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Custom Peptide Microarray Service
MULTIPLEX PROTEIN KINASE ASSAYS
Perform protein kinase reactions on arrays of comprehensive sets of substrates. Measure kinase activity and inhibitor effects. Obtain hundreds of reaction profiles and curves in parallel for parameters such as VMAX, KM, and KI. Use of microarray titer plate format will
increase your workflow by at least 40-fold that of a single microtiter plate.
LARGE SCALE HIGH RESOLUTION EPITOPE MAPPING
Perform large scale parallel epitope mapping from pathogens. Identify high affinity antibody binding peptides. Screen sensitive antibody-detection peptides. Detect autoantibodies/biomarkers from serum or biological samples, determine Kd (binding affinity) of hundreds of binding peptides, obtain titration curves for antibodies.
PATHWAY PHOSPHOPEPTIDE-BINDING PROTEIN STUDIES
Profile SH2-containing proteins in complex biological samples by an array of phosphopeptides which are carefully curated from literature. Screen effective SH2 binding inhibitors and measure inhibitory activities. Screen signature phosphopeptides for protein capture as a tool for signaling pathway characterization.
PEPTIDES AND PEPTIDOMIMETICS FOR PROTEIN CAPTURE
Screen biomarkers (proteins and peptide binding targets) from biological samples such as blood serum or cell lysates. Use novel
protein capture peptides to detect and profile on the same chip platform a wide range of molecular biomarkers: signaling protein kinases, pathway phosphoprotein-binding and domain-binding proteins, immuno-responsive antibodies, metabolites and metabolic molecules, and other small molecules.
THERAPEUTIC SYNTHETIC PEPTIDE SCREENING
Rapidly design, synthesize, and screen diverse peptides, peptide analogs, and peptides modified with glyco-units against important therapeutic targets.
Cost Effective 1-Stop Proteomics Solution
Pico-Liter Peptide Microarray
on a µParaflo® microfluidics microchip
Microarray titer plate format increases your workflow 40X that of a single microtiter plate.
Comprehensive Sample to Data Service This is a comprehensive PROTEOMICS service - send us your sample - we’ll manufacture a peptide microarray of standard content or synthesize a custom designed array, carry out the sample assays you request, perform data collection and analysis, and deliver a results report to you. Our cost effective 1-stop solution can save you tremendous time and money and the use of a microarray titer plate format will increase your workflow to 40X that of a single microtiter plate.
High Throughput Format
Thousands of different peptide sequences are synthesized on one
array (1 cm2)
1 peptide microarray titer plate = 40 X 96-well microtiter plates.
Target thousands of peptide sequences at once - perform thousands
of multiplex parallel assays at addressable chip locations.
Generate hundreds of binding curves in a single experiment.
Scaleable to proteomic scale.
Innovative Microfluidic Array Platform Peptides are synthesized by conventional t-boc chemistry on a proprietary µParaflo® microfluidic biochip. The microfluidic technology ensures:
An engineerable, reproducible, automatable, and scalable
proteomic platform.
Uniform distribution of the sample solutions on the array.
Efficient sample-peptide contact.
Rapid and straightforward optimization.
Low background and specific binding by stringency wash
processes.
Enclosed environment for sample stability and free of
contamination.
Dye oxidation and deterioration are prevented.
Sensitive fluorescence detection.
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Quantitative Results
Customer Designed Sequences
1711.49SRC-1566
1011.49PTPN11-1122
611.47PDGFRB_Y579
411.47GRB2-0521
1621.47SRC-1565
1521.39SRC-1543
521.39IRS1_Y1222
321.39GABI_Y627
1831.11STAT6-1684
131.11CagAD1
241.01EGFR_Y1197
1350.90PTPN6-1211
760.70PTP_N0218
1270.63PTPN11-1178
1170.63PTPN11-1157
980.60PTPN11-1121
890.54PTP_N3235
Series#
Order
#(1=we
akest
binding)
Estimated
Kd
(Releaive
AU)
1711.49SRC-1566
1011.49PTPN11-1122
611.47PDGFRB_Y579
411.47GRB2-0521
1621.47SRC-1565
1521.39SRC-1543
521.39IRS1_Y1222
321.39GABI_Y627
1831.11STAT6-1684
131.11CagAD1
241.01EGFR_Y1197
1350.90PTPN6-1211
760.70PTP_N0218
1270.63PTPN11-1178
1170.63PTPN11-1157
980.60PTPN11-1121
890.54PTP_N3235
Series#
Order
#(1=we
akest
binding)
Estimated
Kd
(Releaive
AU)
0
2500
5000
7500
10000
0.01 0.1 1 10
50% Binding Strength
0
2500
5000
7500
10000
0.01 0.1 1 10
50% Binding Strength
0
2500
5000
7500
10000
0.01 0.1 1 10
50% Binding Strength
0
2500
5000
7500
10000
0.01 0.1 1 10
50% Binding Strength
Protein Assay on a Peptide Microarray
Quantitative Results
Generate information about specific probe sequences - sequences
can be defined to each single amino acid residue and the interpretation of the assay results are taken directly from digital image read out of an addressable microarray.
