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afsaneh_abdolzade-bavil@europe.bd.com
Methods
Protein samples were diluted with the appropriate
FFE separation buffers and loaded via sample inlet
to the separation chamber. The FFE separations
were performed under native conditions using a
voltage of 900-1200 V depending on the current
separation.
Continuous Isoelectric Focusing FFE (CIEF)
buffers were prepared according to manufactures
description (BD™ FFE).
CIEF was performed at 10°C with buffer flow rate
between 30-60 ml/hr
Native isoelectric focusing polyacrylamid gel
electrophoresis (IEF-Native-PAGE) was done
using IEF-Gels from Invitrogen and Serva
according to manufactures description.
Results
In this study we separated protein isoforms from
human Anti-CD3, rabbit L-LDH, Amyloglucosidase
from Aspergillus Niger, ß-Lactoglobulin from
bovine milk and bovine plasma Fetuin by FFE.
Obtained FFE fractions were analyzed by IEF-
A simple way to use a 1D split-free nano-HPLC in an automated 2D LC-MS/MS setup
1 1,3 2 2 2 3
Taylor, P. , Moran, M , Podtelejnikov, A. , Andersen, M. , Vorm, O. and Kislinger, T.
1. Hospital for Sick Children, Ontario, Canada 2. Proxeon, Odense, Denmark 3. University of Toronto,
Department of Medical Biophysics, Ontario, Canada
Introduction
Analysis of complex biological samples often
requires several separation steps. One of the
commonly used technologies in the filed of
proteomics is automated two-dimensional Liquid
Chromatography coupled with Mass Spectrometry.
(2D LCMS) based on on-line strong cation
exchange (SCX) / reverse phase (RP) separations.
That sophisticated system uses ternary or
quaternary gradient generation systems to deliver
the stepped salt concentrations needed to affect
release of the peptides from the SCX resin onto
the RP material and then to elute the peptides
from the RP column followed by MS/MS analysis.
Here we describe a simple, automated SCX/ RP
on-line 2D separation strategy achieved on a split-
free 1D nano LCMS system.
Method
To evaluate the system performance we analyzed
the proteome of mouse placental cells. The
cytosolic fraction was subjected to cysteine
reduction and alkylation with iodoacetamide
followed by trypsin digestion. The lysate was
purified and analyzed by 1D and 2D methods on a
split-free nano LCMS system (EASY n-LC Proxeon
Biosciences, Odense Denmark) coupled to LTQ-
Orbitrap (Thermo-Fisher, Bremen, Germany). In
order to perform 2D separation 10 step injected
salt gradient was used varying from 0.05 to 0.5 M
NH4Acetate.
Results
By using the auto-sampler component and
standard sample injection programs we were able
to accomplish the salt delivery using a split-free
nano LCMS system and therefore transforming the
system into 2D system. The viability of this method
was demonstrated by comparative analysis LCMS
data obtained from 1D and 2D separations. As a
result a 1D analysis yielded about 600 protein
identifications whereas 2D analysis gave
approximately 2000 proteins identified. The
transformation of 1D system into 2D system
makes it possible to obtain much more information
out of a single sample as easily as a traditional 1D
run and making use of the same 1D nano LCMS
setup.
Innovative aspects
These results clearly demonstrate the significant
improvement which can be achieved by slight
modifications of the 1D nano LCMS
A New Stain Free Gel System and its Compatibility with Western Blotting and Mass
Spectrometric Protein Identification
T. Wehr, Y. Yan, K. McDonald, K. Bala, A. Paulus and N. Liu
Bio-Rad Laboratories, Life Science Group, 6000 James Watson Drive, Hercules, CA 94547, USA
Introduction Results
Gel electrophoresis is considered to be a labor The stain-free gels exhibited no difference to the
intensive and cumbersome separation method. To normal gels in western blotting using tested
visualize proteins after the mass separation, antibodies. The WesternC protein standards, LIM
staining is necessary, adding to the time and labor kinases were detected with similar patterns and
requirements. We are introducing Criterion Stain intensities on the stain free and control gels. For
Free gels containing unique components in its MS protein identification, the same set of high
Tris-HCl gel solution which provide fluorescent abundance proteins selected from the stain-free
detection of proteins within 5 min after and control 2-D gels returned the same identities
electrophoresis separation, such shortening the whether by LC-MS/MS or MALDI-TOF MS, even
workflow and reducing the hands-on time of gel through some tryptophan residue-containing
electrophoresis. The unique compounds react with peptides were often missing in the peptide
tryptophans in an UV light-induced reaction to form coverage for the stain free gel samples. Database
fluorescent products in the visible range and thus searching with a dynamic modification of the
allowing protein band detection. The modification tryptophan-residue recovered a few but not all
of the tryptophan residues raises concerns tryptophan-containing peptides. However, this
regarding the compatibility of this method with search modification might help identifying the low
follow-on methods such as western blotting and abundance proteins on the stain free gels.
LC-MS/MS or MALDI-TOF MS protein
identification.
Methods Innovative aspects
HeLa cell total proteins were extracted from o Novel protein visualization method with no
cultures in a urea-containing lysis buffer. The total need for time and labor intensive staining
proteins were separated on either 1-dimensional protocol
(1-D) or 2-dimensional (2-D) stain free gels. The 1- o Compatibility of protein visualization with
D gels were blotted to nitrocellulose membranes follow-up applications such as western
and probed with a selection of antibodies, blotting, LC-MS/MS and MALDI-TOF MS
including an antibody to detect the Bio-Rad analysis
WesternC protein standards. The 2-D gels were
stained with Coomassie following UV light imaging.
Protein spots with different intensities were
randomly selected from the gels for protein
identification by mass spectrometry using either
LC-MS/MS or MALDI-TOF MS. The HeLa total
protein separated on the normal Criterion Tris-HCl
gels served as control.
Proteomics Based on Peptide Fractionation by SDS-Free PAGE.
1 1 1 1 1
Yassel Ramos , Elain Gutierrez , Yoan Machado , Aniel Sánchez , Lila Castellanos-Serra , Luis Javier
1 2 3 1 1
González , Jorge Fernández-de-Cossio , Yasset Pérez-Riverol , Lázaro Betancourt , Jeovanis Gil , Gabriel
1 1 1 2 3
Padrón and Vladimir Besada . Dept. Proteomics, Dept. Informatics, Dept. Bioinformatics, Centre for
Genetic Engineering and Biotechnology, Havana, Cuba
Results
A straightforward method was achieved for SDS-
PAGE of proteins, enzyme digestion, peptide
transfer and fractionation by SDS-free PAGE,
which was named dual-fractionation
polyacrylamide gel electrophoresis (DF-PAGE).
This method increases the number of identified
proteins 2.5-3 fold with respect to the proteins
identified after direct analysis, and more than 80%
of assigned peptides were found in unique SDS-
free gel slices. A vast majority of identified
peptides (93%) have pI values below 7.0 and 7%
have pI values between 7.0 and 7.35. Peptide
digests that were derived from complex protein
mixtures were in consequence simplified as
peptides that are positively charged are not
recovered in the present conditions. Fractionation
of tryptic peptides from casein allowed the isolation
of phosphopeptides in the fraction of highest Figure 1. Tryptic digestion of the recombinant
migration. The use of SDS for protein fractionation Streptokinase fractionated by SDS-free PAGE. A) Non-
allows analysis of highly hydrophobic proteins and fractionated digest, B-I) Lowest to highest migration
minimal protein loses. The analysis of a membrane fractions.
protein extract from Neisseria meningitides by this
approach, where a very few components represent
about 90% of the total protein mass (estimated by
External gradient chromatofocusing for quantitative analysis of complex lysates
Karl Burgess, Kit-Yee Tan, Lachislav Tsonev, Terry Sheehan, Ken Cook and Andrew R Pitt
Functional Genomics Facility, University of Glasgow,
G12 8QQ, Glasgow, Scotland
Methods
Results
A 12000
B 12000
C
Methods 10000 10000
μS
monitor the salt concentration of samples. The salt 6000 6000
4000
2000
‧ E.coli crude extract ‧ E.coli crude extract
2000
‧ Pig liver crude extract ‧ Pig liver crude extract
calibrating the observing conductivity (μS) against 0
0
‧ Chinese Pennisetum crude extract
100 200 300 400
0
0.0 0.2
‧ Chinese Pennisetum crude extract
0.4 0.6 0.8 1.0 1.2
standard curves for various salts, such as NaCl NaCl concentratrion (mM)
0 20 40
PBS dilute ratio
60 80 100 120
27.4 54.8 82.2 109.6 137 164.2
20 30 40 50 60
2.02 4.04 6.06 8.08 10.1 12.12
from swine liver were separated using 7cm IPG Figure 1. Utilization of conductivity to measure the salt
strips (pH 3-10) with different focusing programs. concentration of 2-DE samples. (A) Conductivity meter
The electrophoretic result of the second dimension (B) The relationship between the conductivity (mS) and
12.5% SDS-PAGE gels were revealed using the NaCl concentration (mM) in 2-DE sample buffer. (C)
VisPro 5 minute protein stain. The focusing results The relationship between the conductivity (mS) and the
serially diluted PBS in 2-DE sample buffer. The salt
of IEF were investigated for 2-DE samples
content in three TCA precipitated 2-DE samples (E. Coli,
containing exogenous supplement of NaCl from 0 pig liver and Chinese Pennisetum) were calibrated
to 120 mM. against two standard curves respectively.
Current (μA)
Voltage (V)
Voltage (V)
A)μ
A)μ
A)μ
Voltage (V)
Voltage (V)
Current (
Current (
1750Vhr
100 200
Time (minute)
300 400
0 0
0
1250Vhr
100 200
Time (minute)
300 400
0 0
0 100
750Vhr
200 300
Time (minute)
400
0 0
0
550Vhr
100 200 300
Time (minute)
400
0 0
0
350Vhr
100 200 300
Time (minute)
400
0
5000
120
100
6000
5000
120
100
6000
5000
120
100
6000
5000
120
100
6000
5000
120
100
Current (μA)
Current (μA)
Current (μA)
Current (μA)
Voltage (V)
Voltage (V)
Voltage (V)
Voltage (V)
Voltage (V)
0
0 100 200 300 400
20
0
1000
0
0 100 200 300 400
20
0
1000
0
0 100 200 300 400
20
0
1000
0
0 100 200 300 400
20
0
1000
0
0 100 200 300 400
20
concentration. A pre-washing procedure of the Figure 2. Evaluation the optimal IEF program for a
sample rehydrated IPG strip is a more effective regular 2-DE sample. 50 μg of TCA precipitated proteins
mean to diminish the interference of salts. from pig livers was separated by IEF (7cm IPG strip, pH
Additionally, many suggested IEF programs were 3-10) and 12.5% SDS-PAGE. The IEF programs were
found more than sufficient for focusing proteins. In evaluated from total 350 Vhour (Vhr) to 30750 Vhour.
a 7cm IPG strip, as low as a total 750 Vhour was The IEF program with a total 5750 Vhr is the
recommended by the manufacturer, Amersham
required for a complete focusing of 50 μg proteins Bioscience. A minimal 1250 Vhr was found sufficient to
(Fig 2). Applying high voltage may not improve the focus most proteins in the evaluated samples.
focusing result but bring in the risk of strip burning.
Isoelectric Western Blotting (iWB) after Digital Proteome Chip (dPC) Focusing
† † † † † †
Thomas Miller, James R. Dasch, Malcolm G Pluskal, Russell Garlick, Stephen Haralampu, Bill Skea,
‡
*Bhanu Singh, *David Malarkey and Sun W. Tam
†
Protein Forest, Inc. 100 Beaver St., Waltham, MA, USA; *National Institute of Environmental Health
‡
Sciences; 111 Alexander Drive, Research Triangle Park, North Carolina and Proteomic Fractionation Group,
University of Massachusetts Medical School, 222 Maple Avenue, Shrewsbury, MA, USA
Methods
dPC were run under standard conditions. For this
analysis both pH 4.20-6.20 and pH 6.00-8.00 dPC
were used. Protein lysate extracted from rat livers
was obtained from NIEHS. To electroelute
proteins from dPC onto membranes, two methods Figure1. Reproducibility of dPC Western Analysis. 0.05
were developed, a wet tank transfer system and a μg biotinylated ovalbumin was fractionated on pH 4.20
semi-dry transfer system. For the tank transfer to 6.20 dPC. The ovalbumin was transferred to PVDF
process, the PVDF membrane is adhered to the membrane using the tank method. After blocking, the
dPC at high pressure using linear polyacrylamide blot was probed with HRP-strepavidin and ECL
as a reversible adhesive. The PVDF-dPC substrate.
sandwich is placed back into the specialized
running chamber containing transfer buffer and the
proteins are electroeluted from the dPC onto the
membrane. For the semi-dry method, a specialized
chamber was developed, wherein the dPC is
placed next to a piece of PVDF membrane. This
sandwich is placed directly between two plate
electrodes. Thereafter the proteins are transferred
from the dPC onto the membrane. Good contact
between the electrodes, dPC, and the PVDF Figure2. dPC Western Analysis of F1,6 BPase from a
membrane is maintained by using several sheets liver lysate fractionated on two pH 4.20 to 6.20 dPC. The
of pre-wetted filter paper on both the cathode and lysates was transferred to PVDF membrane using the
anode sides. semi-dry method. After blocking, the blot was probed
with a F1,6 BPase antibody and followed with a anti-Ig
Results HRP conjugate. Blots were visualized using ECL
Biotinylated ovalbumin was used as a test chemiluminescent substrate.
compound to work out elution conditions for
proteins from the dPC. Parameters examined
included time, voltage and current, in addition to
the need for pre-equilibration in a buffer containing
SDS. It was found that efficient transfer of proteins
to the membranes in both systems was
accomplished in less than 20 minutes at low
Fast targeted Proteomics on a chip
1 2 1
Zuzana Demianova , Sami Franssila and Marc Baumann
1
Protein Chemistry Unit, Institute of Biomedicine, University of Helsinki, 00014 Helsinki, Finland
2
Micro and Nanosciences Laboratory, Helsinki University of Technology, 02015 Espoo, Finland
Methods
Our PASGE- and ComPress-chip are based on the
classical technology including the polyacrylamide Figure 1 → Photographic illustration of miniaturized
instruments. A) PASGE-chip and B) ComPress-chip
matrixes. The PASGE-chip (3x2.5x1 cm, width x
length x depth) is capable of running five different
samples. The ComPress-chip (4x5.2x2.2 cm) is A kD HbA2
A
1 2 C
3 HbF HbA1c
able to perform a 2-DE in a single analysis. The HbS
chips separated a set of predefined standards as HbA
50 ctrl
Standard proteins were in-gel alkylated and 37
1 1 2 1 3 2
Xiangming Fang , Lei Huang , Weijun Qian , Sergey Sikora , Kimimichi Obata , Richard Smith , Wei-Wei
1
Zhang
1
GenWay Biotech, Inc., San Diego, CA, United States
2
Pacific Northwest National Laboratory, Richland, WA, United States
3
PSS Bio Instruments, Inc., Livermore, CA, United States
Introduction The wide dynamic range of protein satisfactory; (3) SepproTip can be reused up to 30
concentration in mammalian biofluids posts a times. The turnaround time of 12 samples per 55
formidable challenge for low abundance biomarker minutes allows large number of samples being
detection using MS or 2DE technologies. To tackle processed without decrease in sample preparation
this challenge, we developed an avian IgY quality. The SepproTip system makes “digging
antibody-based immunoaffinity fractionation faster” possible for meeting the needs of HTP
®
platform, Seppro IgY-14 for removal of top 14 sample preparation.
high-abundance proteins (HAP), SuperMix for
separation of moderate-abundance proteins (MAP) Innovative aspects
from Low-abundance proteins (LAP), and • IgY antibody-based immunoaffinity columns
SuperEnrich for capturing of proteins from tissue enable highly-specific and effective capture of
leakage. An automated SepproTip system for HTP target proteins from complex biofluids.
sample preparation and facilitating biomarker • Seppro® fractionation platform enhance
validation. detection of LAP from top-down or bottom-up
approaches.
