http://www.abbs.info e-mail:[email protected] ISSN 0582-9879 ACTA BIOCHIMICA et BIOPHYSICA SINICA 2002, 34(4): 423-432 CN 31-1300/Q |
Protein
Isoforms Observed by Ultrahigh Resolution Capillary Isoelectric
Focusing-electrospray Ionization Mass Spectrometry
(
Research Centre for Proteomic Analysis, Key Laboratory of Proteomics, Institute
of Biochemistry and Cell Biology,
Shanghai
Institutes for Biological Sciences, the Chinese Academy of Sciences,Shanghai 200031,
China )
When
CIEF is coupled to mass spectrometry (MS), information-rich results can be
obtained to facilitate direct protein characterization. The CIEF-MS combination
is equivalent to 2-DE, a separation based on pI followed by an orthogonal
separation based on mass, but with even higher precision. Separation of pI
differences as small as 0.004 pH units by CIEF was reported[5]; MS
allows the precise molecular mass determination with an error of ±0.01%
and has the potential of obtaining structural information when it is operated
in collision induced dissociation[6-8]
(CID) or electron capture dissociation[9] (ECD) mode. The coupling
of CIEF to electrospray ionization (ESI) MS has been accomplished by using
sheath-liquid interface[10-19]
and liquid-junction interface[20-23].
CIEF can also be off-line coupled to matrix-assisted laser
desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) by using
sheath flow fraction collection system[24, 25]. In addition, the
microfabricated IEF device for direct ESI-MS was also reported recently[26].
CIEF-ESI-MS
is extremely useful for the analysis of mixtures of proteins with very close pI
values. Hemoglobin A and hemoglobin F, with a pI difference of 0.05 pH units,
were almost baseline resolved and characterized in CIEF-ESI-MS[11].
CIEF-ESI-MS has been used to analyze glycoform distribution[12],
protein phosphorylation[13], and protein refolding intermediates[14],
and the screening for high-affinity ligands of the Src SH2 domain[15].
One of the most ambitious and promising applications of this technique is the
two-dimensional analysis of the whole cellular proteins by CIEF-ESI-MS[16].
In addition, the use of isotope labeling of the cell culture media can not only
improve the mass measurement accuracy but also provide a means for the
quantitative proteome-wide measurement of protein expres-sion[18].
In
this study, ultrahigh-resolution CIEF-ESI-MS analytical system was established
using long LPA-coated capillary and sheath-liquid interface with active
capillary positioning[19]. The protein isoforms (proteins with same
mass, but different pI) of several standard proteins including cytochrome c,
myoglobin and b-lactoglobulin
A, and hemoglobin variants were analyzed.
1.1
Materials
All
chemicals used were of analytical grade if not mentioned otherwise. Formic
acid, glacial acetic acid, and standard proteins including myoglobin (horse
heart), carbonic anhydrase II (bovine erythrocytes, pI 5.9), b-lactoglobulin
A (bovine milk), human hemoglobin-A (HbA) and human sickle cell hemoglobin
(HbS) were purchased from Sigma (St. Louis, MO, USA); cytochrome c was
obtained from Pierce (Rockford, IL, USA); carrier ampholytes Pharmalyte 3.5-10
and Pharmalyte 5-8 were obtained from Amersham Pharmacia Biotech (Uppsala,
Sweden); HPLC grade methanol (MeOH) was obtained from Fisher (Fair Lawn, NJ,
USA), and all water was distilled and deionized (18 W)
using a Milli-Q system from Millipore (Bedford, MA, USA). HbA and HbS were
desalted using a PD-10 column (Amersham Pharmacia Biotech) equilibrated with
0.6% acetic acid and freeze-dried, other standard proteins were used as
received.
