Highly Sensitive, Robust MS-Based Workflow for

Higher Resolution LC-MS and MS-MS
Analysis of Lipid Extracts Using Benchtop
Orbitrap-based Mass Spectrometers and
LipidSearch Software
David A Peake,1 Yasuto Yokoi, 2 Reiko Kiyonami1 and Yingying Huang1
1
Thermo Fisher Scientific, San Jose, USA; 2Mitsui Knowledge Industry, Tokyo, JAPAN
Overview
Purpose: Benchmark the performance of a new LC-MS/MS system and determine the
effect of full scan MS resolution vs. the number of identified lipids in total lipid extracts.
Methods: Lipid extracts were profiled using LC-dd-MS/MS analysis using a novel
quadrupole-Orbitrap mass spectrometer operated at mass resolution of 30, 60, 120
and 240K.
Results: The data presented here shows that lipidomic profiling at higher full scan MS
resolution provides more identified lipids during an LC-MS run. The higher acquisition
rate of MS/MS spectra also contributes to significantly more lipids being identified.
Introduction
Lipids play a key role in cell, tissue and organ physiology with diseases such as cancer
and diabetes which involve disruption of their metabolic enzymes and pathways.
Identification of unique lipid biomarkers to distinguish healthy humans compared to
those with a disease can have an impact on the early detection of diseases and
personalized medicine.
Because of the complexity of the lipidome, which includes 8 major categories of lipids,
over 80 major classes, 300 sub-classes and thousands of lipid species1, HPLC MS/MS
methods are often used to separate many overlapping isomeric or isobaric molecular
ions in biological samples for increased lipid identification coverage. By employing a
high resolution accurate mass (HR/AM) platform equipped with a ultra-high field
Orbitrap mass spectrometer (Thermo ScientificTM Q Exactive HFTM MS) to detect lipids
after HPLC separation, ultra-high resolution MS and MS/MS analysis provides
unambiguous identification of lipids in biological samples.
However, it is extremely challenging to process all the MS and MS/MS data manually.
A sophisticated software with an extensive database is required to identify all detected
lipids HPLC MS/MS data. The newly-released Thermo ScientificTM LipidSearchTM
software enables automated identification of lipids from biological samples based on its
large lipid database which includes >1.5 million lipid ions and predicted fragment ions.
In addition, relative quantification of identified lipid precursors can be carried out in the
same LC/MS/MS experiment.
In this study, we present that hundreds of lipid species can be simultaneously
identified and quantified in a single LC/MS-MS experiment by using optimized HPLC
separation and HR/AM MS and data-dependent MS2 conditions.
Methods
TABLE 1. HPLC Gradient
Time, min
%A
0.00
68
%B
32
1.50
68
32
4.00
55
45
5.00
48
52
8.00
42
58
11.00
34
66
14.00
30
70
18.00
25
75
21.00
3
97
25.00
3
97
25.01
68
32
33.00
68
32
Data Processin
LC-MS/MS Data Processing
1) Peak Detection. Read raw
2) Identification. Candidate m
database >106 entries of accu
each potential lipid structure a
3) Alignment. The search res
window and the results are co
4) Quantification. The accura
each identified lipid precursor
5) Statistical Analysis. t-Test
sample vs. control groups, and
FIGURE 1. LipidSearch Work
LC-MS Sample Preparation.
Bovine brain, heart, liver and yeast total lipid extracts (2.5 mg/mL in Chloroform) were
purchased from Avanti Polar Lipids. Dilution series of each lipid extract was prepared
by diluting the stock solutions sequentially into 1.25 µg/µL, 500 ng/µL, 250 ng/µL, 125
ng/µL and 50 ng/µL in 50:50 Methanol and Isopropanol (IPA).
HPLC Method.
A Thermo Scientific™ Dionex™ UltiMate™ 3000 Rapid Separation LC (RSLC) system
performed separations using the gradient conditions shown in Table 12. Mobile phase A
was 60:40 Acetonitrile / Water and mobile phase B was 90:10 IPA / Acetonitrile; both A
and B contained 10mM ammonium formate and 0.1% formic acid. The column was an
Ascentis Express C18 (Supelco, 2.1 x 100mm, 2.7µm) operated at 55°C, flow rate of
260 µL/min and the injection volume was 2 µL.
