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APPLICATION NOTE ZM-1008
mixture was incubated for 2, 3, 3.5 and 4 hours between these two peaks is the mass of galactose
at 37oC. due to the different glycosylation on the MAb.
Light chain fragment has a mass of 23,441 Da.
Pepsin digestion
Papain digestion – Fab/Fc separation
Pepsin digestion was performed with a method Papain digestion generated Fab and Fc fragments
modified from the previously reported (3,4). from the intact MAb. A time course of papain
MAb 321 was incubated at a final concentration digestion at 37 oC yielded optimum 3.5 hours of
of 1 mg/mL in 20 mM sodium acetate, pH 4.0 incubation time. Time point material was taken
with a pepsin to MAb 321 ratio of 1:40. The and subjected to SEC analysis similar to figure 5
digestion was carried out at 37 oC for 15.5 hours. (3.5 hour time point). At 3 hours of incubation,
The reaction was stopped by adding 2 M TRIS to based on peak integration from a 7.8 x 300 mm
increase the pH to 8.0. run with 20 g digested MAb injection, there
was a 0.28% intact MAb and 0.5% Fab/Fc dimer
Papain digestion and Pepsin digestion mixtures present. Intact MAb, incomplete digestion
were stored at -20oC until use. Freshly reduced fragments, Fab and Fc were all well separated on
MAb 321 was prepared each time before use. ZenixTM SEC-300 (data not shown here). Figure
All samples were stored in the chilled 5 shows an overlay profile of individually
autosampler for sequenced HPLC runs. injected intact MAb 321, papain digested MAb
321 and papain blank on a 4.6 x 300 mm
Results column. Fab and fc maintained the baseline
separation with 5 g injection. The gel image of
Monoclonal antibody fragment separations on the collected peaks indicates the correct
Zenix SEC-300 with 0.1% TFA, 0.1% formic molecular weight order elution.
acid and 20% acetonitrile
Pepsin digestion – F(ab’)2
Reduced MAb Pepsin digestion generated the F(ab’)2 fragments
Separations of heavy chain and light chain were and many small fc fragments. Figure 6 panel A
achieved using both 4.6 x 300 mm and 7.8 x 300 shows the digested MAb separation on ZenixTM
mm ZenixTM SEC-300 columns. HPLC profiles SEC-300 4.6 x 300 mm. F(ab’)2 eluted as a
in figure 2 and 3 indicate that the elution times of single peak with a small shoulder due to a
heavy and light chains were later than that of smaller fragment which is indicated by the gel
intact MAb. Heavy and light chains were image shown in panel B. This smaller fragment
separated based on their molecular elution order. had an estimated molecular weight of 70 kD.
4-12% Bis-Tris gel image shows the correct There was also a small fraction of undigested
molecular weight for each collected fraction intact MAb 321, indicated by a tiny visible peak
containing heavy (50 kD) and light (25kD) before the F(ab’)2 peak and a faint gel band at
chains. There was a small fraction of the 160 kD in the gel image.
dimerized fragments in each peak according to
the gel bands with the dimer molecular weights. Comparison of mobile phases with different
TFA concentrations in volatile buffer 0.1%
With a 7.8 x 300 mm column at a 0.2 mL/min formic acid with 20% acetonitrile and salt
flow rate and directly coupled to online mass mobile phase
spectrometry, identities of the heavy and light
chains were confirmed. Heavy chain and light Figures 7, 8 show chromatogram overlays for
chain were separated. Sample were directly heavy/light chains, Fab/Fc and F(ab’)2
introduced to the mass spectrometer without a separations with 0.02%, 0.05% and 0.1% TFA in
flow split (LC profile not shown, similar to 0.1% formic acid and 20 % acetonitrile on a 4.6
figure 3 with later retention time due to slower x 300 mm column, respectively. The results
flow rate). Figure 4 represents the deconvoluted indicate that when TFA concentration is reduced
mass spectra of heavy and light chain peaks. to 0.05%, all fragments still can be baseline
Heavy chain has a major fragment with a mass of separated with slightly broader peak width in
50,598 Da. Another prominent peak shown in comparison to 0.1% TFA. At 0.02%, all
the spectra was 50,760 Da with an additional fragments in each sample could not be separated
mass of 162 Da. The possible difference and were merged into the buffer peaks.
