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1. So What’s the Big Deal with
Those Little Tubes?
Capillary Electrophoresis
Exercises for MSU Students
Prepared for Chemistry and Biochemistry Fall 2003
Kevin Olsen

2. Program
• General principles
• Safety
• Obtaining good results
• Example application, CE in drug discovery
• Running your samples on the Beckman
Coulter model P/ACE

3. System Schematic
Anode
+
Cathode
-
Applied Electric Field.
1000 Volts / Centimeter
Velocity = (Field Strength) (Electrophoretic Mobility)
Detector (UV, PDA or LIF)

4. Beckman P/ACE System

5. Electrophoretic Mobility
Z
Uep = ---------------
6 n r
Where:
Z = Net charge on the analyte
n = Viscosity of the medium
r = Stoke’s Radius

6. Variables Governing Electrophoretic
Mobility
• Charge
• Radius*
• Mobility
*The Stoke’s radius is
related to molecular
mass. Heavier
molecules will have a
greater radius.

7. Electroosmotic Flow
(EOF)
This flow is a phenomena resulting
when a solution is contained in a
capillary with fixed charges along its
wall. This is also known as the
Electroendosmotic Flow.

8. Where does the Electroosmotic flow come
from?
Anode
+
Cathode
-
Detector

9. Where does the Electroosmotic flow come
from?
Anode
+
Cathode
-
Applied Electric Field.
1000 Volts / Centimeter
Detector

10. Where does the Electroosmotic flow come
from?
Anode
+
Cathode
-
Detector
The interior wall of the capillary contains
charged sites that are created by the
ionization of Silanol groups on the fused
silica.

11. Where does the Electroosmotic flow come
from?

12. This is where the Electroosmotic flow
comes from.
What happens to the + cations when we turn on the power?

13. pH, Silanol Population, and the rate of
EOF flow.
• At very low pH, not many
silanols are ionized and
the EOF is slow.
• As pH increases the
number of ionized sites
also increases. The EOF
speed rises steadily.
• At very high pH values, a
maximum number of
ionized sites is reached.
The EOF speed also
reaches a maximum.

14. The apparent velocity of any analyte
(u) will be a combination of its
electrophoretic velocity and its
movement in response to the EOF.
u = (Uep + Ueo) E

15. How does apparent velocity help us?
Analytes with a net positive charge will move faster than EOF
EOF
Analytes with no net charge will move at the same speed as the EOF.
(This is a useful tool that helps us to measure the EOF.)
EOF
Analytes with a net negative charge will move slower than EOF
EOF

16. Separation Efficiency
(apparent mobility) (Voltage)
N = ----------------------------------------
2 (diffusion coefficient)

17. Separation Efficiency (Y) and Diffusion
Coefficient (X)
• Note the very dramatic
drop in separation
efficiency with
increasing diffusion
coefficient.
• This means that in
some cases, there is no
real advantage over
conventional HPLC
for smaller molecules.

18. Injections
There are two principle methods:
• Pressure differential works by applying a pressure across the
capillary while it it is dipping into the sample solution.
• Electrokinetic injection works by applying a voltage and
allowing ions to migrate into the capillary because of their
charge.
Injection volumes are typically very small:
• Typically if injection volumes exceed 1% of the column
volume, separation efficiency severely suffers.
• Sample volume can be increased by focusing the ions inside
the capillary. This technique uses a combination of
additives to the medium and selectively applied charges.

19. Preconcentration to Increase Sensitivity
• Attached to front of
column
• Contains a selective
binding agent
• Allows several
capillary volumes to
pass
• Analytes of interest
are then eluted

20. Pressure and Electrokinetic Injections
• One additional advantage of electrokinetic injections is that
if appropriate conditions are set, extended injection times
allow analytes to be concentrated without overloading the
column.
+ + +
+
+ +
+
-
-
+

21. Setting up the Capillary Column
• Cut the ends cleanly.
• Load capillary into
the cartridge
• Place the clear
portion in the
detector window.

22. The Capillary Column’s Cartridge
• Allows the column to
be moved from vial to
vial.
• Contains a cooling
medium.
• Contains gas and
vacuum connections.
• Holds electrodes that
place a charge on the
sample vials.

23. The Advantages of CE are:
• The number of theoretical plates is typically
in the hundreds of thousands.
• There is no mass transfer between mobile
and stationary phases as with HPLC and
GC, therefore the analytes remain in a
“plug” instead of spreading as a result of
laminar flow. (Peaks can still broaden
however.)
• Altering column conditions allows focusing
or concentration of samples.

24. Program
• General principles
• Safety
• Obtaining good results
• Example application, CE in drug discovery
• Running your samples on the Beckman
Coulter model P/ACE

25. SAFETY
• Chemical and Biological
• Remember that solvents will be flowing under high
pressure inside an electrically powered device.
• Aerosols may be generated, work in appropriate enclosure.
• Take all normal safety precautions when working with
toxic, pathogenic, or radioactive materials.
• Electrical
• Never remove covers and expose the electronics.
• Under certain conditions the chemist may have to be
grounded for protection against static electricity.
• Mechanical
• The CE unit features a robotic autosampler with many
moving parts and a sharp needle. Keep hands out of the
sample compartment while the unit is running.

26. Obtaining Reproducible (Good) Results
• Column condition.
• Composition and pH of the medium.
• Viscosity of the medium.
• Operating temperature.
• Adequate sample volume.
• Use of internal standards.

27. The pH must be tightly controlled to
obtain reproducible EOF flow.
• Remember that the
percentage of silanols that
are ionized is dependent
on the pH.