MS Conditions.
Thermo Scientific Q Exactive Plus and Q Exactive HF instruments were employed for
untargeted lipid profiling experiments using the instrument operating conditions shown
in Table 2. Each instrument was operated under optimized conditions providing
sufficient scans across the chromatographic peak profile for accurate relative
quantification using the HR/AM precursor ion while simultaneously acquiring dd-MS2
spectra for lipid identification.
Data Analysis Software.
LipidSearch software was used for lipid identification and relative quantification.
2 Highly Sensitive, Robust MS-Based Workflow for Therapeutic Monoclonal Antibody Analysis from Complex Matrices
•
•
•
•
•
HRAM / Nomin
Infusion & LC-M
ID based on M
DB with 106+ li
Integration of m
W
KO / WT = 0.3
p < 0.0053
KO
S/MS system and determine the
ified lipids in total lipid extracts.
MS analysis using a novel
mass resolution of 30, 60, 120
profiling at higher full scan MS
MS run. The higher acquisition
more lipids being identified.
gy with diseases such as cancer
enzymes and pathways.
ealthy humans compared to
etection of diseases and
es 8 major categories of lipids,
of lipid species1, HPLC MS/MS
isomeric or isobaric molecular
on coverage. By employing a
ped with a ultra-high field
active HFTM MS) to detect lipids
S/MS analysis provides
s.
MS and MS/MS data manually.
required to identify all detected
ScientificTM LipidSearchTM
biological samples based on its
s and predicted fragment ions.
ursors can be carried out in the
can be simultaneously
ent by using optimized HPLC
onditions.
TABLE 1. HPLC Gradient
Time, min
%A
0.00
68
32
1.50
68
32
4.00
55
45
5.00
48
52
8.00
42
58
TABLE 2. Orbitrap Operating Conditions
%B
11.00
34
66
14.00
30
70
18.00
25
75
21.00
3
97
25.00
3
97
25.01
68
32
33.00
68
32
HESI Source
Pos. or Neg. Ion
Aux gas 3
MS Resolution
30K, 60K, 120K,
240K
MS Resolution
17.5K, 35K, 70K,
140K
Spray volt. 4.2 Top15 dd-MS2
R = 35K
kV
Top20 dd-MS2
R = 30K
S-Lens 50
MS2 Isolation
width 1 Da
MS2 Isolation
width 1 Da
Cap. Temp.
320°C
Stepped NCE –
Pos. 25, 30
Neg. 20, 24, 28
Stepped NCE –
Pos. 25, 30
Neg. 20, 24, 28
Heater temp.
300°C
AGC target
1E+6 MS
1E+5 MS2
AGC target
1E+6 MS
1E+5 MS2
Results
Lipid Identification Results from
(1.25 µg/µL) was analyzed by LC/M
modes, respectively (Figure 2). Lipi
data for all common lipid classes us
product ions. For each MS2 spectru
the lipid precursor ion m/z stored in
summarized for the identified lipid s
experimental data (Figure 3).
The speed advantage of Q Exactive
illustrated in Figure 4, compared to
higher resolution (120K) the Q Exac
FIGURE 2. High Resolution (70,00
Total ion Chromatograms of Bov
Positive
Ion
Data Processing
LC-MS/MS Data Processing Workflow using LipidSearch Software (Figure 1).
1) Peak Detection. Read raw files, MSn and precursor ion accurate masses.
2) Identification. Candidate molecular species are identified by searching a large
database >106 entries of accurate m/z (lipid precursor and fragment ions) predicted from
each potential lipid structure and positive/negative ion adduct.
3) Alignment. The search results for each individual sample are aligned within a time
window and the results are combined into a single report.
4) Quantification. The accurate-mass extracted ion chromatograms are integrated for
each identified lipid precursor and the peak areas are obtained.
5) Statistical Analysis. t-Tests determine significantly differences between lipids in
sample vs. control groups, and results are displayed in a whisker plot.
FIGURE 1. LipidSearch Workflow.