Methods To generate plasma protein-based • SepproTip automation system meets the needs
SuperMix IgY antibodies, human plasma was first of HTP sample preparation.
depleted of 12 HAP via IgY-12 column. The protein
mixture in flow-through fraction was used as
antigens to immunize chickens and as affinity
ligands to purify antibodies. The antibodies were
covalently coupled to microbeads. To fractionate
plasma samples, an IgY-14 LC10 column was
tandem connected to a SuperMix IgY LC2 column.
The fractions are analyzed by LC/MS/MS. To
generate cell protein-based SuperEnrich IgY
antibodies, proteins isolated from cell lines were
used as antigens and affinity ligands. The
antibodies were covalently coupled to polymeric
microbeads or magnetic beads. Cell lysates and
plasma samples were processed through
SuperEnrich column, and the resulting fractions
were analyzed by LC/MS/MS.
®
Results By coupling Seppro IgY-12 or 14 HAP
removal with the MAP-separating SuperMix
system, proteins less than 1ng/ml in plasma were
detected by LC/MS/MS analysis. The SuperEnrich Figure 1. Enhanced detection of LAP in plasma using
IgY columns against prostate cancer, lung cancer, IgY-12 coupled with SuperMix columns. The results
and lymphocyte cells were shown to be able to show more than 2 fold increase of protein identification.
capture more than 500 cellular proteins in each
cell line. Cellular proteins, such as membrane,
nuclear, and mitochondria proteins, were captured
in plasma samples, indicating the usefulness of the
columns for tissue leakage biomarker enrichment
from plasma or serum samples. The SepproTip-
treated samples were analyzed by 1DE, 2DE, and
MALDI-TOF-MS. The results demonstrated that
(1) SepproTip specifically removed all target
proteins; (2) the reproducibility of SepproTip is
A multi-approach experiment to analyse aphid salivary proteome
1 1 2 1
Nicolas Harmel , Eric Haubruge , Edwin De Pauw , and Frédéric Francis
1
Gembloux Agricultural University, Functional and Evolutionary Entomology, Passage des Déportés
2, 5030 Gembloux, Belgium
2
University of Liege, Mass Spectrometry Laboratory, Sart Tilman, B22 building, 4000 Liege, Belgium
Marco Galésio, Diana Vieira, Raquel Rial-Otero, Carlos Lodeiro, and José L. Capelo
REQUIMTE, Departamento de Química, FCT-UNL, 2829-516 Caparica, Portugal
Introduction
The development of rapid methods for protein
separation, identification and quantification has
important clinical and toxicological implications. In
the last decades, continuous progress in analytical
methodology has been achieved. New findings in
sample treatment based on ultrasonic assisted
protein enzymatic digestion (USAPED) after
polyacrylamide gel electrophoresis separation
have been developed in our laboratory [1]. The
aim of this work was to compare the overnight and
the new ultrasonic methodologies for protein
digestion when fluorescent dyes are used for
protein visualization.
Methods
For the purpose of this study, a standard protein
mixture of glycogen phosphorylase b, 97 kDa;
bovine serum albumin, BSA, 66 kDa; ovalbumin,
45 kDa; carbonic anhydrase, 30 kDa; trypsin
inhibitor, 20.1 kDa; and α-lactalbumin, 14.4 kDa,
was used.
Stain solutions were prepared diluting the stock
solutions of Sypro Red and Sypro Orange 1:5000
in acetic acid (7.5%, v/v). Protein bands were
observed in an electronic UV transiluminator
radiating at 300 nm. Ultrasonic protein enzymatic
digestion was performed in a sonoreactor system.
Protein identification after sample treatment was Figure 1. Comparison of the overnight protocol (orange
done through Peptide Mass Fingerprint (PMF) color) and the ultrasonic sample treatment with 4 min of
using a MALDI-TOF-MS system model Voyager digestion time (green color) in terms of protein sequence
DE-PRO Biospectrometry Workstation equipped coverage (%) and number of peptides matched. The
with a nitrogen laser radiating at 337 nm. Sypro Red staining was used.
Liang Gao, Zhen Liang, Lihua Zhang, Yushu Huo, Yukui Zhang
National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics,
Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, PR China
Introduction
Deer antler is a well-known traditional Chinese
medicines (TCMs), with the obvious regulation
effects on diseases of nervous system, Innovative aspects
immunologic system, cardiovascular system and • Research on the bioactive components in deer
genital system. The bioactivity of deer antler has antler
been considered to be related with the • Two dimensional method containing SEC and
components, such as peptides and proteins. In IEC for high resolution protein separation with
order to investigate the molecular mechanisms of bioactivity maintained
the regulation effects of deer antler, the separation
of proteins in deer antler was performed with off-
line two dimensional size-exclusion 1000 f1 f2 f3 f4 f5
chromatography (SEC) and ion-exchange
chromatography (IEC), to keep the protein activity, 800
Methods 400
℃
extracted by 50mM Tris-HCl, pH 7.5, at 4 for 72
0
hours. The extracted proteins were firstly
separated on a G3000SW XL column (Tosoh, 0 5 10 15 20
Results
In order to study the bioactive components of deer
antler, the complicated extracted proteins should
mV
Introduction
Obtention of a subset of modified peptides of
interest from very complex mixtures of proteins is
of challenging interest. Protein phosphorylation / Innovative aspects
dephosphorylation is often considered as an • Synergical combination of two techniques
“on/off” molecular switch for cell signaling and yielding improved selection of phosphorylated
many other cellular processes. However, for MS peptides sequenced by MALDI TOF TOF
based identifications, modified peptides represents MS/MS
only an infinitesimal fraction. Enrichment via • Commercially available chromatography
immunoaffinity has greatly helped and so has columns
metal affinity columns(1). Both techniques have
their flaws, the first yields a cohort of non specific References
peptides, and the second looses selectivity when (1) Pinkse et al, Selective Isolation at the
non phosphorylated peptides are too abundant. Femtomole Level of Phosphopeptides
Here we have combined both techniques to from Proteolytic Digests Using 2D-
increase our confidence in peptide identification NanoLC-ESI-MS/MS and Titanium Oxide
and modifications’ localisation. Precolumns; Anal. Chem.2004, 76,3935-
3943
Methods
Proteins from biological samples were extracted
and digested according to the Phosphoscan® kit
protocol from Cell signalling Technology. After C18
purification and concentration, Phophotyrosine-
containing peptides were immunoprecipitated
using mouse mAb (P-Tyr-100) beads. Eluted
peptides were separated on an Ultimate 3000 2D
nanoLC system using a novel Dionex TiO2
µprecolumn (1cm length, 200µm i.d.) and
fractionated on a MALDI plate for MS/MS
identification through Mascot 2.2. Flow-trough (ft)
and eluted (po) fractions were both collected after
separate reverse phase fractionations.
Results
We have compared the same samples with or
without TiO2 filtering. Although immunoaffinity
yielded many peptides bearing phosphate groups,
those were still among an impressive number of
nonphosphoryated ones. The implementation of
the TiO2 column allowed discrimination between
the two species to an almost perfect yield. Thus
we can argue that this supplemental step is
improving separation and selection of
phosphorylated precursors for MALDI MS/MS.
However we still need to determine the limitations
of the TiO2 microcolumn, since a large excess of
nonphosphorylated peptide lead to a partial loss of
selectivity.
We were also able to make a “shortlist” of
phosphorylated species which are identified in
each fraction regardless of the sample treatment,
in other words a kind of “phosphorylated baseline
signal in human cells”.
Separation of Membrane Proteins and Protein-Complexes Using Free-Flow
Electrophoresis
1 1 2 1 1
Hartmann K , Kronbauer S , Islinger M , Eckerskorn C , Nissum M
1
BD Diagnostics, Innovation Center Biotechnology, Martinsried, Germany
2
Department of Anatomy and Cell Biology II, University of Heidelberg, Germany
Methods
Membrane protein extracts from HeLa cells were
prepared including washing steps with sodium
carbonate buffer and dissolving the final pellet in a
low-salt buffer, containing a proprietary cleavable
detergent. The OXPHOS protein complexes were
solubilized in a low-salt buffer, containing digitonin
as detergent. IZ-FFE was carried out at constant
pH 7.8. For further analysis of separated protein
complexes BN-PAGE was performed. Collected
protein fractions were digested and analyzed using
LC-MS/MS (Agilent 1100 binary HPLC system
coupled to a Bruker HCTultra ion trap mass
spectrometer).
Results
We observed precipitation in the separation
chamber when the membrane protein extract from
HeLa cells was separated in the IEF-FFE mode
even when a detergent was included in the
separation media. Application of the IZ-FFE mode
significantly increased protein solubility and
prevented precipitation. The separation media
containing the cleavable detergent facilitated the
coupling to LC-MS/MS since no cumbersome
detergent removal was necessary. Membrane
proteins identified by LC-MS/MS of the individual
FFE fractions were analyzed based on the number
of transmembrane domains using the TMHMM
software (www.cbs.dtu.dk/services/TMHMM/).
The inner mitochondrial membranes extracted
from rat liver mitochondria were chosen as a
model for setting up analytical methods for
Utilization of Immunoaffinity Interaction for Specific Antibody and Peptide Separation
Md. Fida Hasan1*¶, Yoichi Kumada2§, and Shigeo Katoh1, 2
1
Dept. of Molecular Science and Material Engineering, Graduate School of Science and
Technology, Faculty of Engineering, Kobe University, Japan, 2 Dept. of Chemical Science and
Engineering, Faculty of Engineering, Kobe University, Kobe 657-8501, Japan
Present Address: * ¶ Department of Process Engineering and Applied Science, Food Science
and Technology Program, 1360 Barrington Street, P.O. Box 1000, Halifax, NS, B3J2X4,
Canada, Fida.Hasan@Dal.Ca; Tel: 1-902-494-3211, Fax: 1-902-420-0219
§ Department of Chemistry and Materials Technology, Kyoto Institute of Technology, Kyoto
606-8585, Japan
ABSTRACT: In recent years, immunoaffinity, using methods that are both sensitive and
specific, has challenged classical techniques. The highly specific antibodies constitute a
promising tool in the isolation of functionally homologous peptides from protein hydrolysates.
The separation of antihypertensive fragments from water extracted bonito protein hydrolysates
(WEBPH) has been studied by using antibodies. We produced antipeptide antibodies against
modified C-terminal peptide (KKPTHIKWGD, PC-IACE) from tuna glyceraldehydes-3-
phosphate dehydrogenase (GAPDH). The GAPDHs are a family of novel peptides with strong
antihypertensive properties. This modified peptide was used as a model to demonstrate the
immunoaffinity screening strategy. An efficient procedure for the separation of high
immunoaffinity peptides from a WEBPH with inhibitory activity was developed. Polyclonal
antibodies have been generated by immunization of rabbits with chemically synthesized PC-
IACE conjugated to the carrier protein keyhole limpet hemocyanin (KLH). An antipeptide
antibody was purified against a PC-IACE by CNBr activated Sepharose peptide column
chromatography. Both antibodies were used in competitive enzyme-linked immunosorbent assays
(ELISA) to binding characteristics against peptide-BSA conjugate. The specificity of antibodies
was evaluated by a indirect ELISA and a competitive indirect-ELISA. The ELISA was valuable
for detecting the existence of PC-IACE specific antibodies in the sera and purified products and
quantifies the antibodies. In Dot blot analysis, the purified antibody also recognized a peptide-
BSA conjugate.
This highly specific and sensitive antipeptide antibody provides an important tool for the
separation of peptide drug, with immunoaffinity interaction from the other members of the similar
peptides. Immunoaffinity chromatography columns with the immobilized purified antipeptide on
CNBr activated Sepharose gel retained the homology peptide from the WEBPH. Monitoring the
purification of hydrolyzed peptide with antipeptide antibodies suggests that while the
performance of the evaluated purification procedures would be reasonably acceptable in terms of
their yield, recovery and purity are attractive. Applications of these antibody tools are suggested
for the rapid detection and purification as well as evaluation of specific binding dynamics.