1.2
Methods
CIEF-ESI-MS Beckman P/ACE system 5500 (Beckman,
Fullerton, CA, USA) was coupled on-line to a Finnigan MAT LCQ electrospray ion trap
mass spectrometer (San Jose, CA, USA) via a sheath-liquid interface supplied by
Finnigan. For the combination of CIEF with ESI-MS, a BioCAPTM linear
polyacrylamide (LPA) coated capillary (80 cm ×
50 mm
I.D., 360 mm
O.D., Bio-Rad, Hercules, CA, USA) assembled in Beckman eCAPTM
capillary cartridge was mounted within the electrospray probe. A micrometer
head attached to the ESI probe allowed fine positioning of the capillary. The
polyimine coating at the outlet side of the capillary was burned off 2-3 mm and
washed off with ethanol to ensure the electric contact. The LCQ was tuned and
calibrated by infusing an aqueous solution of angiotensin (Sigma) and UltramarkTM
(Finnigan), respectively.
On-line
coupling of CIEF to ESI-MS was established by using a strategy of “active
capillary positioning”
modified from the method described by Kirby et al.[19].
Before CIEF, the whole CE apparatus was placed on a height-adjustable platform
and care was taken to ensure that the CE buffer reservoir and the electrospray
end of the capillary were at the same level to avoid the influence of gravity
flow. To start a run, the focusing catholyte[1% NH4OH (v/v)] used as
liquid sheath was delivered at a flow rate of 2 mL/min
by syringe pump on LCQ, and the gas sheath was set to 20 arbitrary units to
prevent liquid accumulation on the electrospray needle. Next, the capillary was
filled with a mixture of sample and ampholyte[≈0.1
mg of protein per mL of 1% Pharmalyte in H2O (w/v)], and the inlet
was placed in a buffer reservoir containing focusing anolyte[1%HAc (v/v)]. The
outlet was retracted 1.5 mm inside the liquid sheath tube with the aid of
micrometer to form a microreservoir at the end of the tube. The tube was
flushed with focusing catholyte for 2 min to remove any residual sample and
ampholyte in the microreservoir. The gas sheath was decreased to 7 arbitrary
units to allow a standing drop of focusing catholyte to form and stabilize on
the end of the liquid sheath tube, while the liquid sheath was still delivered
at the same flow rate. A constant focusing voltage of +30 kV (375 V/cm) was
then applied until the focusing was complete after about 40 min, as shown by a
minimum CE current of 1.0 mA.
After switching off the voltage, the capillary tip was extruded 1 mm outside
the liquid sheath tube with the aid of micrometer. Then, the liquid sheath was
quickly replaced by mobilization catholyte (0.25 / 75 / 25, HAc / MeOH / H2O,
v/v/v), and the inlet was placed in another reservoir containing mobilization
anolyte[0.5% HAc(v/v)]. To combine gravity with cathodic mobilizations, the
inlet reservoir was raised 8 cm above the electrospray needle. Finally, the gas
sheath was shut off, an ESI voltage of +4.25 kV was applied to the electrospray
tip, and a voltage of +30 kV was applied immediately to the capillary
(effective mobilization voltage gradient was 322 V/cm), and the data collection
was begun.
The
ion trap was scanned from m/z 1100 to m/z 2000 at a scan rate of
0.33 s/scan and detected in positive ion mode. Other parameters were as
follows: electron multiplier voltage, -950 V; heated capillary temperature, 180
℃; capillary voltage, +24 V; tube lens
offset, -5 V.
2.1
CIEF-ESI-MS analysis of model protein mixtures
A
mixture of model proteins, cytochrome c, myoglobin, and b-lactoglobulin
A was analyzed by ultrahigh resolution CIEF-ESI-MS. The mixture contains 1%
(w/v) Pharmalyte 3.5-10, and the following proteins: 8.0 mmol/L
cytochrome c; 1.5 mmol/L
myoglobin; 8.0 mmol/L
b-lactoglobulin
A. The protein mixture was focused in an 80 cm long LPA-coated capillary for
about 40 min under a constant voltage of 30 kV. The current decreased from 4.5 mA
at the beginning to 1.2 mA
when the focusing was finished. Figure 1 shows the base peak of CIEF-ESI-MS
analysis of the protein mixture. It can be seen that all three proteins were
well focused into narrow bands and all eluted within one minute, thus allowing
the resolving of proteins with very close pI values. Interestingly, it was
observed that each of these three proteins contained two isoforms with almost
the same molecular masses, even with longer time of focusing (Data not shown).