FIGURE 3. Search Results for m/z
329.2483 PC(18:0_22:5)
Peak
Detect
283.2640
820.5
Separation LC (RSLC) system
own in Table 12. Mobile phase A
90:10 IPA / Acetonitrile; both A
ormic acid. The column was an
operated at 55°C, flow rate of
nd relative quantification.
Q Exactive HF
Sheath gas 35 Pos. or Neg. Ion
2.5 mg/mL in Chloroform) were
ach lipid extract was prepared
µL, 500 ng/µL, 250 ng/µL, 125
(IPA).
nstruments were employed for
ent operating conditions shown
zed conditions providing
e for accurate relative
ultaneously acquiring dd-MS2
Q Exactive Plus
508.3407
Identify
•
•
•
•
•
HRAM / Nominal mass
Infusion & LC-MS data
ID based on MSn
DB with 106+ lipid species
Integration of multiple runs
KO
500
Align
400
300
WT
KO / WT = 0.36
p < 0.0053
FIGURE 4. Increase in the Number
Lipid Extract using dd-LCMS2 with
Quan
QE Plus (top
QE HF (top 2
200
100
0
100ng
Thermo Scientific Poster Note • PN-64137-ASMS-EN-0614S 3
250ng
Orbitrap Operating Conditions
Q Exactive Plus
5 Pos. or Neg. Ion
MS Resolution
17.5K, 35K, 70K,
140K
2 Top15 dd-MS2
R = 35K
Q Exactive HF
Pos. or Neg. Ion
MS Resolution
30K, 60K, 120K,
240K
Top20 dd-MS2
R = 30K
MS2 Isolation
width 1 Da
MS2 Isolation
width 1 Da
Stepped NCE –
Pos. 25, 30
Neg. 20, 24, 28
Stepped NCE –
Pos. 25, 30
Neg. 20, 24, 28
AGC target
1E+6 MS
1E+5 MS2
AGC target
1E+6 MS
1E+5 MS2
Results
Improved ID and Relative Q
Higher MS resolution lipid pr
related lipids overlap even u
resolution for identification o
two Lyso phospholipid speci
during analysis at 2.2 minute
needed to separate these tw
smaller LPE 18:1 peak (m/z
is only partially resolved at 2
required for unequivocal iden
lipid species is challenging w
Lipid Identification Results from LC/dd-MS2 Data. Bovine heart total lipid extract
(1.25 µg/µL) was analyzed by LC/MS and dd-MS/MS in positive and negative ion
modes, respectively (Figure 2). LipidSearch software was used to search the LC-MS
data for all common lipid classes using a mass tolerance of ±5 ppm for precursor and
product ions. For each MS2 spectrum matching a predicted fragmentation pattern from
the lipid precursor ion m/z stored in the LipidSearch database, search results are
summarized for the identified lipid species with m-score indicating the fit to the
experimental data (Figure 3).
The speed advantage of Q Exactive HF (120K resolution) and TOP20 dd-MS2 is
illustrated in Figure 4, compared to Q Exactive Plus (70K) and TOP15 dd-MS2. At the
higher resolution (120K) the Q Exactive HF obtains 20% more lipid identifications.
The number of lipids identifie
results are shown in Table 3
exceed the sum of positive a
where lipids are identified in
FIGURE 2. High Resolution (70,000) Accurate Mass Positive and Negative
Total ion Chromatograms of Bovine Heart Total Lipid Extract.
FIGURE 5. Increased Reso
PC and PE Lipid Species. R
500ng_pos_15K_30kms2_top15_200_1200_01
Positive
Ion
SM:
5B
Rt = 2.2 min
LipidSearch Software (Figure 1).
480.15764
ecursor ion accurate masses.
15K
are identified by searching a large
ecursor and fragment ions) predicted from
ive ion adduct.
+2.1 ppm
43K
Negative Ion
100
Relative Abundance
vidual sample are aligned within a time
gle report.
d ion chromatograms are integrated for
as are obtained.
ficantly differences between lipids in
ayed in a whisker plot.