Solid Phase Extraction - Liquid Chromatography (SPE-LC) Interface for Automated
Peptide Separation and Identification by Tandem Mass Spectrometry
O.B. Hoerning; M.B. Andersen; O. Vorm
Proxeon A/S, Staermosegaardsvej 6, DK-5230, Odense M, Denmark
Introduction
Solid phase extraction (SPE) is a simple, widely
used technique for desalting and concentrating
peptide and protein samples prior to mass
spectrometry analysis. Often, SPE sample
preparation is done manually and the samples
eluted, dried and reconstituted into 96 well titer
plates for subsequent LC-MS/MS analysis. To
reduce the number of sample handling stages and
increase throughput, we developed a robotic
system to interface off-line SPE to LC-ESI-MS/MS.
Method
Samples were manually loaded onto disposable
SPE tips that subsequently were connected in-line
with a capillary reverse phase (RP) column.
Peptides were recovered from the SPE step and
separated on the RP column using isocratic elution
conditions and analyzed by electrospray tandem
mass spectrometry. Flow was delivered by two
nanoflow piston pumps operated with Advanced
Flow Control (AFC) (Proxeon, Denmark). Using a
modified autosampler for mounting and disposal of
the SPE tips, the SPE-LC-MS/MS system could
analyze 8 samples per hour. Up to 96 SPE tips
can be processed in one batch.
Results
The chromatographic performance of the SPE-LC
system was evaluated in terms of peptide ion peak
widths, column peak capacity and retention time
reproducibility based on the analysis of tryptic BSA
and a 12 protein component mixture. Peptide
mixtures eluted within approximately 5 minutes,
with individual peptide peak width of ~5 seconds
(FWHM), making the SPE-LC suited for high
throughput analysis. The MS/MS data was
extracted and searched against a protein database
using the Mascot search engine resulting in
confident identification of the standard proteins.
The relatively high sample throughput, separation
power and high sensitivity makes the automated
SPE-LC MS/MS setup attractive for proteomics
experiments as demonstrated by the identification
of the components of simple protein mixtures and
of proteins recovered from SDS-PAGE and 2DE
gels.
Innovative aspects
Sensitive, high throughput analysis of peptide
samples by a novel SPE-LC - MS/MS set-up.
2D protein and peptide separation of serum by preparative monolithic
chromatography
1 2 3 1 1
Linda IJsselstijn , Deborah Kronenberg , Remco Swart , Peter J. Koudstaal , Peter A. E. Sillevis Smitt ,
2 1
Monique M. B. Breteler and Theo M. Luider
1 2
Department of Neurology and Department of Epidemiology and Biostatistics, Erasmus Medical Center,
Dr. Molewaterplein 50, 3015 GE Rotterdam, the Netherlands
3
Dionex Benelux B.V., Abberdaan 114, 1046 AA Amsterdam, the Netherlands
Methods References
Serum was diluted 25 times in 0.05% TFA water (1) This work was supported by the
and 1 μl was injected onto a nanoLC system Netherlands Proteomics Centre
(Ultimate 3000). A custom-made monolithic
column with size 500-μm i.d. × 100 mm was used.
A 25 min gradient of 24-48% ACN was applied and
the fractionation time was varied resulting in 24, 48
and 96 fractions, respectively. The fractions were
enzymatically digested. Separation in the second
dimension was done on an identical system with a
monolithic column with size 200-μm i.d. × 50 mm.
A 10 min gradient of 0-48% ACN was applied and
the flow through was spotted on PAC-plates
(Bruker Daltonics). The fractions obtained in the
first dimension were also spotted on PAC-plates
without further separation. Subsequently, mass
Figure 1: Flow chart of the 2D approach. Dashed line
spectra of the spots were obtained by automated
indicates the 1D approach.
MALDI-TOF/TOF (Ultraflex).
Results
The separation of serum proteins on the monolithic
column was reproducible with an average CV of
0.23 ± 0.18% for retention time. The CVs were
calculated using the retention time of the eight
highest peaks in the UV trace of five successive
runs. This high reproducibility opens the possibility
to run the separations in a repetitive way, enriching
lower abundant proteins. Mass spectrometric
analysis of the 24, 48 and 96 digested protein
fractions showed that by increasing the number of
fractions from 24 to 96 twice the amount of Figure 2: UV-traces (214 nm) of the separation in the
compounds were picked by WarpLC software first dimension (protein level) of five successive runs of
(Bruker Daltonics). In addition, a higher number of the same sample on a preparative monolithic column.
fractions resulted in a relatively higher S/N for low Human serum albumin elutes after 15 min and
abundant peptide peaks. Results of the second apolipoprotein A after 22 min.
separation of 48 protein fractions showed a large
MSRAT, A Proteomic Sample Software Analysis Tool
Oren Kagen, James R. Dasch, Russell Garlick, Bill Skea, Andrew L. Johnson, ∗§Yakov Chudnovsky,
† † † †∗ †
∗§
David M. Sabatini, ∗Eric Spooner, William C. Hahn, Milan G. Chheda and Howard A. Fine
§# §# ‡
† ∗
Protein Forest, Inc. 100 Beaver St., Waltham, MA,02453; Whitehead Institute for Biomedical Research,
Cambridge, MA 02142; Broad Institute, Cambridge, MA 02139; #Department of Medical Oncology, Dana-
§
‡
Farber Cancer Institute, Boston, MA 02115; and Neuro-Oncology Branch, National Cancer Institute, National
Institutes of Health, Bethesda, MD 20892
Results
Introduction
Understanding cellular regulation requires insight References
in the relationship between mRNA expression and (1) Kiick et al, Incorporation of azides into
protein expression. Although the availability of the recombinant proteins for chemoselective
complete genome of various species has resulted modification by the Staudinger ligation; Proc
in a shift from the level of a single gene or protein Natl Acad Sci USA 99, 19-24 2002
to genomics and proteomics, analysis of post- (2) Dieterich et al. Selective identification of
transcriptional regulation on a genome-wide scale newly synthesized proteins in mammalian
is still a daunting challenge. For this purpose we cells using bioorthogonal noncanonical amino
are developing a chemical pulse-chase labeling acid tagging (BONCAT) Proc Natl Acad Sci
system. USA 103, 9482-7 (2006)
(3) Back et al, Mild and chemoselective peptide-
Methods bond cleavage of peptides and proteins at
We employ the tolerance of the methionyl-tRNA azido homoalanine Angew.Chem. Int. ed.
synthetase towards the methionine analogue 117, 8160-8164 (2005)
azidohomoalanine (Azhal) to label the E. coli
proteome (1,2). By using a selective and mild
chemical reaction directed against azides (3) in
combination with diagonal chromatography we
separate labelled peptides from unlabeled species,
thereby enabling mass spectrometric identification
of newly synthesized proteins. Quantification of
proteins labelled by a pulse of Azhal will allow
determining both the relative rates of synthesis
and the half lives of proteins on a genome wide
basis.
Results
To look at protein synthesis on a small timescale, figure1: structure of the methionine analogue Azhal
E. coli cells are grown in mineral medium for 15 used to label newly synthesized proteins in E. coli.
minutes in the presence of Azhal to label newly
syntesized proteins. Under the conditions used,
growth rates of E. coli are the same on Azhal or
methionine during the labeling time used.
Separation of the labeled peptides from the
unlabeled species by diagonal chromatography
resulted in more than 500 newly synthesized
proteins identified with a low false discovery rate.
This for the first time allows proteome wide
detection of newly synthesized proteins in
prokaryotes. Comparison of these findings with
micro-array data will provide valuable insights into
the regulation of protein expression at the
translational level and shed new light upon the
regulation of proteins in the bacterial cell.
figure 2: mild chemical cleavage of azhal containing
Innovative aspects peptides by TCEP, inducing either reduction from an
• Proteome wide analysis of protein azide to an amine or cleavage after Azhal resulting in a
peptide with a c-terminal homoserine lactone residue
synthesis rates in prokaryotes.
and a peptide with a normal n-terminus.
• Diagonal chromatography of azide
labeled peptides proteome wide.
SDR HyperD® Resin for Detergent Removal Prior to Mass
Spectrometry Analysis
Hongshan Li, Saurabh Nagpal, Gurpreet Kaur, Brian Miller and Lisa Bradbury; Pall Corporation
Biological detergents frequently play a critical role in the preparation of protein containing
samples, most commonly for protein solubilization, denaturation, and/or stabilization.
Unfortunately detergents often interfere with downstream applications and analytical techniques,
e.g., mass spectrometry (MS) analysis, thus requiring detergent removal prior to use. There are
many methods for detergent removal including dialysis, gel filtration and ultrafiltration. In this
study, Pall SDR HyperD® resin is evaluated for rapid, efficient detergent removal from protein
samples using Nanosep® spin device, 96-well plate, and 1ml pre-packed column formats. The MS
experimental data shows that SDR HyperD® treatment significantly improves the protein signal
quality and intensity after detergent removal. The sensitivity of MS protein detection increases
more than 20-fold (BSA in the presence of CHAPS, Nonidet P40 or Triton X-100) after SDR
HyperD® treatment. Additionally, high protein recovery (>99% BSA recovery with Triton X-100
removal), efficient detergent capture, and removal of nonionic, cationic, and anionic detergents is
demonstrated. Based on results from this highly sensitive MS based performance
characterization approach, the rapid and efficient detergent removal by SDR HyperD® resin
shows a great deal of potential for use prior to detergent sensitive applications and analyses.
Additionally, the flexibility in choice of format, accommodating low to high throughput and small to
large fluid volumes, makes this resin an ideal sample preparation choice for many protein
applications.
Microchip-based monolithic immobilized pH gradient
isoelectric focusing for protein analysis
Introduction References
With the development of μ-TAS techniques, CIEF [1] C. Yang, G. Zhu, L. Zhang, W. Zhang, Y.
has been applied on microfluidic chips, and shown Zhang, Electrophoresis, 2004, 25, 1729–1734.
the potentials of rapid protein analysis and further [2] G. Zhu, H. Yuan, P. Zhao,L. Zhang, Z. Liang,
integration with other operation units or separation W. Zhang, Y. Zhang, Electrophoresis 2006,
modes. Typically, IEF is performed in aqueous 27, 3578–3583.
ampholyte solution. However, carrier ampholytes
(CAs) added in the running buffer might interfere
the following sample detection and even the
multidimensional separation. To overcome such
shortcomings, in our recent work, monoliths with
immobilized pH gradient (M-IPG) was prepared in
the microchannel by UV initiation.
Methods
M-IPG was prepared by photoinitiated
polymerization of acrylamide, glycidylmethacrylate
and N,N-methylenebisacrylamide with 1,4-
butinediol, dodecanol and DMSO as porogens,
within the 100μm-width channels of a glass chip,
followed by the attachment of Ampholine to the Figure1 Photograph of the microchip with monolithic
surface of the porous monolith via epoxide groups immobilized pH gradient (M-IPG) for isoelectric focusing
(Figure 1). To illustrate the performance of such a of proteins
microchip-based M-IPG IEF, several FITC-labeled
proteins were isoelectric focused and concentrated
with monoliths in the channel of glass chip. The
35
focused zones were subsequently mobilized by
replacing NaOH (catholyte) with H3PO4 (anolyte), 30
and detected by a LIF detector.
25
Results
mv
20
With M-IPG materials in the microchannel, a
mixture of 3 proteins was enriched and separated 15
Innovative aspects
• Photoinitiated polymerization of monoliths with
immobilized pH gradient (M-IPG) on
microfluidic chips
• Microchip-based IEF with M-IPG for protein
analysis
Depletion of high abundance proteins in serum by
Introduction
Current research trends are focused on the Innovative aspects
exploration of proteins in serum to gain insights • Selective binding of serum albumin by MIP
into the molecular behavior of diseases through chromatographic column and monolithic
the proteomics. A key technical challenge materials
confronting the comprehensive analysis of proteins • A rapid, inexpensive and simple method for
in serum is the broadly dynamic range of proteins. depleting high abundance proteins
Since high abundance proteins could undermine • Great potential in the selective enrichment of low
the detection of low abundance ones, it is urgent to abundance proteins.
develop rapid, effective and simple methods to
deplete the high abundance proteins. References
(1) Simpson, R. J., Proteins and Proteomics: A
Methods Laboratory Manual, Cold Spring Harbor
In our recent work, two kinds of molecular Laboratory Press, New York 2003
imprinting polymers (MIPs) for the depletion of (2) Shi, H., Tsai, W. B., Garrison, M. D.,
human serum albumin (HSA) were prepared by Ferrari, S., Ratner, B. D., Nature 1999,
molecular imprinting technique. Hydrogels with 398, 593-597
BSA imprinted were synthesized under low
temperature in a chromatographic column, and
worked as the stationary phase to distinguish the
imprinting and non-imprinting proteins. Another
kind of monolithic imprinting material was prepared
with porcine serum albumin (PSA) as the template.
After grinded into particles, they were used as the
packing materials for SPE to selectively remove
HSA in serum.
Results
In selective test, both imprinted hydrogels and 1
grinded monolithic materials showed specific
binding to the template proteins. Although both
MIPs and non-imprinting polymers (NIPs)
monolithic columns were prepared and evaluated
under the same conditions, the former one could
recognize the template protein from a mixture of
proteins, which could not be accomplished by the
latter one (Fig. 1, Fig. 2). In addition, the selective
binding test for MIP and NIP monolithic materials
was carried out, and MIPs adsorbed more
template protein than other competitive proteins
and NIPs adsorbed proteins equally. These results 2
indicated that imprinted materials showed high Chromatogram of Selective recognition of proteins on
affinity and specific recognition for the target MIP column (Fig. 1) and NIP column (Fig. 2)
protein. Since MIPs are less expensive and Column: 4.6×50 mm Mobile phase (A) pH 6.5 10mM
quicker to prepare than biological receptors, such phosphate buffer (B): (A) +2M NaCl; gradient condition:
0-60 min, 6-100% (B).
materials have great potential in the depletion of
high abundance proteins and even in the
enrichment of low abundance proteins in proteome
study.
Vascular wall profiling addresses deep proteome from minute samples.