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APPLICATION NOTE ZM-1008
When the mobile phase was switched to a 150 20% acetonitrile, as shown in figure 13. The
mM sodium phosphate buffer, only the papain other fragment peak, next to the Fab peak, was
digested sample was analyzed; Fab/Fc fragments visible at 0.1 g.
were eluted as one peak with a delayed retention
time as shown in figure 9. Conclusion
Effect of formic acid concentration on
ZenixTM SEC-300 4.6 x 300 mm can successfully
monoclonal antibody fragment separations
separate MAb fragments including heavy/light
With 0.02% TFA, 0.1% formic acid and 20% chains, Fab/Fc and F(ab’)2 from their reaction
acetonitrile, there is no separation of heavy/light, mixtures, respectively. Volatile mobile phases
Fab/ Fc and F(ab’)2. When the concentration of were optimized for the separation of MAb
formic acid was increased to 1% in 0.02% TFA fragments. To minimize the TFA MS signal
and 20% acetonitrile, all fragments were suppression effect, TFA concentrations can be
separated again on the same column. Figure 10
reduced to lower than 0.05%. At 0.02% TFA,
and 11 show the heavy/light, Fab/Fc, and F(ab’)2
separations under three different mobile phases 1% formic acid and 20% acetonitrile, all
(A. 0.02% TFA in 1% formic acid and 20% fragments can be separated from their reaction
acetonitrile; B. 1% formic acid in 20% mixtures with similar separation efficiency as
acetonitrile; C. 0.1% TFA in 0.1% formic acid 0.1% TFA. Even without TFA, all MAb
and 20% acetonitrile). When 0.02% TFA was fragments can be separated with some reduced
omitted from the mobile phase, heavy and chains column performance. Both mobile phases are
were baseline separated while F(ab’)2 exhibited a
much broader peak width, indicating a stronger suitable for the MAb fragment separation and
retention on the column. Both Fc and Fab peaks SEC-MS online analysis. With low sample
were eluted earlier and there was a slight overlap loading and mass spec friendly mobile phases,
between the two peaks without the 0.02% TFA the on‐line SEC‐MS method can be applied to
as shown in figure 11. Table 1 summarizes the general protein separation and mass detection.
column performances using the three different
mobile phases. 0.02% TFA in 1% formic acid
and 20% acetonitrile has similar effect on the
separation of Fab and Fc as 0.1% TFA in 0.1%
formic acid and 20% acetonitrile.
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APPLICATION NOTE ZM-1008
+ +
DTT reduction
Fc Fc small
50 kD 2x + 2x fragments
Light chain Heavy chain
25 kD 50 kD
mAU
160
140
Buffer peaks
MAb 321
120
Intact MAb 321
100
Heavy Light
80 chain chain
40
20 DTT blank
0
7.5 10 12.5 15 17.5 20 22.5 25 min
Figure 2. Reduced MAb 321 separation on ZenixTM SEC-300, 4.6 x 300 mm. Mobile phase was 0.1%
TFA, 0.1% formic acid with 20% acetonitrile. Flow rate was at 0.2 mL/min. UV detection was set at 280
nm. 5 g of intact MAb 321 and 20 g of reduced MAb 321 were injected.
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APPLICATION NOTE ZM-1008
A. B.
kD
23.386
mAU Zenix-300 7830
260
70 0.5mL/min
160
UV280nm
60 110
0.1%TFA, 0.1% formic acid, 20% ACN
80
30 g reduced MAb321
60
25.869
50
Peak1 Peak2 50
40 Heavy Light 40
15.849
30 30
18.949
20
20 15
16.523
22.056
10 10
0
3.5
10 12.5 15 17.5 20 22.5 25 27.5 min
1 2 3 4
Figure 3. Panel A shows a separation profile of reduced MAb 321 on ZenixTM SEC-300, 7.8 x 300 mm.
Peak 1 and Peak 2 were each collected and speed-vac dried. Dried samples were then dissolved in
Invitrogen LDS sample buffer. Panel B. shows the 4-12% Bis-Tris gel image of reduced MAb sample and
Peak 1, 2 fractions. Lane 1 protein marker; lane 2 reduced MAb sample mixture; lane 3 peak 1 heavy
chain; lane 4 peak 2 light chain.
Light chain
162 Da mass
difference-Galactose
% %
50760
24883
48763
30626 37322 72873 7713779983 90646 9744399534
64282
5408856348 11720
0 0
30000 50000 70000 90000 20000 40000 60000 80000
mass mass
Figure 4. Online MS analysis of heavy and light chain from SEC separation of reduced MAb 321. A 7.8 x
300 mm Zenix™ SEC-300 column was used to separate the heavy and light chains. Flow rate was 0.2
mL/min with 0.1% TFA, 0.1% formic acid and 20% acetonitrile as the mobile phase. Samples were
directly introduced to online Q-TOF after SEC. Deconvoluted mass spectra of peaks were shown as in
heavy chain and light chain.