LPE 18:1
480.15664
C23H47NO7P
80
+0.1 ppm
R = 83K
60
40
480.15713
20
0
480.05
FIGURE 3. Search Results for m/z 880.6068, PC(40:5) M+HCO2329.2483 PC(18:0_22:5)
30K
480.15639
R=
480.10
480.15
60K
120K
480.20
480.25
m/z
TABLE 3. Comparison of L
Bovine Brain, Heart, Liver
Bovine Brain
Lipid
Class Neg Pos Merged
CL
283.2640
820.5862
Match
Details
508.3407
Identify
FIGURE 4. Increase in the Number of Lipid Species Identified in Bovine Heart
Lipid Extract using dd-LCMS2 with Q Exactive HF Compared to Q Exactive Plus
500
Align
400
300
QE Plus (top 15)
QE HF (top 20)
200
100
0
100ng
250ng
500ng
1000ng
2500ng
4 Highly Sensitive, Robust MS-Based Workflow for Therapeutic Monoclonal Antibody Analysis from Complex Matrices
LPC
13
34
40
PC
49
152
242
LPE
14
15
24
PE
88
73
171
LPS
PS
LPG
PG
LPI
PI
PA
SM
So
Cer
CerG1
CerG2
ChE
ZyE
DG
TG
CoQ
Total
6
4
7
35
24
63
8
2
9
19
19
33
34
41
62
2
31
34
2
2
2
4
8
2
2
4
33
5
26
284
2
4
13
5
37
5
35
86
147
552
936
1
1
Improved ID and Relative Quantitation Results Obtained with Q Exactive HF
Higher MS resolution lipid profiling translates into improved identification when closely
related lipids overlap even under chromatographic conditions. The effect of MS1
resolution for identification of lipid species at the same retention time is illustrated for
two Lyso phospholipid species, 18:1 LPE and 16:0p LPC. These two lipids overlap
during analysis at 2.2 minutes at m/z in positive ion of 480.3. The mass resolution
needed to separate these two lipids is illustrated in Figure 5. At a resolution of 10K, the
smaller LPE 18:1 peak (m/z 480.3085) is overlapped by LPC 16:0p (m/z 480.3449) and
is only partially resolved at 22K. The 60K setting giving an actual resolution of 42K is
required for unequivocal identification of both M+H ions. Thus, identification of minor
lipid species is challenging without sufficient mass resolution, leading to fewer ID’s.
. Bovine heart total lipid extract
S in positive and negative ion
e was used to search the LC-MS
ance of ±5 ppm for precursor and
edicted fragmentation pattern from
database, search results are
ore indicating the fit to the
ution) and TOP20 dd-MS2 is
(70K) and TOP15 dd-MS2. At the
20% more lipid identifications.
The number of lipids identified in positive and negative ion, and the aligned (merged)
results are shown in Table 3. Note that the number of lipid species after alignment may
exceed the sum of positive and negative ion species because of the correlation step
where lipids are identified in multiple samples and isomers are present at the MS2 level.
ss Positive and Negative
Lipid Extract.
FIGURE 5. Increased Resolution Improves Identification of Overlapping Lyso
03/28/14 03:31:06
PC and PE Lipid Species. Resolution (m/z 200) = 15K, 30K, 60K and 120K
500ng_pos_15K_30kms2_top15_200_1200_01
SM:
5B
Rt = 2.2 min
480.34361
15K
+2.1 ppm
43K
Negative Ion
480.34454
Relative Abundance
LPE 18:1
480.15664
C23H47NO7P
80
+0.1 ppm
R = 83K
60
40
480.15713
20
0:5) M+HCO2-
480.34458
30K
480.15639
R=
100
0
480.05
480.30710
480.10
480.15
60K
120K
480.20