Introduction
Over the last 6 years 2DE has been the gold Results
standard for proteomic characterization of with Using this approach we can identified with
excellent results in terms of publications. statistical significance up to 16 proteins from a
2
Particularly in cardiovascular biomarkers tissue area as low as 10000 μm from a cryostat-
identification, the last proteins incorporated to the section of 15 μm thickness. A trypsin droplet of
biomarkers validation pipeline had been obtained about 100 pl were added in our area of interest
by electrophoretic techniques. In highly and after 2h incubation, it were aspirated using the
heterogeneous samples, homogenization prior to reverse phase capilar. The protein quantity was
its analysis masks local variations criticals for our estimated on 0.8 μg.
understanding of these pathologies. In parallel we compare this direct approach with
those obtained using 2DE gel from vascular
Development of Peptide/protein profiling smooth muscle cells excised from the same
techniques to overcome this limitation, by direct sample. Using in this case a 100-fold increase
coupling of proteins or peptides obtained “in situ” both quantity and surface dissected.
from small homogeneous areas within the tissue, Just 3 proteins were found in both lists and even
had provide a new set of data completely different more important some striking proteins as prolargin
from those obtained in previous studies. The and interleukin-25 were found by in-situ digestion
present research, carried out in human while 2DE only lists abundant structural or
atherosclerotic plaques, has shown an equivalent transport proteins.
area studied by standard proteomic approach Further improvements of this approach could lead
using silver-stained bidimensional electrophoresis in better protein identification in very small areas of
in parallel with protein profiling of intimal vascular highly heterogeneous samples.
muscle cells leads to the identification of a
completely different set of proteins, and more Innovative aspects
remarkable many low-abundance proteins • Samples as low as 100 cells can be subjected
potentially involved in the pathophysiological to proteomic analysis
process. • Most of proteins that were identified by
nanoLC-MS/MS are absent in 2GE.
Methods • Some low abundant proteins were identified
Human Carotid endarterectomy samples cell from with confidence.
the innermost layer were either excised or
digested in situ from thin-slice frozen samples.
Microdissected samples were analysed using a
conventional approach combining two-dimensional
electrophoresis with MALDI-TOF identification,
while in situ digestion sample were extracted using
a 100 um capillar followed by an on-line analysis
using nanoLC-MS/MS. Data from both approaches
were compared under the same searching
conditions.
Use of 1ml Prepacked AcroSepTM Q
Ceramic HyperD®F Resin Combined
with Albumin and Antibody Depletion
Results in Significant Improvement in
Protein Detection by 2D Gel
Electrophoresis and Mass
Spectrometry Analysis
AUTHORS
1 2
Masilamani Selladurai Saurabh Nagpal , Chitra
3 4 5
Thangavel , Gurpreet Kaur , Hongshan Li and
6
Lisa Bradbury
1,2,3,4
Proteomics Group, Pall India Pvt. Ltd,
Bangalore, INDIA,
5, 6
Proteomics Group, Pall US Pvt.Ltd. Woburn,
Boston, USA
ABSTRACT
1 2 2 1
Dr Judit Nagy , Fiona Pereira Dr Stuart Hassard , Tony Cass ,
1 2
Institute of Biomedical Engineering, Imperial College London, deltaDOT Ltd. London UK
human plasma. 25
20
15
Methods
10
Sample Preparation: Human plasma was obtained
by centrifugation at 1300 g for 10 minutes at 4 ºC.
Protease inhibitor cocktail was added to plasma
samples.
Figure 1. 1-DE-PAGE analysis with different
Preparation of low molecular plasma proteins: buffering reagents in the urea buffer system. Plasma
Three milliliters of human plasma were diluted by was diluted 1:4 by adding different buffering reagents to
adding of 12 ml of various buffer systems. The the urea buffer system, then ultrafiltrated using COM.
diluted sample was then loaded onto a filter Ultrafiltrated samples were concentrated using 3 KDa
membrane, and centrifuged at 3000g. The filtrate membranes and 5 ul aliquots of samples were subjected
was concentrated to 200ul using a cut off to SDS-PAGE. lane 1 and 2: 25mM NH4HCO3 + 20%
membrane (Vivaspin, MWCO 3,000) proteins were ACN (pH 8.2); 3 and 4: 40mM Tris-HCl + 20% ACN (pH
separated by SDS-PAGE or 2-DE. 8.2); 5 and 6: 7M Urea, 2M Thiourea + 20% ACN; 7 and
Protein identification: LMPP were digested with 8: 7M Urea, 2M Thiourea, 25mM NH4HCO3 + 20% ACN
(pH 8.2); 9 and 10: 7M Urea, 2M Thiourea, 40mM Tris-
trypsin and were analyzed by FT-ICR MS.
HCl +20% ACN (pH 8.2). The buffer system containing
7M Urea, 2M Thiourea, 25mM NH4HCO3 +20% ACN
Results (pH 8.2) produced the highest recovery rate of plasma
we used various buffer systems, including urea proteins.
buffer solution to determine which one provided
the highest recovery of LMPP using a 30 KDa of
cut off membrane and found that the buffer system
containing 7M Urea, 2M Thiourea, 25mM
NH4HCO3 +20% ACN (pH 8.2) produced the
highest recovery rate (Fig.1). Total LMPP proteins
prepared by urea buffer system were analyzed by
ESI-LTQ FT MS. Among the total 168 proteins
identified, 99 proteins (59%) were belong to the
under 30 kDa. Although this technology will not be
solved completely current problem of biomarker
Fig.2. Distribution of identified proteins by molecular
discovery using human plasma, we expect that this weight. The 99 proteins were
technology represents an opportunity to discover belong to the under 30 kDa (58.9%)
Selective purification of azide-containing peptides from complex mixtures
1,2 1 2 1 1
Merel A. Nessen , JaapWillem Back , Jan H. van Maarseveen , Gertjan Kramer , Leo J. de Koning , Luitzen
1 2 1
de Jong , Henk Hiemstra , Chris G. de Koster
1
Mass Spectrometry of Biomacromolecules - Swammerdam Institute of Life Sciences (SILS)
2
Biomolecular Synthesis - Van ‘t Hoff Institute for Molecular Sciences (HIMS)
Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.
Introduction References
(1) Agard, N.J., et al., A Comparative Study of
To answer the question to which extent gene Bioorthogonal Reactions with Azides, ASC
expression is regulated post-transcriptionally, we Chemical Biology 2006, 1, 644-648
have developed a pulse-chase labelling method (2) Kiick, K.L., et al., Incorporation of Azides into
that will allow us to determine the relative rates of Recombinant Proteins for Chemoselective
protein synthesis and degradation. Newly Modification by the Staudinger Ligation, PNAS
synthesized proteins are labelled with a bio- 2002, 99, 19-24
orthogonal methionine analogue, bearing an azide
(see figure 1), and selectively captured on a
specially designed resin (figure 2A). Subsequent
MS analyses will provide identity of proteins and
their de novo translational rates. Here we show the
selective enrichment of azide-containing peptides
from different origin.
Methods
Figure 1, Azidohomoalanine is an analogue of
The designed affinity purification method was methionine and readily accepted by methionyl-
tested for a single (synthetic) peptide containing tRNA synthetase in Escherichia coli and
azidohomoalanine (Azhal) and then applied to incorporated into proteins (2).
digests of an Azhal-labelled single protein and an
A
Azhal-labelled Escherichia coli proteome. Azide-
containing peptides were selectively captured on
the Cyclooctyne-resin (Cyco) (figure 2A) via the
strain-promoted [3+2]-cycloaddition (1). Coupled
peptides were released upon reduction and
alkylation of the disulphide-linker (figure 2B). The B
enriched Azhal-peptide mixtures were then
analysed by MALDI-TOF and LC-Q-TOF MS(MS).
Results
A. Paulus(1), T. Wehr (1), N. Liu(1), K. Academia (1), S. Freeby (1), E. Boschetti (2)
1 Bio-Rad Laboratories, Life Science Group, 6000 James Watson Drive, Hercules, CA 94547
2 Bio-Rad Laboratories, c/o CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
Introduction
Biomarker discovery projects are typically conducted We also show that the quantitative information for
with serum or plasma samples. The high dynamic range proteins in the ng/ml range is retained after ProteoMiner
of 10–12 orders of magnitude surpasses the capabilities treatment using SAA spiked samples. Finally, we are
of existing separation and analysis techniques. Serum using an artificial blood to examine the retention
and plasma are dominated by 20 or so high-abundance mechanism of ProteoMiner beads for select known
proteins that make up 95–99% of the protein mass. proteins. We find that we can detect tissue leakage
Typically, immodepletion methods are used to remove proteins such as retinol binding protein after
high abundance proteins. ProteoMiner treatment on 1D and 2D gels.
We developed an alternative to antibody-based methods
with ProteoMiner™, which is based on treatment of Innovative aspects
complex protein samples with a library of hexapeptides o Novel method to dramatically reduce high
bound to chromatographic supports. Each unique abundant proteins in serum and plasma
hexapeptide binds to a unique protein recognition site. samples
In this presentation, we explore the use of ProteoMiner o Retention of quantitative information for
for high abundance protein reduction in plasma and medium to low abundance proteins to allow
serum in biomarker studies, its ability to retain biomarker discovery
quantitative information on medium to low abundance o Application of high abundant protein reduction
proteins, applications to non-blood samples and work in biomarker discovery projects, non-blood
with an artificial serum to understand mechanisms of samples and artificial serum
action.
Methods
We subjected human plasma and serum, some from
patients with known disease status of cardiac arrests and
diabetes, to ProteoMiner treatment. Subsequent analysis
was done via SELDI, 1D LC-MS-MS and 2D LC-MS-
MS. In addition, we used Western blots to track
quantitative measurement of select medium to low
abundance proteins such as SAA. Protein identification
was done after spot or band excising and trypsin
digestion using a nanospray LC coupled to a Thermo
LTQ iontrap MS. The artificial serum was composed by
mixing of 17 commercial proteins both in equimolar
amounts and in the mass ratios found in serum and
plasma.
Results
Using ProteoMiner reduces the initial protein mass in
serum and plasma by 97%. The remaining 3% protein
mass represents all proteins including the high
abundance proteins, albeit at a lower concentration in
the sample. The procedure is reproducible as
demonstrated via SELDI and 2D analysis. We show that
ProteoMiner treatment increases the 2D spot count from
about 200 for a control to close to 500 after the
treatment. Applied to cardiac arrest and diabetic
samples, the quantitative difference in expression levels
increases roughly 10 fold compared to a control. Data of
excised spots identified via LC-MS-MS will be shown.
First results of using ProteoMiner to non-blood samples
with the presented using plant and cell extract samples.
The Secretome of H460 non small cell lung cancer cells: comparing workflows
Sander Piersma, Simone Span, Frank Kruyt, Remond Fijneman, and Connie Jiménez
Oncoproteomics lab and medical oncology, Cancer Center Amsterdam, VU medical center, De Boelelaan
1117, 1081 HV Amsterdam, The Netherlands
Results 29 35 35 121
IGD SCX
One of the key points in obtaining a good 876 693
secretome fraction is replacing the medium by
serum-free medium, thus minimizing interference 37 16 24 47
89 26
by bovine serum-derived proteins. However,
serum-free incubation time has to be optimized to
minimize apoptosis and cell lysis. For H460
NSCLC cells we found 24 hours to be optimal with SCX 45 934 158 IGD
respect to protein yield and cell viability.
We compared 3 workflows. Intact proteins
separation by C2 hydrophobic interaction resin
method yielded 580 proteins (N=3 experiments) Figure 1. Venn diagrams of N=3 biological replicates of
with 416 proteins in all 3 experiments. Conversely, H460 secretomes analyzed by TC2, SCX and 4-12%
the 10% SDS PAGE IGD analysis yielded 895 SDS-PAGE followed by LC-MS/MS. Reproducibility of
proteins (N=3) with 699 proteins identified in all 3 identification was 72% for TC2, 71% for the SCX
experiments. Comparing this with 4-12% gradient workflow and 80% for the 4-12% IGD workflow. The
gel and off-line SCX gave 1092 and 979 identified lower panel shows the overlap between the 2 most
proteins with 876 and 693 proteins in all 3 successful data sets (all protein ID’s in N=3 included)
ALTERNATIVE TWO DIMENSIONAL ELECTROPHORESIS – OFFGEL
ELECTROPHORESIS COMBINED WITH HIGH SENSITIVITY MICROFLUIDIC ON-CHIP
PROTEIN DETECTION
Tobias Preckel, Andreas Ruefer, Christian Wenz, Martin Greiner, Agilent Technologies R&D and Mktg.
GmbH & Co.KG, Hewlett Packard Strasse 6, Waldbronn, Germany
Results
1 : Biophysique et Biochimie des Systèmes Intégrés, iRTSV/ LBBSI, CNRS UMR 5092, CEA Grenoble,
17, rue des martyrs, 38054 Grenoble France
2 : Laboratoire de Spectrométrie de Masse, UMR CNRS 7178, Strasbourg
Jeffrey H. Ringrose, Wouter W. van Solinge, Shabaz Mohammed, Martina C. O’Flaherty, Albert J.R. Heck,
and Monique Slijper
Biomolecular Mass Spectrometry and Proteomics Group, Utrecht University, Sorbonnelaan 16, 3584 CA
Utrecht, The Netherlands, Fax (+31) 30 2518219, e-mail: j.h.ringrose@uu.nl
Results
We developed an efficient and specific Hb
depletion column based on sepharose. SDS-
PAGE analysis revealed that after Hb depletion the
number of visible protein bands was greatly
increased (Figure 1). Using IEX chromatography
we could also deplete for CA-1 which after Hb
depletion became the most abundant protein.
Under the conditions used the CA-1 was present in
Figure 1. SDS-PAGE analysis of RBC lysate (lane1), Hb
the IEX flow through whereas almost all other affinity column bound fraction (lane 2), Hb depleted RBC
proteins were retained and subsequently eluted fraction (lane 3), CA-1 containing IEX flow-through
from the columns. We analyzed all fractions by fraction (lane 4), and double depleted RBC fraction (lane
SDS-PAGE and subsequent MS/MS. The number 5). Coomassie stained gel.
of identified proteins from RBC lysate increased
from 167 before depletion to 677 after depletion for
both Hb and CA-1. In the Hb and CA-1 fractions
we detected 20 and 39 proteins respectively.