The isoforms of myoglobin with pI values of 7.2 and 6.8 are well known and are
often used as the IEF standard, while cytochrome c can only be detected
as a single band with a pI value of 9.6. Yang et al[23]
reported that two isoforms of cytochrome c could be found in CIEF-ESI-MS
by using the highly efficient microdialysis junction interface, but only one
kind of protein could be detected when coaxial liquid sheath interface was
used. In our experiment, two cytochrome c isoforms were well resolved
although a common sheath liquid interface was used; the increased resolution
might be due to the use of long capillary, in which a narrower pH gradient
could be established than that in short capillaries using the same ampholyte
mixtures. These results indicate that the increased resolution of analytical
method may contribute to the detection of protein isoforms separated in IEF
process. Besides cytochrome c and myoglobin, a minor isoform of b-lactoglobulin
A with very low abundance could also be detected by sensitive CIEF-ESI-MS. The
full mass spectra of these isoforms are shown in Figure 2. It can be seen that the
charge distribution patterns (and hence the molecular masses) of these protein
isoforms are quite similar but their migration times (and hence pIs) are
different.
Fig.1 CIEF-ESI-MS base peak of a mixture of
cytochrome c (8.0 mmol/L),
myoglobin (1.5 mmol/L),
and b-lactoglobulin
A (8.0 mmol/L)
Remark: Capillary, 80 cm total length, 50 mm
I.D. and 360 mm
O.D.; applied voltages, 30 kV for focusing and mobilization, 4.25 kV for
electrospray; sheath liquid, acetic acid/methanol/water (0.25/75/25), 2 mL/min;
mass scan, m/z 1 100-2
000 at 0.33 s/scan. The inlet reservoir is raised 8 cm above the electrospray
needle for the introduction of gravity flow.
Fig.2 Summed mass spectra from the labeled
peaks in the base peak in Fig.1
(A1)
cytochrome c 1, (A2) cytochrome c 2; (B1) myoglobin 1, (B2)
myoglobin 2; (C1) b-lactoglobulin
A 1, (C2) b-lactoglobulin
A 2.
Fig.3 Calibration curves of migration time
versus protein pI in CIEF-ESI-MS in different pH range
Fig.4 CIEF-ESI-MS base peak of a mixture of
cytochrome c (8.0 mmol/L),
myoglobin (2.5 mmol/L),
and carbonic anhydrase II (3.0 mmol/L)
Other
conditions are the same as in Fig.1.
Hemoglobin
is well known of the existence of a large number of variants, some variants can
result in the malfunctioning of the red cells, such as sickle cell hemoglobin.
Studies on hemoglobin variants are of great significance not only in basic
research but also in practice. The combined use of pI and mass data can greatly
facilitate the identification of different variants. For example, although the
mass shift between Hb C variant and Hb A is only 0.94 amu, which is not so easy
to differentiate them singly by ESI-MS, but the pI shift of 0.5 pH unit between
them can be easily detected by CIEF. The pI values of the most common four
hemoglobin variants were determined previously (Hb C, 7.45; Hb S, 7.20; Hb F,
7.0; Hb A, 6.95).
In
this study, a mixture of Hb S and Hb A was analyzed by high-resolution
CIEF-ESI-MS. Figure 5 shows the base peaks of the separations using Pharmalyte
3.5-10 and Pharmalyte 5-8. There were only two proteins in the mixture, but the
base peaks of the separations were more complicated. However, when selected ion
monitoring (SIM) was used to locate Hb S and Hb A (+12 charged ions with m/z
values of 1320.9 and 1323.4 were chosen for themonitoring of Hb S and Hb A,
respectively), it was found that the complexity of the base peak of separation
was due to the presence of 6 isoforms of hemoglobins with very close pI values
(3 isoforms of each variant). Moreover, the three isoforms of the same
hemoglobin (nominate as Hb 1, Hb 2 and Hb 3 according to their migration times)
was baseline resolved. Closer inspection revealed that the three isoforms of Hb
S had the same charge distribution pattern and molecular mass, the same results
were also observed in isoforms of Hb A (Fig. 6). Two isoforms of Hb S (Hb S2
and Hb S3) were contaminated by two isoforms of Hb A (Hb A1 and Hb A2), because
their pI values were too close. When ampholytes with narrow pH range was used
in CIEF-ESI-MS, the resolution of different isoforms could be further
improved[Fig. 5(B)].