480.25
m/z
480.30946
2500ng
Neutrals
Unknown
3
1
10
5
42
17
7
2
11
3
22
1
8
59
100
2
7
50 20
32
100 100
1
1
19
2
1
5
13
4
45
6. Composition of Lipid
480.30854
480.30
480.35
480.40
480.45
TABLE 3. Comparison of Lipid Species Identified in Total Lipid Extracts of
Bovine Brain, Heart, Liver and from Yeast
CL
1000ng
Brain Heart Liver Yeas
Total
Bovine Brain
Bovine Heart
Bovine Liver
Yeast
Lipid
Class Neg Pos Merged Neg Pos Merged Neg Pos Merged Neg Pos Merged
s Identified in Bovine Heart
Compared to Q Exactive Plus
Wt %
PA
LPC
PC
LPE
PE
PG
LPI
PI
PS
CL
Chol
NL: 2.58E5
500ng_pos_15K_30kms2_top15_200_12 FIGURE
00_01#1162-1333
+3.6 ppm RT: 2.13-2.43 AV:
35 T: FTMS + p ESI Full ms
R = 10K
[250.00-1200.00]
NL: 2.43E5
500ng_pos30k_30kms2_top15_200_120
0_01#1087-1253
-2.6 ppm RT: 2.01-2.29 AV: 28
T: FTMS
p ESI Full ms
R = +22K
[250.00-1200.00]
NL: 2.97E5
500ng_pos60k_30kms2_top15_200_120
LPC 16:0p
0_01#1100-1263
C24H51NO6P RT: 2.14-2.42 AV: 25
T: FTMS + p ESI Full ms
-0.6 ppm
[250.00-1200.00]
R = 86K
NL: 2.82E5
500ng_pos120k_30kms2_top15_200_12
00_01#999-1144 RT: 2.14-2.43 AV: 18
T: FTMS + p ESI Full ms
[250.00-1200.00]
480.34658
480.15764
TABLE 4. Typical Composition o
Total Lipid Extracts (Avanti Lipid
LPC
9
1
2
2
13
34
40
14
28
30
18
36
39
13
25
40
PC
49
152
242
78
141
253
61
137
294
26
58
92
LPE
14
15
24
14
8
17
15
10
17
9
9
12
PE
88
73
171
92
45
165
74
51
248
19
19
34
1
1
7
1
LPS
PS
LPG
PG
LPI
PI
PA
SM
So
Cer
CerG1
CerG2
ChE
ZyE
DG
TG
CoQ
Total
9
6
4
7
35
24
63
37
8
2
9
19
19
34
41
2
2
4
8
2
53
23
26
4
35
33
31
25
62
37
31
34
1
2
2
2
4
33
5
26
284
2
6
2
4
13
5
37
5
3
147
552
936
1

Higher resolution and speed
identification and relative qu
3

1
At least 20% more lipid ID’s
Orbitrap.

LipidSearch provides autom
single LC-ddMS2 experimen
lipid species.
24
6
38
17
5
48
10
3
10
55
34
33
98
27
41
55
39
56
37
39
91
6
7
12
17
18
5
41
46
3
3
1
2
1
32
351
Four different total lipid extra
lipidomics experiments, sepa
65
4
5
3
2
1
5
9
5
3
5
9
5
35
3
45
174
329
528
1087
5
5
29
310
5
9
11
5
9
5
44
1
4
9
2
3
3
2
2
4
27
5
18
1.
LIPID MAPS comprehensiv
Lipid Res. 2009, 50, S9-S1
3
2.
Lipidomics profiling by high
dissociation fragmentation:
cardiolipins and monolysoc
940–949. dx.doi.org/10.102
2
2
31
248
161
241
568
1297
153 374
607
3
4
References
3
155
3
Conclusion

1
5
86
1
4
7
2
3
Lipid Search is a registered trademark of MKI
All other trademarks are the property of Therm
This information is not intended to encourage
intellectual property rights of others.
Thermo Scientific Poster Note • PN-64137-ASMS-EN-0614S 5
Obtained with Q Exactive HF
mproved identification when closely
conditions. The effect of MS1
me retention time is illustrated for
p LPC. These two lipids overlap
of 480.3. The mass resolution
Figure 5. At a resolution of 10K, the
ed by LPC 16:0p (m/z 480.3449) and
ving an actual resolution of 42K is
ions. Thus, identification of minor
resolution, leading to fewer ID’s.
tive ion, and the aligned (merged)
of lipid species after alignment may
s because of the correlation step
somers are present at the MS2 level.