Using our depletion strategy we could in total
Guided Gas-Phase Fractionation: a Strategy to Tackle Duty-Cycle Limitations
Anne Rokka (1), Aschwin van der Woude (1), Santosh Gupta (2), Matthias Nees (2), and Garry Corthals (1)
1)Turku Centre for Biotechnology, University of Turku & Åbo Akademi University,
Tykistökatu 6A, 20520 Turku, Finland
2) Medical Biotechnology, VTT Technical Research Centre of Finland and
University of Turku, Turku, Finland
Introduction
The relationship between the duty-cycle of an MS Innovative aspects
instrument and the number of peptides that can be • Easy peptide pre-fractionation by IEF
identified from a single LC-MS experiment is • Improved protein identification by guided
relatively straightforward: the faster the duty-cycle, GFP
the more peptides will be identified for a given • Quality assessment on any LC-MS run by
data-dependent acquisition experiment. For most pepRecon tool
proteome-scale experiments we are severely
limited in our analyses, and attempts at complete
analysis are not immediately foreseeable. Thus we
face a formidable challenge in developing methods
that make the step towards full-scale analysis.
Methods
In an attempt to maximize proteome coverage we
used an integrated approach that allowed for
gentle fractionation of peptides in to two phases:
the liquid-phase and gas-phase. Liquid-phase
fractionation was achieved by peptide isoelectric
focusing (pepIEF) prior to MS analysis and gas-
phase fractionation (GPF) was achieved in the MS
instrument.
Results
Peptide isoelectric focusing (pepIEF) was used for
pre-fractionation of the complex peptide sample
prior to MS analysis because it is simple,
reproducible and do not involve chemical or
structural modifications to peptides and is suitable
for practically any proteomics approach. Its
performance as a pre-fractionation step for
peptides prior to LC-MS-MS is less common, even
though it is as successful as commonly employed
SCX procedures. Three of the twelve IEF fractions,
containing either acidic, neutral or basic peptides,
were chosen for GPF analyses.
We found GPF as a simple analytical approach
that can be used to increase the number of
identifications without the need for hardware
modifications. GPF iterative LC-MS/MS analyses
of a sample were performed on selected m/z
ranges that had been determined following a
normal wide m/z range scan (typically 400–1800
m/z). In other words, the proteome complexity was
determined empirically prior to GPF. We have
written a suite or R scripts that enable the detailed
and rapid evaluation of empirical data and
concurrent quality assessment of any LC-MS run.
We will present data on the principle and
application of guided GPF and give examples of
how a massive increase in the number of
identifications is achieved for peptide
identifications.
Proteomics on a chip for monitoring autoimmune diseases
Richard B.M. Schasfoort, Bianca Beusink, Dietrich Kohlheyer, Angelique Lokate, Ger Pruijn, Ad de Jong,
Wout van Bennekom, Linda Silvertand, Natasja Carol-Visser, Albert J.R. Heck and Albert van den Berg.
BIOS Lab on a chip Group, MESA+ Institute for nanotechnology,
P.O. Box 217, 7500 AE Enschede, the Netherlands
Protein phosphorylation is the major mechanism by which diverse cellular processes are
regulated. Despite its importance, the paucity of phosphorylated proteins in a biological
sample poses a major hurdle in studying these processes. Immunodetection method,
based on the use of phospho amino acid specific antibodies to detect phospho-proteins
blotted onto either polyvinylidene fluoride (PVDF) or nitrocellulose (NC) membranes,
offers highly sensitive yet relatively simple way of studying global protein
phosphorylation.
A431 cell lysates (EGF stimulated and non-stimulated) were separated by SDS-PAGE
and blotted onto either hydrophilic PVDF or NC membranes. Analysis of global p-Tyr/p-
Ser proteomics were performed by western immunodetection using monoclonal antibody
4G10 (p-Tyr) and recently developed p-Ser monoclonal antibody 4A4. Two different
detection methods were employed: traditional chemiluminescence or multiplexed
fluorescent detection using a near infrared laser scanner.
Results demonstrate hydrophilic PVDF membranes exhibit instant and uniform wetting in
water and aqueous buffers without the alcohol pre-wetting step, while maintaining a level
of immunodetection performance comparable to NC membranes. In contrast to the
conventional PVDF membrane, the new membrane exhibited substantially reduced
background auto fluorescence making it suitable for multiplexed fluorescent
immunodetection. Use of hydrophilic PVDF membrane offered selective and sensitive
detection of serine and tyrosine phosphorylation when combined with 4A4/4G10
immunodetection, enabling global profiling of protein phosphorylation. While shown its
utility in EGF signaling pathway in A431 cells, the combined use of hydrophilic PVDF
membrane with phospho-immunodetection can be easily applied to other biological
systems.
Observing Rapid H/D Exchange of The Reactive Hydrogen on the Protein Molecules
by Electrospray-Assisted Laser Desorption Ionization (ELDI) Mass Spectrometry
1
Jingyueh Jeng
2,3 2 2 2
Jentaie Shiea , Li-Hua Lo , Yi-Tzu Cho , Cheng-Hui Yuan
1
: Department of Biotechnology, Chia Nan University of Pharmacy & Science
2
: Department of Chemistry, National Sun Yat-Sen Univ., Kaohsiung, TAIWAN
3
: National Sun Yat-Sen University-Kaohsiung Medical University Joint Research Center, Kaohsiung, TAIWAN
Methods
Aqueous sample solutions containing protein
standards were prepared. Ten microliters of the
sample solution were deposited on a stainless
steel sample plate by a micropipette. After being
dried, the sample spot was irradiated with a pulsed
nitrogen laser beam. The laser- desorbed analyte
molecules entered an ESI plume generated from a
capillary located 5 mm above the sample spot. The
solution containing different ratio of D-solvents
(D2O, MeOD, and CH3COOD) and H-solvents
(H2O, MeOH, CH3COOH) was used for
electrospray. The protein ions were detected by an
ion trap mass analyzer attached to the ELDI
source.
Results
Hypothetically, the time between molecular
desorption and ion production in ELDI is estimated
to be in milliseconds. This time scale will only allow
the reactive or outmost hydrogen atoms on the
desorbed protein molecule to be exchanged with
the deuterium in the ESI plume. Hydrogen atoms
in peptide bonds and secondary amines showed
no H/D exchange, for they required longer time to
exchange with the deuterium. It was found that the
H/D exchange number of cytochrome c in the ELDI
was much less than that found through
conventional methods. However, the exchange
H/D number of the cytochrome c with different
origin shows slight differences. For example, 42
hydrogen atoms were exchanged for the
cytochrome c from a rabbit and 46 atoms for the
cytochrome c from a horse. This may be due to
Top-Down Proteomics analysis using Automated 2D LC and Fractionation
Evert-Jan Sneekes, Bas Dolman, and Remco Swart
Dionex Corporation, Amsterdam, The Netherlands
Methods
We describe an automated two-dimensional LC
workflow for the separation and identification of
proteins. The workflow involves a first dimension
ion-exchange separation and second dimension
reversed-phase separation, both performed on
polymeric monolithic columns and both dimensions
were fractionated in well plates. The application of
monolithic columns allows for fast and highly
efficient protein separations and the resulting
chromatograms are presented in a 2D retention
map. In-well digests of selected fractions are
subsequently analyzed by capillary LC-MS/MS for
their identification. This LC based top-down
workflow was validated with an E.coli protein
extract and the recently introduced Universal
Proteomics Standard Set (Sigma).
Results
The complete 2D LC separation of intact proteins
was achieved in 4 hours, including fractionation of
both first and second dimension. Tryptic digestion
was performed immediately after the second
dimension fractionation and quenched after 3
hours. A 2D retention map was generated based
on the UV data of the protein separations and was
used to select fractions of interest.
The tryptic peptides in these fractions were then
analyzed by capillary LC-MS/MS for protein
identification. Evaluating the analyzed fractions
revealed a high efficient protein separation with
minimal overlap between fractions. In well
digestion of the collected LC fractions and
subsequent LC-MS/MS analysis provided
confident protein identifications.
Optimization of separation power in one-dimensional LC
in analysis of proteomics samples
Introduction
9.00
One of the main challenges in proteomics research mAU WVL:214 nm
Results
Using 15 cm long columns packed with 3 μm silica
C18 particles the effect of gradient time on peak
capacity and peak width was investigated. Longer
gradient times yielded higher peak capacities. A
steep initial increase in peak capacity is observed
when increasing the gradient time from 5 to 40
min. At longer gradient times the rate of increase is
less steep, and peak capacity tends to reach a
maximum around 300, which is caused by the
increase in average peak width of peptides at
longer gradient times.
With increasing temperature from 25 to 40°C a
strong increase in peak capacity was observed
(∼35%). At elevated temperatures the viscosity is
reduced and diffusion in the mobile and stationary
phase is greatly enhanced, leading to narrower
peaks.
In addition, the effect of column length on peak
capacity was investigated. In general, longer
columns yielded higher peak capacities. An
example of the separation power of long packed
columns at optimized LC conditions in one-
dimensional LC is shown in Figure 1. Over 320
different peptides were separated within 125 min.
Study of β-Catenin-associated Complex by Nanoprobe-Based Affinity Mass
Spectrometry
1 1,2 3 3 4 1
An-Kai Su , Hsin-Hung Huang , Po-Chiao Lin , Chun-Cheng Lin , Jeou-Yuan Chen , and Yu-Ju Chen
1,4 2
Institute of Chemistry and Biomedical Sciences, Academia Sinica, Institute of Biochemical Sciences,
3
National Taiwan University, Department of Chemistry, National Tsing Hua University, Taiwan
Introduction
As well known, β-catenin involves in the Wnt References
pathway and acts as a transcriptional co-activator (1) Lin et al, Ethylene glycol-protected
in the control of cell proliferation and migration magnetic nanoparticles for a multiplexed
during metastasis. Cancer metastasis is regulated immunoassay in human plasma; Small, 2,
by complex interplay between the β-catenin- 485-489, 2006.
mediated adhesion pathway and β-catenin/TCF
complex formation within the nucleus. Taking
advantages of high surface-to-volume ratio and
easy separation of magnetic nanoparticles (MNPs),
we present a nanoprobe-based affinity mass A B
pre-clean + + + +
spectrometry (MS) strategy that simultaneously _ _ _
pre-clean + MNPs + +
isolate and identify β-catenin-associated protein Ab@MNPs + + Ab@MNPs _ + _ +
complexes in gastric cancer cell.
kDa
Methods 250
Antibody of β-catenin was conjugated on MNPs
surface and the MNPs were incubated with lysate
130
of the tumorigenic gastric cancer cell AZ521 for
extraction of β-catenin-included protein complexes. β-catenin
95
The synthesis of antibody-conjugated magnetic
nanoparticles (Ab@MNPs) can be found in the 72
literature (Lin et al. Small, 2, 485-489, 2006). After
incubation, the extracted multiplex protein
complexes were directly analyzed by SDS-PAGE 55
separation for trypsin-digestion and identified by
LC/MS/MS, thereby, achieving multiple protein
screening and the characterization of complex
variants. Figure 1. Enrichment of β-catenin and its associated
protein complex with Ab@MNPs in AZ521 cells. (A) The
silver staining result showed that nonspecific binding
Results proteins were pre-cleaned with MNPs only. (B)
As shown in SDS-PAGE analysis in Figure 1, the Compared with MNPs, amounts of β-catenin was
preliminary results show that using Ab@MNPs can enriched using Ab@MNPs precipitation after MNPs pre-
enrich β-catenin and its interacting partners (Fig. cleaning by western blotting (left). Patterns of
1B). The binding capacity of Ab@MNPs and IP precipitated proteins were compared by silver staining
beads has been compared; the former strategy (right). Western blot analysis was performed using anti-
demonstrated easier purification process for the β-catenin IgG.
follow-up MS identification. In addition, nonspecific
binding of MNPs (Fig. 1A) cab be improved by pre-
clean step with blank MNPs and washing steps
(Fig. 1A). The new analytical method will be
applied to study the different β-catenin-associated
complexes in cancer cells with different metastasis
potential. We expect that the newly developed
assay may have implementations to study
bimolecular interactions in targeted proteomics.
Innovative aspects
• Develop a nanoprobe-based proteomic assay
for simultaneously enrich and identify protein
complexes associated with cancer metastasis.
A Facile Buffer Exchange Interface
for On-line Hyphenation with Trypsin Microreactor
1,2 1,2 1,2 1 1 1
Liangliang Sun , Xiaoqiang Qiao , Dingyin Tao , Zhen Liang , Weibing Zhang , Lihua Zhang *,
1
and Yukui Zhang
1
National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics,
Chinese Academy of Science, 457 Zhongshan Road, Dalian 116023, China
2
Graduate School of Chinese Academy of Sciences, Beijing 100039, China
Introduction
For shotgun method, protein digestion is one of the Innovative aspects
most important steps, which is usually performed • A facile microdialysis interface for adjusting pH
in solution, but recently more focus is put on the and acetonitrile concentration of protein
trypsin microreactor because of the high digestion solutions within 30 seconds.
efficiency. However, in most cases, the pH and • On-line hyphenation of the buffer exchange
organic reagent concentration of protein solutions, interface with trypsin Microreactor.
especially for eluants from HPLC separation, are • Enrichment of proteins during buffer exchange
not compatible with immobilized trypsin. Therefore, process.
it is indispensable to develop on-line buffer
exchange interfaces (1). In our work, a novel on- References
line buffer exchange interface based on (1) David C. Schriemer et al, Blending protein
microdialysis was developed, and successfully separation and peptide analysis through real-
applied into the adjustment of pH and acetonitrile time proteolytic digestion; Anal. Chem. 2005,
concentration successfully within 30 seconds. 77,1572-1579.
