140
Extracted ionSM: 7G
RT: 5.00 - 50.00 chromatograms [M-3H]
RT: 0.00 - 39.40 SM: 7G
3-
11/3/2011 7:31:40 PM
11/3/2011 7:31:40 PM
NL: 9.57E5 Ion assignment Peak I (m/z) Peak II (m/z)
26.07 NL: 9.57E5
26.07
treatment of the capillary inner wall and, (ii) polymerization of PS-DVB monolithic capillary column.
100
100 25.10 m/z=
25.10 m/z=
(b) Extracted ion chromatograms [M-3H]3- (a) 90
90
(a)
1772.98-1773.98 F:
1772.98-1773.98 F:
- p ESI Full ms
- p ESI Full ms
W2 - 634.40 634.53
80 [700.00-2000.00]
80 [700.00-2000.00]
W3 - 947.67 947.67
Only those silica capillaries which have contact angle, θ >85° were used further for subsequent in-situ Peak 1 Peak 2 MS
70 MS
Relative Abundance
70 data05_1111031931
Relative Abundance
data05_1111031931
40
60 40
NL: 4.86E5
60
50
50
CCC CGA GCA ATC TCA AT CCC CGA GCA ATC TCA AT W4 - 1236.809 1236.809
25 mM triethylammonium Bicarbonate
W5 - 1540.93 1541.07
polymerization at 70°C for 16 hours by treating with a mixture of divinylbenzene, styrene, decanol, and
40
40
30
30
20
20 W6 - 1830.191 1830.191
THF at a volume ratio of 3.33::3.33::9.0::1.0 and 10mg/mL of α,α′-Azobisbutyronitrile (AIBN).
10
25 mM N,N dimethylbutylammonium Bicarbonate NL: 7.76E5 10
0 W72- 1067.194 1067.194
0
D:01_2012...data05_111103193140 8
0
6
2
8
4
10
6
12 14 16
10
18
12
20
14
22 11/3/2011 1826
16
24 7:31:40 20
PM
28
22
30 32
24
34
26
36
28
38
30
40
32
42
34
44
36
46 48
38
50
RT: 5.00 - 50.00 SM: 7G
26.07
RT: 5.00 - 50.00 SM: 13G
NL: 9.67E5 NL:
Time (min)
Time (min) W82- 1223.47 1223.80
100 25.10
26.13
NL: 2.75E5 NL:4.86E5 m/z= 100 RT: 0.00 - 39.40 SM: #522-536 RT: 24.81-25.36 AV:
data05_1111031931407G
(c) (d) 7.29E4 data05_111103193140 #1 RT: 0.01 AV: 1 NL: 1.55E3 5 NL: 2.32E3
W92- 1379.93 1380.47
Relative Abundance
25.12
25 mM N,N hexylammonium Bicarbonate 80 1772.90-1773.90 F: -
80 26.57 NL:7.29E4 m/z= F: -- p d Full ms2 1773.47@cid30.00 [475.00-2000.00]
T: 100 Full ms [700.00-2000.00]
p ESI
26.07 NL: 9.57E5
p ESI Full ms 1772.90- 908.47 W3- - 25.10 1525.00 m/z=
(a) (b)
100 947.67
25 mM triethylammonium 100
Peak 1 (a8-B8)2- (a5-B5) (a10-B10)2-
- 1772.98-1773.98 F:
W102-
dT12-dT18 mixture
[700.00-2000.00]
60 60 1773.90 MS 90
1540.93 W5 (a6-B6)- W 2-
1524.93 1525.07
MS
+ 10 mM ammonium data01_1111 12 - p ESI Full ms
van deemter H-u curve
90
90
40 988.00
40
Bicarbonate data05_1111031931 01105747 80