tification of Overlapping Lyso
= 15K, 30K, 60K and 120K
TABLE 4. Typical Composition of
Total Lipid Extracts (Avanti Lipids)
Wt %
Brain Heart Liver Yeast
PA
LPC
PC
LPE
PE
PG
LPI
PI
PS
CL
Chol
Neutrals
Unknown
Total
NL: 2.58E5
500ng_pos_15K_30kms2_top15_200_12 FIGURE
00_01#1162-1333
+3.6 ppm RT: 2.13-2.43 AV:
35 T: FTMS + p ESI Full ms
R = 10K
[250.00-1200.00]
NL: 2.43E5
500ng_pos30k_30kms2_top15_200_120
0_01#1087-1253
-2.6 ppm RT: 2.01-2.29 AV: 28
T: FTMS
p ESI Full ms
R = +22K
[250.00-1200.00]
NL: 2.97E5
500ng_pos60k_30kms2_top15_200_120
LPC 16:0p
0_01#1100-1263
C24H51NO6P RT: 2.14-2.42 AV: 25
T: FTMS + p ESI Full ms
-0.6 ppm
[250.00-1200.00]
R = 86K
NL: 2.82E5
500ng_pos120k_30kms2_top15_200_12
00_01#999-1144 RT: 2.14-2.43 AV: 18
T: FTMS + p ESI Full ms
[250.00-1200.00]
3
1
10
5
42
17
7
2
11
3
22
1
8
59
100
2
7
50 20
32
100 100
1
1
19
2
1
5
13
4
45
Composition of Total Lipid Extracts
Composition information for the total lipid
extracts listed on Avanti Polar Lipids website are
shown in Table 4.
The LC-MS2 results for each lipid extract
injected in duplicate were searched using
LipidSearch, and positive and negative ion data
were aligned within a 0.4 min window (Table 3).
The peak areas for each lipid class were
summed and the relative amounts of each lipid
class were plotted as % Area from the full scan
MS (Figure 6). As expected from the 50 wt % of
neutral lipids, the bovine heart extract contained
the highest amount of TG (65% by peak area),
and the yeast extract contained 61% TG. Brain,
liver and yeast extracts contained the most PC.
6. Composition of Lipid Extracts by LC-HRMS Peak Area (%)
Brain
Liver
Yeast
Heart
70
60
50
40
30
20
10
Bovine Liver
Yeast
eg Pos Merged Neg Pos Merged
1
2
2
2
Four different total lipid extracts were profiled and are suitable for benchmarking
lipidomics experiments, separation conditions and instrumental optimization.

Higher resolution and speed of Q Exactive HF provides more confident
identification and relative quantification in a single positive and negative ion run.
3

1
At least 20% more lipid ID’s were obtained using a ultra-high field benchtop
Orbitrap.

LipidSearch provides automated identification of more than 500 lipid species in a
single LC-ddMS2 experiment, and alignment of multiple samples gives over 1000
lipid species.
36
39
13
25
40
61
137
294
26
58
92
15
10
17
9
9
12
74
51
248
19
19
34
7
1
7
3
1
65
24
6
38
17
5
48
10
3
10
34
33
98
27
41
55
37
39
91
6
7
12
5
41
46
3
3
5
9
5
10
3
5
9
5
29
5
9
11
5
9
5
44
1
4
9
2
3
3
2
2
4
27
5
18
1.
LIPID MAPS comprehensive classification system for lipids. E Fahy et al., J.
Lipid Res. 2009, 50, S9-S14. doi: 10.1194/jlr.R800095-JLR200.
3
2.
Lipidomics profiling by high-resolution LC-MS and high-energy collisional
dissociation fragmentation: focus on characterization of mitochondrial
cardiolipins and monolysocardiolipins. S Bird, et al., Anal. Chem. 2011, 83,
940–949. dx.doi.org/10.1021/ac102598u.
2
2
31
248
161
241
568
1297
153 374
607
3
4
References
3
155
3
Conclusion

18
23
Heart
Yeast
d in Total Lipid Extracts of
Brain
0
480.45
Liver
480.40
3
Lipid Search is a registered trademark of MKI and Ascentis Express is a registered trademark of Sigma-Aldrich.
All other trademarks are the property of Thermo Fisher Scientific and its subsidiaries.
This information is not intended to encourage use of these products in any manners that might infringe the
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