Fig.5 CIEF-ESI-MS base peak (top panel) and SIM (middle and bottom
panels) of a mixture of hemoglobin S (3.0 mmol/L)
and hemoglobin A (3.0 mmol/L)
using (A) Pharmalyte 3.5-10 and (B) Pharmalyte 5-8
Fig.6 Summed mass spectra from the labeled
peaks in Fig. 5(A)
(A) Hb S1; (B) Hb A3. The insets show the
mass of hemoglobin a-chain
(labeling with A), bs-chain
(labeling with Bs), and (ba-chain
(labeling with Ba)
Fig.7 CIEF-ESI-MS base peak (top panel) and SIM (middle and bottom
panels) of a mixture of hemoglobin S (3.0 mmol/L),
hemoglobin A (3.0 mmol/L),
and model proteins cytochrome c (4.0 mmol/L)
and myoglobin (0.8 mmol/L)
using Pharmalyte 3.5-10
Other
conditions are the same as in Fig. 1.
The
mechanism of the formation of such protein isoforms in CIEF process is not
clear, but the possibility that it is formed due to the protein precipitation
can be eliminated. For example, the hemoglobin variants have been separated by
CIEF-ESI-MS at the concentration ranging from 10-5-10-7
mol/L, but no such isoforms were found[11], yet the protein
concentration used in this study is at the range of 10-6-10-7 mol/L.
In addition, two isoforms of cytochrome c could be detected when a
microdialysis junction interface was used even at a concentration of 10-7
mol/L[23].
Comparing
to other techniques, CIEF-ESI-MS can easily resolve isoforms with tiny pI
difference. For example, Hb A2 and Hb A3 with a pI difference of 0.04 pH units
can be baseline resolved by this technique. Other advantages of CIEF-ESI-MS
include simple sample preparation, high sensitivity, and the possibility of
automation. The information-rich data collected in CIEF-ESI-MS can greatly
facilitate the identification of proteins. CIEF-ESI-MS combination also
provides another orthogonal separation possibility in addition to capillary
zone electrophoresis-mass spectrometry (CZE-MS), liquid chromatography-mass
spectrometry (LC-MS), and 2-DE techniques. For example, the protein isoforms
found in this study cannot be detected by CZE-MS or LC-MS. The complementation
of these techniques not only can make the characterization of proteins more
reliable but also may contribute to the discovering of interesting molecular
processes.
Another
interesting phenomenon found in this study is: some proteins, such as
cytochrome c, myoglobin, and b-lactoglobulin
A, have two isoforms with identical molecular masses, in the case of
hemoglobin, even three isoforms were found for each variant; while other
proteins (e.g. carbonic anhy-drase II) do not have such isoforms.
Although theories of structural biology and dynamics may help to explain the
reason why such protein isoforms can form after IEF, deep-going investigations
in different fields, such as protein behavior in IEF, structural study of such
isoforms, are still need to perform to further explore the exact mechanism.
Acknowledgements The authors thank Prof.
WANG Ke-Yi in our institute and Dr. ZHU Ming-De in Bio-Rad laboratories for the
helpful discussion.
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Received:
December 6, 2001
Accepted: January 30, 2002
The
work was supported by grants from the Special Funds for Major State Basic Research Project (973) of China
(No.2001CB5102), and by State 863 High-Technology R&D Project of China (No.2001AA233031)
*Corresponding
author: Tel, 86-21-64374430; Fax, 86-21-64338357; e-mail, [email protected]