Methods
The microdialysis interface for on-line buffer 50
exchange was made of hollow fiber membrane Cytochrome c
with MWCO 3000, and the dead volume was about
2 μL. The counterflow exchange buffer was 40
applied to accelerate the mass transfer and
improve the buffer exchange performance. In our
30
experiments, 0.1% trifluoroacetic acid and
Signal
Results
In PMSIEF, 5 chambers with well-defined pH
range, pH 3.0-4.6, 4.6-5.4, 5.4-6.2, 6.2-7.0 and
7.0-10.0, were generated by isoelectric
membranes, which could be used for protein
fractionation according to their isoelectric points Figure 1. Number of identified unique peptides and
(pIs). Proteins focused in each chamber were proteins in each fraction and in total
digested, and further separated and identified by
long column μRPLC-MS/MS. The coupled long
column could obviously improve the separation
efficiency of peptides. Even with single
dimensional separation by μRPLC, 202, 263, 282,
203 and 181 proteins were respectively identified
in each chamber (as shown in Fig. 1),
corresponding to 835 unique proteins identified
from E. Coli. The detailed information was shown
in Fig. 1. The overlapping of proteins in neighbor
chambers was shown as Fig. 2, and the average
percentage of unique proteins identified by each
fraction was calculated to be 73.82%, In addition,
compared to gel based protein separation, the
protein recovery as high as 95.06% was obtained,
which was quite useful for the analysis of low Figure 2 Protein overlapping of identified proteins in
abudnace proteins. In conclusion, with the each fraction chamber.
combination of off-gel protein prefactionation by
PMSIEF, peptide separation by long-column
An Alternative 2D-LC-Separation Scheme for Shotgun Proteomics Coupled to
ESI or MALDI MS/MS
1
The BioCentre Facility, University of Reading, Whiteknights, Reading RG6 6AS, UK.
Email: a.tiss@reading.ac.uk;
2
Cancer Proteomics Laboratory, Department of Gynaecological Oncology, University College of London,
Gower Street, London, WC1E 6BT, UK.
3
Dept of Computer Science, Royal Holloway, University of London, Egham TW20 0EX, UK
4
Institute of Women’s Health, UCL, Maple House, 149 Tottenham Court Road, London, W1T 7DN, UK.
peaks (more than 100 peaks per profile). The
results show that this easy and fast method of
using ZipTips, tested over a whole year, is more
Introduction reproducible and more suitable for serum profile
screening than magnetic bead-based
Blood metabolites and peptides are potential
methodologies used for comparison.
indicators of progression from a normal to a
diseased state. However, the presence of salts, An extra step of ultra-filtration was found to further
lipids and highly abundant proteins in blood serum increase the number and the intensity of low mass
can adversely affect sensitive proteomic analysis peptides (up to 6 kDa) without sacrificing the
using mass spectrometry. robustness of the technique. This last step also
Several pre-fractionation strategies using improved the MS/MS data acquisition.
chromatographic adsorbents have been employed The automated ZipTip platform is now used to
to desalt samples and remove abundant proteins. process thousands of serum samples collected
We describe here the adaptation and validation of from post-menopausal women as part of the UK
a simple and fast solid-phase extraction technique Collaborative Trial of Ovarian Cancer Screening
using ZipTips followed by ultra-filtration for peptide (UKCTOCS) trial.
serum profiling and identification.
For method optimisation and comparison, we used • Robust, easy and sensitive method for
3 commercially available human sera and purification and enrichment of peptides
fractionated them using pipette tips packed with from biofluids, using ZipTips and ultra-
various solid phase materials. The sample filtration prior to biomarker pattern
preparations were run both manually and diagnostics using MALDI- or ESI-MS and
automatically. A CyBi™-Disk robot (CyBio AG) MS/MS.
equipped with a 96-piston head was adapted for
• Suitable method for use in a high-
automated sample preparation using ZipTips.
throughput and potentially clinical
Microcon centrifugal filters (Millipore) with various
environment, only requiring 5 to 10 μl of
cut-offs were used for the ultrafiltration either
serum.
before or after ZipTips.
MS data (from 700 to 10000 Da) were collected
using an Ultraflex MALDI-TOF mass spectrometer
(Bruker Daltonics). MS spectra were analysed
using FlexAnalysis and ClinProTools software
(both from Bruker Daltonics). MS/MS spectra of
the major peaks were collected using the MALDI-
QTOF Premier (Waters).
Results
Methods
Membrane protein extraction from human colon
HCT-116 cell line was investigated using sodium
dodecyl sulfate-based buffer and the proteins were
separated on modified gels with the N,N'-
dimethylacrylamide monomer. Each gel was totally
sliced in 50 bands and each band was
enzymatically hydrolyzed. The peptides generated
by the trypsin hydrolysis are separated on a LC-
Packings nanoLC using a C18 trap-column (300
μm i.d., 5 mm length, Dionex) and a C18 capillary
column (Pepmap C18, 75 μm i.d., 15 cm length). Figure 1. HCT-116 membrane proteins separated on
classical and hydrophobic gels. The hydrophobic gel
The peptides are on-line transferred to the
presents higher resolving power than classical one.
nanoESI-Qq-FT-ICR MS instrument (Apex 9.4 T,
Bruker), separated and sequenced for protein
identification.
Results
A total of 227 proteins separated on hydrophobic
gel versus 195 on the classical gel were identified
(Fig 1). More hydrophobic proteins were globally
identified in the new gel (GRAVY -0.25) compared
Figure 2. MS/MS spectrum identifying the sequence
to the classical acrylamide one (GRAVY -0.42). 52
LAVEALVR corresponding to the peptide 194-201 of the
proteins were identified on the hydrophobic gel Hyaluronan synthase 1 protein (Accession number:
containing 1 to 10 transmembrane domains (vs 9 Q92839). The identified peptide is very hydrophobic, i.e.,
in classical gels). For example, the GRAVY value: 1.450. The Hyaluronan synthase 1 is a
sodium/potassium-transporting-ATPase-alpha-1- protein with 7 transmembrane domains located in the
chain-precursor (10-transmembrane-domains) or plasma membrane.
the glutamate-receptor (4-transmembrane-
domains) were identified only in the hydrophobic
gel with MS/MS mean errors inferior to 1 ppm.
Other proteins involved in
intracellular/extracellular-trafficking were identified
as the clathrin located onto the cytoplasmic side of
the plasma membrane. Focusing more particularly
on sequenced peptides, very hydrophobic peptides
could be observed, as the peptide 194-201 of the
Hyaluronan synthase 1 (Fig 2) identified despite its
very high GRAVY value of 1.45. Globally, most of
the membrane proteins identified with the classical
procedure are well documented in the literature
while membrane proteins strictly identified with the
Selective detection and enrichment of serum albumin in human erythrocyte and urine by
capillary electrophoresis
1,3 1 2,3
W.-L. Tseng, C.-Y. Lin, H.-C. Chang
1. Department of Chemistry, National Sun Yat-sen University, Taiwan
2. Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University
3. National Sun Yat-sen University-Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan
Methods:
Before separation, 70-cm capillaries were filled
with 1% dextran sulfate, which was prepared in 10
mM phosphate buffer at pH 10.0. A plug of
different concentrations of the sodium alkyl sulfate
solution was injected hydrodynamically by raising
Figure 1. On-line concentration of (A, B) 1 μM and
the capillary inlet 20-cm height for 10 s before
(C) 5 nM HSA by capillary electrophoresis (A)
proteins were injected by raising the capillary inlet
without and (B, C) with a plug of 1% SOS. The
20-cm height for a period of time up to 240 s. The
sample injection volume is 190 nL. Peak identifies:
ends of the capillary were then immersed in the
1, EOF marker; 2, HSA.
cathodic and anodic vials containing 1% dextran
sulfate (pH 9.0). Once a high voltage (17.5 kV)
was applied, the solution of dextran sulfate in the
anodic reservoir entered the capillary under
electroosmotic flow.
Results:
We have carefully investigated the effects that the
alkyl chain length on the electrophoretic mobility of
the proteins. An increase in electrophoretic
mobility was only discovered in the case of HSA
when applying a short plug of 1% sodium octyl
sulfate (SOS). The complete unfolding for HSA
occurs at 1% SOS. The formation of SOS-HSA
complexes shows at least 100-fold improvement in
peak efficiency. Our proposed method is
appropriate for on-line concentration of HSA.
Under injection a large-volume sample, the limit of
detection at signal to noise of 3 was 1.0 nM for Figure 2. On-line concentration of HSA in
HSA when using low cost absorbance detection erythrocytes by capillary electrophoresis (A)
coupled with capillary electrophoresis. With high without and (B, C) with a plug of 1% SOS. The
sensitivity and efficiency, the proposed method erythrocytes were spiked (A, B) without and (C)
has been shown for analyses of serum albumin in with 1 μM HSA.
human erythrocyte and urine.
Ultrasonic Assisted Protein Enzymatic Digestion for Selenium amino-acids
1 4 2 3 2 1
G. Vale , R. Rial-Otero , A. Mota , L. Fonseca , M. L. Gonçalves , J.L. Capelo
1
REQUIMTE, FCT, Universidade Nova de Lisboa, Monte de Caparica, Portugal.
2 3
Centro de Química Estrutural, and IBB-Institute for Biotechnology and Bioengineering, Centre for Biological
and Chemical Engineering, from the Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
4
Nutrition and Bromatology Group, Analytical and Food Chemistry Department, University of Vigo, Ourense
Campus, E32400 Ourense, Spain
Introduction: Ultrasonic assisted protein Table 1 – Influence of sonication on enzyme activity
enzymatic digestion, USAPED, is a new sample (n=3)
treatment, for fast protein digestion. The
Applicationrelatively of USAPED accelerates, from Sonication Enzyme Enzyme activity
hours to minutes the sample treatment for: time (s) Activity (%)
a)identification of proteins by mass spectrometry (U/mg solid)
based techniques b) identification of amino acids 0 4.81±0.03 100
joined to metals such as selenium (Se-AA) [1,2]. 60 3.8±0.4 78±8
In this work the performance of USAPED for Se- 120 0.06±0.003 1.2±0.6
AA determination through hyphenated techniques
such as High Performance Liquid Chromatography Retention times –HPLC- for the different Se-AA
(HPLC) plus Electrothermal Atomic Absorption Species after enzymatic treatment
Spectrometry (ET-AAS)) is compared with HPLC-
MS/MS techniques. The retention times were studied using standards.
The enzymatic treatment with US seemed not to
Methods: change the integrity of the Se-AA species.
Each sample [Reference Materials BCR-414
plankton, ERM-CE 278 mussel tissue] was
prepared mixing 10 mg of the biological material
with 10 mg of enzyme in 1mL of ultrapure water.
The mixture was: 1) sonicated for 120s at 50%
sonication amplitude with a 1mm probe; 2)
centrifuged at 4000 rpm for 4 minutes and 3)
1 2 3 4
Passed through a 0,22μm Cut-off filter. 5
Hyphenated techniques: I) the extracts were
injected in an HPLC and fractions containing the
Se-AA, were recovered at retention times,
Figure 1 – Chromatogram of different Se-AA
previously determined with the adequate
mixture. 1 – Selenocystine ; 2- Selenio Methil Selenio
standards. II) the samples were analyzed for its Cysteine; 3- Selenite (Se IV); 4- Selenio Methionine; 5-
content in Se through ET-ASS. Selenate (SeVI)
HPLC-MS/MS: The extracts were injected in the
HPLC and the Se-AA, previously identified as USAPED arise as a robust fast sample treatment
targets, were further fragmented for Se containing for the proteomic applications of metallomics.
residue determination. Through this innovative sample treatment, other
techniques different from those using mass
Results spectrometry can be used for proteomic studies in
a routine basis, i.e. environmental and food
Influence of ultrasound in protease activity. control.
The influence of the ultrasonic energy in the Innovative aspects
enzymatic activity (casein hydrolysis) of protease
XIV was studied by applying ultrasound at • Acceleration of Se-AA extraction from solid
amplitude of 50% in intervals of 30–120 s. matrices
Interestingly, 30 s of sonication does not affect • USAPED-HPLC-ET-AAS Hyphenation.
enzyme activity, however, after 60 s, the activity
decreases ca. 20%. A sonication time 400of 120 s References
led to the complete inactivation of the enzyme [1] H. M. Santos, R. Rial-Otero, L. Fernandes, G.
(Table 1). Vale, M. G. Rivas, I. Moura, J. L. Capelo, J.
Proteome Res. 6 (2007) 3393.
[2] P. Bermejo, J. L. Capelo, A. Mota, Y.
Madrid and C. Cámara, Trac Trends Anal.
Chem., 23 (2004) 65.
Potential of long capillary monolithic columns for the analysis of protein digests
Introduction A B
Mass spectrometry of protein digests is an
important tool for protein identification in
proteomics. Analysis of protein mixtures requires
efficient separation of the peptides for optimal
protein identification, this can be achieved by using
monolithic columns. The gain in separation
efficiency for monolithic columns was evaluated by C D
the analysis of a mixture of bovine serum albumin,
α-casein and β-casein tryptic digests using an LC-
MS system and capillary columns of different
lengths (150 and 750 mm).
Methods
A protein digest mixture was separated by
Reversed phase liquid chromatography using
capillary monolithic silica columns of different Figure 1:
lengths at various gradient times. Both Top figures – base peak chromatograms of digest
chromatographic performance and efficiency of mixture. A: 150 x 0.1 mm column, 5-50% ACN (15 min)
gradient. B: 750 x 0.1 mm column, 5-50% ACN (75 min)
protein identification were compared for both
gradient.
columns. Peak capacities were determined from Bottom figures – Averaged mass spectra of α-Casein
MS base-peak chromatograms and MS/MS data peptide YLGYLEQLLR (m/z 1267.7, MH+). C: 150 x 0.1
were used for protein identification by Mascot mm column, 15 min gradient. D: 750 x 0.1 mm column,
database searching. 75 min gradient.
Results
Analyses with similar gradient slope for the two
columns produced ratios of the peak capacities
which were slightly higher than the expected value
of the square root of the column length ratio. Peak
capacity and protein identification scores were
higher for the long column, peak capacity ratios
varied from 2.58-3.23 for four different gradient
slopes, while protein identification scores were 1.3-
3.0 times higher. Only use of the longest gradient
on the long column led to identification of all three
proteins, which demonstrates the advantage of
increased separation efficiency. The use of long
monolithic columns improves peptide separation
and increases reliability of protein identification.
Innovative aspects
• Comparison of long and short silica monolithic
columns for peptide separation
REPRODUCIBILITY OF 2D GEL-BASED PROTEOMICS EXPERIMENTS
1 2 3 4 5 6
David Bramwell , Mary Caponite Hurley , Alamgir Khan , Katrin Marcus , Jules A. Westbrook , Hans Voshol
6
Novartis Inst. for BioMedical Research, WSJ-88.805, CH-4002 Basel, Switzerland
Correlation coefficient
complexity of ‘the proteome’, reproducibility
continues to be an important issue in proteomics
[1]. Consequently, proteomic studies have not yet
resulted in the once anticipated quantum jump in
the discovery of validated disease targets and
biomarkers. Here we demonstrate the validation of
2D-PAGE as a reproducible approach for
differential proteome analysis through a cross-lab
1 2 3 4 5
experiment.