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APPLICATION NOTE ZM-1008
A. B.
mAU
kD
160 MAb321 260
160
140 110
Intact MAb 321 80
120
Fab 60
100 Fc 50
80 40
Papain digested MAb 321
60 30
20
40
15
20 10
Papain blank
0
5 7.5 10 12.5 15 17.5 20 22.5 min 3.5
Fc Fab
Figure 5. Panel A shows the papain digested MAb 321 (3.5 hour incubation time) -Fab/Fc separation on
ZenixTM SEC-300, 4.6 x 300 mm. Mobile phase was 0.1% TFA, 0.1% formic acid with 20% acetonitrile.
Flow rate was 0.2 mL/min. UV detection was set at 280 nm. 5 g of intact MAb 321 and 5 g of papain
digested MAb 321 were injected. Panel B shows the 4-12% Bis-Tris gel image of collected Fc and Fab
fractions separated on a ZenixTM SEC-300, 7.8 x 300 mm column at 0.5 mL/min (LC profile not shown).
A. B.
mAU kD
A. Pepsin digestion blank 260
120 B. Pepsin digested MAb 321 160 a
C. Intact MAb 321 110
b
100 MAb 321 80
60 c
80 C 50
F(ab)’2 40
60
Undigested MAb
30
40 B
20
Small fragments and 15
20
buffer peaks
A 10
0
6 8 10 12 14 16 18 20 22 24 min 1 2 3
Figure 6. Panel A showed the pepsin digested MAb 321-F(ab’)2 separation on ZenixTM SEC-300, 4.6 x 300
mm. Mobile phase was 0.1% TFA, 0.1% formic acid with 20% acetonitrile. Flow rate was 0.2 mL/min.
UV detection was set at 280 nm. 5 g of intact MAb 321 and 15 g of papain digested MAb 321 were
injected. Panel B shows 4-12% Bis-Tris gel image. 5 g of each sample were loaded. Lane 1 protein
markers; lane 2 undigested MAb 321; lane 3 pepsin digested MAb 321. Band (a) is undigested MAb, band
(b) is F(ab’)2, and bands (c) are smaller fragments from the digestion.
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APPLICATION NOTE ZM-1008
mAU
Mobile phases:
A. 0.02% TFA, 0.1% formic acid, 20% ACN
160 B. 0.05% TFA, 0.1% formic acid, 20% ACN
140
C. 0.1% TFA, 0.1% formicHeavy
acid, 20% ACN
Light
120 Heavy
Light
100
C Heavy Light
80
60
B
40 Heavy+light
Heavy + light
20
A
0
8 10 12 14 16 18 20 22 24 26 min
Figure 7. Effect of different TFA concentrations on the separation of heavy and light chains on a ZenixTM
SEC-300, 4.6 x 300 mm column. Flow rate was 0.2 mL/min. UV detection was set at 280 nm. 20 g of
reduced MAb 321 was injected. At 0.05% TFA, heavy and light chains can be baseline separated.
However, at 0.02% TFA, heavy and light chains are not separated.
A. B.
mAU mAU Mobile phases:
Mobile phases:
160 A. 0.02% TFA, 0.1% formic acid, 20% ACN A. 0.02% TFA, 0.1% formic acid, 20% ACN
B. 0.05% TFA, 0.1% formic acid, 20% ACN B. 0.05% TFA, 0.1% formic acid, 20% ACN
140 120
C. 0.1% TFA, 0.1% formic acid, 20% ACN C. 0.1% TFA, 0.1% formic acid, 20% ACN
120 100
Fab
100 F(ab’)2
Fc 80
80
60 C
C
60
Fc Fab
40
40
B B
20 20
A
A
0 0
8 10 12 14 16 18 20 22 24 min 7.5 10 12.5 15 17.5 20 22.5 25min
Figure 8. Effect of different TFA concentrations in 0.1% formic acid and 20% acetonitrile on the
separation of Fab/ Fc and F(ab’)2 on a ZenixTM SEC-300, 4.6 x 300 mm column. Flow rate was 0.2 mL/min.