28. Column Condition
• As time goes on, certain
molecules will block or
otherwise neutralize the
ionized silanol sites.
This will change the
EOF and alter retention
times.
• It is also very important
to condition the column
properly before use.
Follow the directions in
the published method.

29. Internal Standards
• The main advantage of an internal standard is
that it is subject to the same conditions as the
analyte.

30. Program
• General principles
• Safety
• Obtaining good results
• Example application, CE in drug
discovery
• Running your samples on the Beckman
Coulter model P/ACE

31. Courtesy of Cetek Corporation

32. Courtesy of Cetek Corporation
20,000 Compounds Tested per Day
6,000,000 Tested since 1998

33. Other Applications
• Analysis of molecules that are not suited to
HPLC.
• Chiral separations of enantiomers.
• Determination of drug molecules in biological
fluids.
• Separating bacteria.
• Expect the unexpected.

34. Program
• General principles
• Safety
• Obtaining good results
• Example application, CE in drug discovery
• Running your samples on the Beckman
Coulter model P/ACE

36. Setting Up Methods
• Use File|Method|New from the menu bar to
create your method.
• When finished use File|Method|Save as from
the menu bar.

37. Tray Layout
A1 B1 C1 D1 E1 F1
A2 B2 C2 D2 E2 F2
A3 B3 C3 D3 E3 F3
A4 B4 C4 D4 E4 F4
A5 B5 C5 D5 E5 F5
A6 B6 C6 D6 E6 F6

38. A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
Manipulating Tray Layouts

39. A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
A1 B1 C1 D1 E1 F1
Manipulating Tray Layouts
Blue = Rinse
Green = Multiple use
Orange = Fraction
collection
Dark purple = Sample
Light purple = Other
injection
Red = Selected vial
Yellow = Separation

40. Manipulating Tray Layouts
• Vials positions can be designated under
“instrument set-up”. Afterwards, you will be
prompted to save the changes to your method.
• Vial positions can also be designated while setting
up the “Timed events” table in your method.
• In either case, the software commands and
procedures are the same.

41. P/ACE System Control
• Select your method from the drop-dow method
under FILE
• You may then change the tray layouts but all
changes become part of the method.
• In this class, we will have two control options:
1. Direct Control
2. Single Run

42. THE EXERCISES
• Each team will create one method that will rinse
and condition the column, then inject a sample.
• Each team’s method parameters will be slightly
different.
• Your instructor will string the methods together
for an overnight run.
• When the class meets again, the results will be
compared. Each student will submit a report
comparing and contrasting the results.

43. Generic Test Solution Method
• Rinse: 0.5 minutes, Regenerator sol’n A, 20 psi.
Destination = waste vial.
• Rinse: 1.5 minutes, Run buffer A, 20 psi.
Destination = waste vial.
• Inject: 10 Seconds, Test mix, 0.5 psi. Destination
= Run buffer A on outlet tray.
• Separate: 7 minutes, Run buffer A, 25 kV. Ramp
time 0.2 minutes. Destination = Run buffer A on
outlet tray.

44. Team 1, Variation
• Rinse: 0.5 minutes, Regenerator sol’n A, 20 psi.
Destination = waste vial.
• Rinse: 1.5 minutes, Run buffer A, 20 psi.
Destination = waste vial.
• Inject: 10 Seconds, Test mix, 0.5 psi. Destination
= Run buffer A on outlet tray.
• Separate: 7 minutes, Run buffer A, 25 kV. Ramp
time 0.2 minutes. Destination = Run buffer A on
outlet tray.

45. Team 2 Variation
• Rinse: 0.5 minutes, Regenerator sol’n A, 20 psi.
Destination = waste vial.
• Rinse: 1.5 minutes, Run buffer A, 20 psi.
Destination = waste vial.
• Inject: 10 Seconds, Test mix, 0.5 psi. Destination
= Run buffer A on outlet tray.
• Separate: 7 minutes, Run buffer A, 25 kV. Ramp
time 0.2 minutes. Destination = Run buffer A on
outlet tray.

46. Team 3 Variation
• Rinse: 0.5 minutes, Regenerator sol’n A, 20 psi.
Destination = waste vial.
• Rinse: 1.5 minutes, Run buffer A, 20 psi.
Destination = waste vial.
• Inject: 10 Seconds, Test mix, 0.5 psi. Destination
= Run buffer A on outlet tray.
• Separate: 7 minutes, Run buffer A, 25 kV. Ramp
time 0.2 minutes. Destination = Run buffer A on
outlet tray.

47. Team 4 Variation
• Rinse: 0.5 minutes, Regenerator sol’n A, 20 psi.
Destination = waste vial.
• Rinse: 1.5 minutes, Run buffer A, 20 psi.
Destination = waste vial.
• Inject: 10 Seconds, Test mix, 0.5 psi. Destination
= Run buffer A on outlet tray.
• Separate: 7 minutes, Run buffer A, 25 kV. Ramp
time 0.2 minutes. Destination = Run buffer A on
outlet tray.

48. Team 5 Variation
• Rinse: 0.5 minutes, Regenerator sol’n A, 20 psi.
Destination = waste vial.
• Rinse: 1.5 minutes, Run buffer A, 20 psi.
Destination = waste vial.
• Inject: 10 Seconds, Test mix, 0.5 psi. Destination
= Run buffer A on outlet tray.
• Separate: 7 minutes, Run buffer A, 25 kV. Ramp
time 0.2 minutes. Destination = Run buffer A on
outlet tray.