Participating labs
Methods
Figure 1. Intra-lab reproducibility - whole gel
The experiment was designed to meet one key correlation.
goal: perform a 2D gel-based comparison between Average whole gel correlation coefficients (Pearson),
two biologically relevant, complex samples and within labs but across multiple experiment runs and
reproducibly identify differential spots. control/treated conditions: 0.92 (lab 1), 0.95 (lab 2), 0.86
Haemophilus influenzae, a Gram-negative (lab 3), 0.87 (lab 4), 0.89 (lab 5). The first submitted gel
bacterium, was treated with actinonin, a peptide from each lab was used as a reference for that lab.
deformylase inhibitor [2]. Control and treated
samples were extracted and distributed to 5 expert
labs, where they were separated by 2D PAGE Innovative aspects
using a procedure that was kept constant within • Validation of 2D PAGE at the level of the final
the instrumental restrictions of the respective analysis result
laboratories. Participants were asked to identify • Basis for establishing standard samples and
the 200 most significant differences using protocols for 2D PAGE
Progenesis SameSpots software. Images were • Paradigm for other proteomics approaches
also provided to a third party for an independent such as LC-MS
analysis. After completion, a meta-analysis was
carried out to compare the identified differentials. References
1. Rifai N, Gillette MA, Carr SA. Nat. Biotech.
Results 2006, 24, 971.
Participants provided at least one experiment, 2. Bandow JE et al., Proteomics, 2003, 3, 299.
defined as 5 replicate gels of each sample, with
some labs including multiple repeats. Intra-lab Author affiliations:
1
reproducibility was excellent for each of the Nonlinear Dynamics, Newcastle upon Tyne NE1
datasets, as illustrated by whole image correlation 2ET, UK
2
coefficients of 86 - 95% (Fig. 1), with scatter plots Michigan Proteome Consortium, Ann Arbor, MI
of spot volumes showing standard deviations 48109-0404, USA.
3
below 0.09. Inter-lab parameters were equally Australian Proteome Analysis Facility (APAF),
impressive, allowing a significant number of gel Macquarie University, Sydney NSW 2109
images to be aligned at the pixel level across labs. Australia.
4
Most importantly, lists of differential spots were Medical Proteom-Center, Ruhr-University of
highly consistent across all participating labs, Bochum, D-44801 Bochum, Germany.
5
demonstrating that 2D PAGE is a reliable Proteome Research Centre, UCD Conway
approach for the identification of differentially Institute of Biomolecular and Biomedical
expressed proteins. Research, University College Dublin, Ireland
In conclusion, this study validates 2D gel-based
comparative analysis by reproducibly deriving tens
to hundreds of differentially expressed proteins
across labs. We highly recommend repeating a
similar experiment in an LC-MS setting, in order to
An Integrated M-IPG-CIEF-microenzymatic reactor-CZE platform for protein analysis
Methods
As shown in Figure 1, an integrated 2D-CE Figure 1. Schematic of the Integrated M-IPG-CIEF-
microenzymatic reactor-CZE platform.
platform was established with monolithic
immobilized pH gradient (M-IPG) CIEF for protein
separation, trypsin immobilized microenzymatic
reactor for on-line protein digestion, and CZE for
peptide separation via two proper interfaces. The
hollow fiber membrane interface between M-IPG
CIEF and microenzymatic reactor was used for the
adjustment of buffer pH to improve the
compatibility of protein separation and digestion.
The Teflon tubing interface between
microenzymatic reactor and CZE was used to
change the buffer to that suitable for peptide
separation and introduce an electric field for CZE
as well.
Results
With such an integrated M-IPG CIEF-
microenzymatic reactor-CZE platform, proteins
were hydrodynamically introduced into the M-IPG
column by a syringe pump and off-line focusing
was performed. Subsequently, the separated
proteins were transferred to the microreactor by a
syringe pump at the flow rate of 500 nl/min for 1.5
min. Finally, the resulting peptides from each
fraction were separated by CZE in 12 min. The
performance of such a system was demonstrated
by the analysis of myoglobin. In 7 of 12 fractions of
protein separation, peptides were observed by
CZE, and a total peak capacity of 2000 was
obtained. Further work on the analysis of complex
protein samples by such a platform is undergoing,
and the primary data indicates that it might offer a
useful way for proteome study.
Quantitative Proteomics for 2D Gel Electrophoresis using Multiple Saturation Dyes
1,2 2 1,2 1
John E. Wiktorowicz , Susan Stafford , Alexander Kurosky , Dept. Biochemistry and Molecular Biology ,
2
and the Biomolecular Resource Facility , The University of Texas Medical Branch, Galveston, TX, USA
Methods
Cysteine content of standard or tissue extracted
proteins was estimated by amino acid analysis.
Sufficient dyes (BODIPY FL- and BODIPY 577-
maleimide) were incubated with the cysteine-
containing and cysteine-free (as negative control)
proteins under variable conditions as described
below. Gels were imaged for fluorescence and
then stained for total protein with Coomassie.
Where appropriate, specific fluorescence (SF) was
calculated as the ratio of the sum of pixel
intensities of each fluorescent protein band and
the corresponding Coomassie band minus the SF
of the non-cysteine containing protein. Both
intensities were background corrected.
Results
Labeling in thiourea with iodoacetamides versus
maleimides confirmed the observations of
iodoacetamide inhibition (2, 3). Other conditions,
such as the linearity of labelling, the effect of dye
concentration, pH, and reaction time on
completeness and specificity of labeling were
optimized, and the impact on protein mobility, and
the effect of additional, unconventional additives
were assessed. In addition, the sensitivity,
reproducibility, and quantitative accuracy were
also investigated and will be presented.
References
1. Pretzer, E., and Wiktorowicz, J. E. (2008)
Saturation fluorescence labeling of proteins for
proteomic analyses, Analytical Biochemistry
374, 250-262.
High Sensitivity Porous Sprayer (HSPS) in Capillary Electrophoresis-Mass
Spectrometry (CE-MS) for the Analysis of Phosphopeptides.
1 2 2
C. C. L. Wong , The Scripps Research Institute C. Ratnayake , J. Chapman , Beckman Coulter, Inc. J. R.
1
Yates III , The Scripps Research Institute.
1
The Scripps Research Institute, La Jolla, CA 92037, USA 2Discovery Products, Beckman Coulter, Inc., Fullerton CA,
USA
Relative Abundance
80 MS
28.06
26.32 22908Run4_
Relative Abundance
80 MS
28.06 28.36
26.32 22908Run4_
25.51 28.70
80
60
23.18 N L:
9.50E5
B ase P eak m/z=
1031.33-1032.33
MS
22908Run4_0802
29104110
40
25.91
20 27.88 29.46
32.49 35.18 36.97 52.84
0.19 3.93 4.84 6.42 8.61 10.85 12.11 15.25 19.28 22.33 41.52 41.98 44.05 47.57 51.02 53.57 58.44 59.77 60.81 65.03
80
um ID and 150 um OD (Polymicro Technologies) were 200 300 400 500 600 700 800 900 1000 1100
m/z
1200 1300 1400 1500 1600 1700 1800 1900 2000
3Department of Chemistry, National Sun Yat - Sen University, 804, Kaohsiung, Taiwan
Metallic nanoparticles have been intensively However, the weak hydrophobic interactions take
applied as affinity probes in sample preparation for a long time (1.5hour) for extraction. Therefore, in
proteins or other biomolecule analysis in mass this study, we applied the electrostatic approach of
spectrometry. However, these nanoparticle based siliver nanoparticles via SDME technique in the
washing of the nanoparticles from protein sample peptides from sample solution before MALDI-MS
before mass spectrometry analysis. The analysis in order to compare with our previous
extraction may lead to serious sample losses and extraction time, sample pH and agitation rate were
chance of interference of matrices from samples optimized for best extraction efficiency and
because these techniques prepared the nano sensitive detection of peptide mixtures. In addition,
particles in aqueous phase. Thus, the application the applicability of the proposed method has been
biomolecule analysis from biological matrices such biological samples and in high concentration of
as urine and blood is difficult. Therefore, in 2005, matrix interferences such as urea and Triton X-
probes for rapid analysis and signal enhancement the same procedures from our previous study [1].
of peptide mixtures in the AP-MALDI atmospheric Briefly, the stock solutions of peptides were
desorption/ionization mass spectrometry (AP- Peptides with desired concentrations were spiked
MALDI/MS) [1]. This approach is simple and into a glass vial filled with 20 mL sample solution.
samples can be directly deposited on target plates A 10 μL of microsyringe (Hamilton co., Reno,
for MALDI-MS analysis after extraction. In 2008, Nevada, USA) was taken and 2 μL toluene
we continually applied modified silver containing AgNPs was drawn into it. The
nanoparticles (AgNPs) with hydrophobic ligands microsyringe was inserted into sample solution
including dodecanethiol (DT) and octadecanethiol through the PTFE-coated silicon septum of screw
(OT) prepared in toluene via liquid-liquid cap of glass vial as shown in Fig. 1. As soon as
microextraction (LLME) to analyze neutral peptides the sample was extracted into 0.8 μL of droplet of
organic solvent or silver nanoparticles in toluene, The AP-MALDI/MS spectra of Leu-enk, and Met-
the droplet was drawn back into the microsyringe enk mainly show two protonated molecules at m/z
(Hamilton Co., Reno, NV) and directly placed on to values 556, 574 for Leu- and Met-enk,
the target plate for subsequent AP-MALDI/MS respectively. The AP-MALDI/MS of GrD spectra
analysis. Mass spectrometry experiments were mainly appear three ions at m/z 1883, 1906 and
carried out using a Finnigan MAT ion trap mass 1922 from GrA which were assigned [Val-GrA+H]+,
Jose, CA, USA). The ESI ion source was replaced Gramicidins are neutral peptides and therefore
with an AP-MALDI ion source. Matrix solution was exhibit no charge at any pH. Leu-enk and Met-enk
prepared by using CHCA (10 mg/mL) dissolved in show net negative charge above the pI value since
methanol and water (2:1 ratio), then TFA was their pI value is 5.4. Based on the neutral property
added to the solution with a final concentration of of gramicidins and pI dependent charge exhibition
0.1%. Following the dried droplet method, 2 μL of of Leu- and Met- enkephalins, the following
nano silver extraction solution was placed on experiments were performed to demonstrate the
target plate with the addition of equal volume of application of AgNPs for peptide identification.
attenuated to 60% was used for the illumination at Effect of selection of solvent
10 Hz of repetitions. Capillary temperature was Several organic solvents including hexane,
maintained at 250 oC. 1.8 kV voltage was applied chloroform and toluene which are typical solvents
to the target plate. Capillary voltage and tube lens applied in traditional SDME experiments were
offset voltage were applied with 40V and 70V, examined for the extraction of the Leu- and Met-
respectively. A pulsed nitrogen laser with UV enkephalin peptides. The SDME were performed
radiation of 337 nm was used to desorb and ionize with extraction time of 2 min and agitation rate at
the deposited molecules. Each spectrum was 240 rpm. Met- and Leu- enkephalin peptides were
scanned for 2 min. However, any difference was spiked into aqueous solution with equal
not observed between 2 and 3 min of scanned concentration (3 μM). After extraction, the analysis
Parameters optimization for SDME and peptide The results only two ions of m/z 568 and 524.1
The SDME extraction of peptide mixtures from revealed that they are coming from the CHCA
aqueous solution to organic solvent was influenced matrix. The m/z 568 is assigned as [3CHCA+H]+
by several parameters including solvent selection, and m/z, 524 is identified as [3CHCA-CO2+H]+.