UV detection was set at 280 nm. Panel A shows the chromatogram overlays of 5 g of papain digested
MAb 321 with the mobile phases indicated. Panel B shows the chromatogram overlays of 15 g pepsin
digested MAb 321.
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APPLICATION NOTE ZM-1008
mAU
Buffer
Fab peak
100
Fc
80
A. 0.1% TFA, 0.1%
60 formic acid, 20% ACN
Fab
40 Fc Buffer
peak
20 B. 150 mM phosphate
buffer, pH 7.0
0
4 6 8 10 12 14 min
Figure 9. Organic mobile phase vs. salt mobile phase for Fab/Fc separations on ZenixTM SEC-300, 4.6 x 300
mm. Flow rate was 0.35 mL/min, 5 g of papain digested MAb 321 was injected for both runs. LC profile
A was obtained with 0.1% TFA, 0.1% formic acid in 20% acetonitrile, while profile B was generated with
150 mM sodium phosphate buffer, pH 7.0.
A. B.
mAU
mAU A. 0.02% TFA, 1% formic acid, A. 0.02% TFA, 1% formic acid,
20% ACN 100 20% ACN
Heavy
B. 1% formic acid, 20% ACN B. 1% formic acid, 20% ACN
120 C. 0.1% TFA, 0.1% formic acid, Light C. 0.1% TFA, 0.1% formic acid, F(ab’)2
20% ACN 80 20% ACN
100 C
C
60
80
60 B 40
B
40
20
20 A A
0
8 10 12 14 16 18 min 6 8 10 12 14 16 18 min
Figure 10. Heavy/light chains, F(ab’)2 separations on ZenixTM SEC-300, 4.6 x 300 mm. Flow rate was 0.2
mL/min with UV 280 nm detection. Panel A shows the chromatogram overlays of reduced MAb 321
separation (heavy and light chains). Panel B shows the chromatogram overlays of pepsin digested MAb
321 separation (F(ab’)2). Mobile phase A was 0.02% TFA, 1% formic acid, 20% acetonitrile. Mobile
phase B was 1% formic acid and 20% acetonitrile. Mobile phase C was 0.1% TFA, 0.1% formic acid and
20% acetonitrile.
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APPLICATION NOTE ZM-1008
mAU
A. 0.02% TFA, 1% formic acid,
120 20% ACN
Fab
B. 1% formic acid, 20% ACN
100 C. 0.1% TFA, 0.1% formic
acid, 20% ACN Fc
80
C
60
40
B
20
A
0
6 8 10 12 14 16 18 min
Figure 11. Fab and Fc separations on ZenixTM SEC-300, 4.6 x 300 mm with different mobile phases. Flow
rate was 0.2 mL/min, 5 g of papain digested MAb 321 was injected for all three runs.
Table 1. ZenixTM SEC-300 4.6x300mm column performance dependence on mobile phase compositions for
Fab/Fc separations.
0.1% TFA, 0.1% formic acid, 20% ACN 13.25 5884 1.08
Fab 0.02% TFA, 1% formic acid, 20% ACN 13.89 7551 1.09 1.77
0.1% TFA, 0.1% formic acid, 20% ACN 14.58 6322 1.19 1.85
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APPLICATION NOTE ZM-1008
40
30 Fab
20 B
Fc
10
A
0
6 8 10 12 14 16 18 20 22 min
Figure 12. Acetonitrile concentration effect on Fab/Fc separations on ZenixTM SEC-300, 4.6 x 300 mm.
Flow rate was 0.2 mL/min, 5 g of papain digested MAb 321 was injected for both runs. LC profile A was
obtained with 20% acetonitrile, while profile B was generated with 50% acetonitrile.
A. B.
mAU Papain digested Fab mAU
25 0.1 g papain Fab
MAb loading: 1 digested MAb
0.1 g
20
0.25 g 0.8
15 0.5 g Fc Fc
0.6
1g
10 3g 0.4
5g
5 0.2
0 0
11 12 13 14 15 16 11 12 13 14 15 16
min min
Figure 13. Panel A shows the chromatogram overlays of different sample loadings of papain digested MAb
from 0.1 g to 5 g on ZenixTM SEC-300, 4.6 x 300 mm. HPLC mobile phase was 0.02% TFA in 1%
formic acid and 20% acetonitrile. Flow rate was 0.2 mL/min with UV 280 nm detection. Panel B shows
the separation profile with 0.1 g loading. Fab and Fc maintained a baseline separation at 0.1 g loading.
Reference:
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APPLICATION NOTE ZM-1008
Order information
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