extraction time, agitation rate and sample pH. The spiked concentration of the peptides was
Thus, these factors were optimized for all the increased to 12 μM and SDME was performed
SDME experiments. To evaluate this technique, a again with various organic solvents as mentioned
mixture of peptides containing gramicidin D (GrD), above. However, after extraction, the subsequent
Leu-enkephalin (Leu-enk) and Met-enkephalin AP-MALDI-MS analysis of all organic solvents can
(Met-enk) were selected as model compounds. not successfully to extract any enkephalins since
GrD consists of a group of different types of these organic solvents are nonpolar in nature and
gramicidin peptides known as GrA, GrB and GrC. therefore can not extract the polar enkephalin
peptides. Further, we applied SDME with toluene adding 0.1 N HCl and observed no signal
containing AgNPs to extract these peptides from corresponding to the peptides. The increase in the
aqueous solution since it is believed that pH to 9.0 by adding 0.1 N NaOH to the sample
nanoparticles exhibit surface charge and both Leu- solution obtained similar results as observed at pH
and Met-enkephalins were extracted and detected 7.0. The two model peptides were successfully
from the AP-MALDI/MS analysis. The Leu- and extracted from aqueous solution to AgNPs in
Met-enkephalins exhibited protonated molecules at toluene droplet at the pH values above their
m/z 556.2 and 574.1 respectively. These results isoelectric point (pI 5.4.) as the peptide molecules
reveal that AgNPs used for SDME exhibit charge exhibit net negative charges. Below the pI values,
on their surface to capture the peptides via these two peptides carry net positive charge and
electrostatic attraction forces. were thus kept away from positively charged
To optimize the best extraction efficiency for charged species can be extracted by AgNPs,
extraction time of sample solution for this mixtures of neutral peptides (GrD) with Leu- and
technique, SDME using AgNPs liquid droplet was Met-enk were spiked into sample solution and
carried out with different time intervals from 30 sec SDME coupled with AP-MALDI/MS analysis was
to 7 min. The signal was increased with increasing performed at different pH values with a range from
time from 30 sec to 2 min and then decreased 5.0 to 11.0 again. However, AP-MALDI/MS
since the equilibrium between the peptides and analysis of the toluene droplet containing AgNPs
AgNPs has been reached at 2 min. These results did not show any signal for gramicidin peptides,
suggest that the equilibrium of peptides between which confirmed that peptides containing pI and
aqueous solution and the droplet of AgNPs in exhibit charge at a certain pH only were captured
toluene was extremely fast due to the electrostatic by AgNPs and subsequently identified by AP-
interaction. Therefore, we selected 2 min as the MALDI/MS. This result indicates that this
optimum extraction time for both enkephalin technique is based on the surface charge of
process of how the peptides are extracted into the Effects of stirring rate
droplet of AgNPs in toluene by electrostatic To optimize the extraction efficiency, the agitation
interactions. The SDME extractions were of sample solution was carried out with varying
performed at both acidic and alkaline from pH 5.0 stirring rates ranging from 60 - 360 rpm at different
– 11.0. The pH effect on signal intensity was intervals. Maximum extraction efficiency was
shown in Fig. 4B. The pH of the aqueous solution observed when the sample solution was agitated
was adjusted with 0.1 N HCl and 0.1 N NaOH. The at 240 rpm and then the extraction efficiency was
SDME/AP-MALDI/MS technique was successfully decreased with increasing agitation rate (300 and
applied to identifie both Leu- and Met-enkephalins 360 rpm), which is due to the instability of the
from aqueous sample solution with pH 7.0. The pH microdroplets at higher stirring rate (300 and 360)
sample agitation rate for the extraction of peptides. AP-MALDI/MS analysis as in Fig. 5B and Fig. 6,
Detection limits of SDME-AgNPs/AP-MALDI/MS urea and 1.2% Triton X-100, the extraction
By means of optimized conditions, (2min, 240 rpm rapidly as the droplet of toluene containing AgNPs
and pH 7) the peptide mixtures of Met- and Leu- became unstable. In addition, since the AP-
enkephalins were identified at lower MALDI/MS with excellent tandem mass capability,
concentrations with the detection limits for Met- the identification of peptides in presence of high
and Leu-enkephalins for 160 and 210 nM matrix interference such as 1% Triton X-100 and
technique in high interference samples enk (m/z, 574.1) produced several fragment ions
One of the problems experienced in MALDI-MS including [Met-enk-H2O+H]+ (m/z 556), b4 (m/z
analysis of protein samples is suppression of 424.93), a4 (m/z 397.01), y3 (m/z 353.91), and b3
signal intensity by surfactants such as Triton X-100 (m/z 424.93). The MS/MS spectra of protonated
and urea. Triton X-100 is a commonly used molecule of Leu-enk (m/z, 556.0) generated
surfactant for hydrophobic membrane proteins fragment ions including [Leu-enk-H2O+H]+ (m/z
solubulization during biological sample preparation 538.05), b4 (m/z 424.93), a4 (m/z 397.01), y3 (m/z
whereas urea is useful to denature the proteins 335.87) and b3 (m/z 278.88) ions. These observed
ahead of tryptic digestion in proteomic MS/MS results are consistent with those results
approaches. However, the presence of Triton X- observed in previous studies. These results
100 and urea in the samples dramatically affects revealed that this technique is a powerful tool for
the quality of mass spectra for subsequent protein peptide identification at high interfercnce matrix
identification when concentrations exceeding 0.1% even at the concentrations of 1% Triton X-100 and
and 1M of Triton X-100 and urea, respectively. To 6 M urea, which are sufficient for solubulization of
overcome this problem, an application has been hydrophobic membrane proteins and protein
tried to identify 3 μM of both Met-enk and Leu-enk Comparison of mass spectra obtained from silver
peptides from aqueous solution in the AP-MALDI- and gold naoparticle-assisted SDME coupled with
MS analysis of sample solution containing either AP-MALDI-MS
1% of Triton X-100 or 6.0M of urea without SDME We previously reported the use of modified gold
and did not observe any peaks related to both enk- nanoparticles assisted with single drop
peptides in the AP-MALDI mass spectra. The microextraction (SDME) in the separation and
mass spectrum obtained without SDME analysis of preconcentration of these peptide mixtures from
sample solution containing urea was not shown in sample solutions before AP-MALDI/MS analysis
this article since no signal was obtained. However, [1]. This is because AuNPs prepared in toluene
the two peptides were successfully extracted by exhibits positively charged tetraalkyammonium
means of AgNPs-assisted SDME from exactly the ions on their surface and therefore exhibit net
same of sample solution containing 1% Triton X- positive charge [1]. In this study, we compared this
similar approach by changing the AuNPs to AgNPs. neutral peptides and proteins by hydrophobic
Thus, the AgNPs exhibit positive charge on their interactions [2]. The LODs of gramicidin detected by
surface and this is due to the interaction between using this approach in urine and plasma samples
dispersion medium (toluene, dodecanethiols, was 0.13 and 0.16 μM, respectively. Comparison of
tetraalkylammonium bromides) and AgNPs, that AgNPs acting as an electrostatic affinity probe
provoke AgNPs to act as electrostatic affinity (current approach) with AgNPs acting as a
probes for peptides. The mass spectra obtained hydrophobic affinity probe (previous work) [2] for
from AuNPs as well as AgNPs-assisted SDME peptide analysis in the AP-MALDI/MS, the AgNPs
techniques were compared and the main as electrostatic affinity probe is suitable to analyze
difference between them is that in our previous neutral peptides such as gramicidin while the
study with AuNPs-assisted SDME, the AP- current AgNPs was further stabilized by
MALDI/MS shown higher signal intensity for Leu- tetraalkyammonium ions which exhibits positively
enk than Met-enk. To our surprise, in contrast to charged ions on their surface and therefore we can
AuNPs, in exactly the same conditions such as in analyze peptides or proteins by electrostatic
aqueous sample solution, in presence of 1% Triton attraction forces based on controlling the pH of
X-100 or in the 6.0 M urea, all mass spectra solution. In addition, since the electrostatic
obtained with AgNPs exhibited higher signal interaction is much stronger than the hydrophobic
intensity for Met-enk although equal concentration interaction, we found that the extraction time can be
of peptides were spiked into sample solution. The greatly reduced in this current approach using
possible reason for the higher efficiency of AgNPs SDME-AgNPs (2 min) compared with that of our
towards Met-enk could be due to silver is highly previous LLME-AgNPs method (1.5 hour).
consists of sulfur atom. A recent report also Approach of using silver naoparticle prepared in
demonstrated that the most attractive sites for toluene as matrix for AP-MALDI ion trap mass
AgNPs would be the sulfur containing residues of spectrometry for peptide analysis
the glycoproteins of HIV-1. The above results AgNPs prepared in aqueous phase have been
show that AgNPs are more efficient to extract Met- successfully applied as matrix for peptide analysis
enk peptide relative to AuNPs. Another advantage in the MALDI –TOF- MS. Thus, we also examined
of using AgNPs in SDME is that the cost for this AgNPs as matrix in the AP-MALDI/MS.
AgNPs-SDME method is less expensive when Unfortunately, none of signal can be observed. Up
compared with AuNPs. Thus, it is worthy and also to date, none of the report has been shown that
of interest to introduce AgNPs for peptide any the nanoparticles can be applied as matrix in
We previously using modified AgNPs with purification and identification of proteins and
samples.
References
(1) Sudhir, P.R., Wu, H.F., Zhou, Z.C., Anal
80 (in press).
Results
Effects of various experimental parameters, Figure 1 The layout of the 2-D microchip
including the electric field strength, channel length electrophoresis.
and injection frequency from the first to the second The first dimension separation (IEF) was performed in
dimensional separation channel, were studied. It the channel between reservoirs 1 (anolyte) and 2
was found that the increase of electric field (catholyte); the second dimension separation (CZE) was
strength was helpful to enhance the resolution of performed in the channel between reservoirs 3 and 4.
the separation, and. a longer channel length could
lead to higher resolution of CZE. The focused
sample zones were introduced into the second one
in sequence by switching the voltage. Smaller
volume of sample introduced lead to higher peak
capacity of the 2-D system.
Under the optimized condition, the peak capacity
of 795 was obtained for the separation of three
labeled proteins, which was greatly increased
compared with each single dimensional
separation. The capacity of such a platform was
further demonstrated by analyzing proteins Figure 2 Analysis of proteins extracted from E. Coli by 2-
extracted from E. Coli (Fig 2), and All these results D microchip electrophoresis
showed the promising of multidimensional Experimental conditions: IEF: cathode solution, 20 mM
separation on microchip in the high throughput and NaOH containing 0.2% MC; anode solution, 20 mM
high resolution analysis of complex samples. H3PO4 containing 0.2% MC; separation voltage,
1300v/cm; CZE: buffer: 20 mM H3PO4 (pH=2.1)
Innovative aspects containing 0.2% MC; injection and separation voltage,
3oov/cm and 500v/cm; sampling and separation time: 4s
and 56s. Sample: 1mg/mL extracted proteins in solution
of 1.0 % MC and 2% v/v Pharmalyte. Image b was the
processed planer images corresponding to a
Column switch recycling size exclusion chromatography for high
efficientt protein separation
efficien
Huiming Yuan 1,2, Lihua Zhang 1, Zhen Liang 1, Yukui Zhang 1
(1 National Chromat ographic Reasearch and Analysis Center, Dalian Institute of Chemical
Physics, The Chinese Academy of Sciences, Dalian ,P.R.China. 2Graduation university of
chinese Academy of Sciences, Beijing, P.R.China)
Introduction orthogonally integrated with RPLC. With a
Due to the good biocompatibility, seven-protein as a simple sample, high peak
conventional size exclusion chromatography capacity of 2D-plat f orm was achieved.
(SEC) has been widely used for the Innovative aspects
separation and purif ication of biomolecules. Novel approach based on size
However, its existing shortcomings, such as excluson chromatography for high
poor resolution, low efficiency and narrow efficiency separation of proteins.
separation window, limited its application in Construction of consecutive 2D-
proteome research. platform based on column switch
Recently, we developed a novel approac h Recycling size exclusion
for protein separation based on column chromatography.
switch recycling size exclusion High peak capacity of 2D-platform
chromatography (CSRSEC), by which could be achieved.
proteins were alternatively switched from References
one SEC column to another, and then (1) Al-Somali, A. M.; Krueger, K. M.;
separated in terms of close-loop recycling. Falkner, J. C.; Colvin, V. L. Anal. Chem.
Such a system demonstrated improved 2004 , 76 , 5903-5910.
resolution for proteins and was further
applied for the construction of
multidimensional protein separation platform .
Methods
For CSRSEC analysis, pumps, SEC
columns, UV detector and two-position,
high-speed ten-port valves (Valco were Figure 1. Scheme of column switch
connected in terms of closed-loop (Figure1), recycling size exclusion chromatography
by which the late eluted components were (CSRSEC) platform.
first kept onto another column, and injected
after the early eluted ones were completely
separated. The CSRSEC approac h was
further integrated with RPLC to construct a
consecutive multidimensional platform for
proteome analysis.
Result s
By CSRSEC analysis, proteins with wide
molecule weight distribution were completely. Figure2. Separation of myoglobin and
The resolution of proteins with minor MW ribonuclease (2500Da difference) by
difference was greatly improved (Figure2). CSRSEC
Furthermore, the CSRSEC approac h was
DEVELOPMENT OF MULTI-DIMENSIONAL CHROMATOGRAPHY-MASS
SPECTROMETRY TECHNIQUES FOR PROTEIN COMPLEX ANALYSIS
National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of
Introduction
The analysis of proteomes is a challenge, because Innovative aspects
the presence of high-abundance proteins can • Capability to deplete high-abundance proteins
overwhelm the signals of low abundant ones. Thus in unknown samples in which the specific
various methods for the depletion of high abundant antibodies of high-abundance proteins are not
proteins have been developed. Protein equalizer discovered.
technology is another means to reduce protein • Easy and low cost to prepared such sample
concentration differences, thus improving the preparation materials, suitable for the analysis
detection sensitivity of low abundance proteins. In of various proteome samples.
our recent study, a new protein equalizer based on
M13 scFv displaying library was developed, and
successfully applied to simultaneously deplete a References
number of high abundant proteins in human serum (1) Arvidsson. P et al, Direct chromatographic
and urine of nephropathy patients. capture of enzyme from crude
homogenate using immobilized metal
affinity chromatography on a continuous
Methods supermacroporous adsorbent. J.
The epoxy-containing supermacroporous Chromatogr. A, 2003, 986, 275–290.
monolithic cryogel was prepared according to (2) Kumar. A et al, Affinity fractionation of
reference (1). Then the amplified and purified lymphocytes using a monolithic cryogel. J.
whole M13 scFv displayed library was coupled to
cryogel by the “glutaraldehyde method” (2).
Immunol. Meth. 2003 ,283: 185–194.
Human serum and urine proteins of nephropathy
patient were selected to study the high abundance
protein depletion capacity of the new protein
equalizer. Each sample was added to the M13-
coupled cryogel for 60 min, then the eluants were
collected and analyzed by SDS-PAGE and MS.
Finally the cryogel was regenerated by 2M NaCl.
Results
Figure 1 showed the analysis of human serum and
urine proteins of nephropathy patients treated with
the protein equalizer by SDS-PAGE. It could be A B
seen that the concentration of proteins was
obviously equalized, by sharply reducing the Figure 1 .The results of depletion of high abundant
concentration of the most abundant components, proteins using the new protein equalizer.
while simultaneously enhancing the concentration Samples were loaded onto each lane and separated by
of the low abundance species. In addition, the 12% gels. A: human serum proteins after depletion of
high abundant proteins. Lanes: 1, Marker (97, 66, 43,
MS/MS identification results also demonstrated
31, 20 and 14kDa); 2, depleted serum using M13-
that after the treatment, more low concentration uncoupled cryogel; 3, depleted serum using M13-
proteins could be identified. Compared with affinity coupled cryogel; 4, crude serum. B: urine proteins of
depletion methods, the new protein equalizer with nephropathy patient after depletion of high abundant
M13 scFv displaying library immobilized is more proteins. Lanes: 1, Marker; 2, depleted urine proteins
suitable for the depletion of various high- using M13-uncoupled cryogel; 3, depleted urine proteins
abundance proteins in unknown complex samples. using M13-coupled cryogel; 4, crude urine proteins of
At the same time, different low abundance proteins nephropathy patient.
could be enriched without bias. All these results
demonstrate that such a novel protein equalizer
might pave a new way for exploring more proteins
in proteome.