Make use of convenient, safe, sensitive fluorescence detection.
Achieve reliable and quantifiable results through the highly stringent
design and use of negative and positive control references. False positive readings are minimized.
Ultra-low Sample Consumption
Miniaturized array features reduces consumption of valuable samples
to the sub-nanoliter to picoliter level per reaction.
Perform thousands of peptide assays per array using only sub-µg of
protein.
Flexible Design
Completely customizable design of peptides according to your
needs. All arrays are synthesized to order.
Choose from our standard microarray content, customer specified
sequences and layout, or sequences custom designed by LC Sciences.
Quickly revise microarray design and content to keep experiments
moving forward based on previous results.
Conventional t-boc synthesis chemistry is completely compatible
with amino acid analogs. Incorporate analogs to expand the range of applications.
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Microfluidic Array Platform These are not spotted arrays! A proprietary µParaflo® microfluidic biochip is used and custom peptide sequences are synthesized on-chip. The microfluidic technology produces a uniform distribution of the sample solutions on the array, ensures efficient sample-peptide contact and enhances binding reactions and stringency wash processes. The microarray chip consists of thousands of three-dimensional chambers and is a closed system. Under these conditions multiplex protein assays are carried out in a way much like in thousands of pico-liter tubes, enclosure keeps the proteins in a stable environment, in solution and protected from air– oxidation/contamination. The miniaturized system provides automation, sample/reagent-savings and simplicity in operation.
In situ Parallel Synthesis In situ peptide synthesis using PGA (photogenerated acid) coupled with conventional t-boc chemistry and a programmable process means high probe quality, tight process control, and complete content flexibility. Our advanced manufacturing process ensures highly uniform spots and high reproducibility from array to array and yet permits total customization of contents on each individual array. In comparison, spotted microarrays tend to suffer from poor spot uniformity and large spot to spot and array to array variations, which lead to large data deviations. The spotting process requires significant up-front investment for peptide libraries and spotting equipment and thus is inflexible for customization.
Complete Control of Peptide Microarray Quality We ensure reliable and quantifiable results through the use of multiple negative and positive controls as well as reference peptides. Multiple QC measures are implemented at various stages of array manufacturing and assay processes. The evaluation of signal intensities of these control spots allows assessment of spot uniformity, cross-array spot-to-spot uniformity, and binding specificities and strength.
Comprehensive and Current Peptide Content Each peptide of a predetermined sequence is synthesized on a long spacer. The peptide sequences may be standard catalog content (from LC Sciences’ library containing database and/or literature validated peptides) or custom content (customer defined sequences). We use the most updated information on proteins for peptide microarray design to deliver arrays of comprehensive, systematic and up to date content. Sequence repeats are used on each array to allow statistical analysis of the data.
Multiple-Time Repetitive Assays on the Same Chip Peptide microarrays can be used for time-, protein/antibody/enzyme concentration-, or co-factor/inhibitor-dependent measurements. The array can be used multiple times, each time assay is carried out and assay signals are collected by fluorescence scan. These assays generate a very large set of data for proteomic assays and valuable information which would take weeks and months to produce using a conventional single protein/antibody/enzyme assay kit.
Innovative Microfluidic Array Platform
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Plate 1
Plate 2
Plate 3
Repeat
Repeat
Repeat
Seq001 002 003 004 005 006 007 008
Seq011 012 013 014 015 016 017 018
Seq101 102 103 104 105 106 107 108
Spots D
ensity
Spots D
ensity
Spots D
ensity
Pico-liter Scale Microarray Titer Plates
A G
Peptide Concentration Variation Across the Microarray Titer Plate
Pos. Conc. 1 0.125
2 0.25
3 0.5
4 1
5 2
6 4
7 8
8 16
9 32
10 64
11 128
12 256
LRR(AG)SLG
Close up view of a µParaFlo® biochip
Peptide Concentration Variation On-Chip Our unique synthesis chemistry makes it possible to vary the substrate density of reaction sites to create a gradient across the array. This array can generate the same amount of data equivalent to that of 40 conventional microtiter plates! This form of miniaturized multiplex parallel protein/antibody assays saves assay samples, reagents, labor and time in generating binding affinity or enzymatic reaction curves with a single experiment, allowing cross comparison of the systems assayed. The use of comparisons provides a more comprehensive picture and more reliable results.
Pico-liter Scale Microarray Titer Plate Peptide sequences are synthesized on the array at different molecular densities and thus are presented at different “concentrations”.
A 4000 feature microarray titer plate contains the molecular content equivalent to 40 microtiter plates.
Titration curves are obtained by concentration variations of the peptide substrates or the binding proteins.
Similarly, time-curves and inhibition curves can be measured simultaneously for a large number of peptides.
1 Microarray = 40 Plates
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Multiplex Protein Kinase Assays LC Sciences provides a comprehensive kinase analysis service utilizing high density protein kinase substrate (PKS) peptide microarrays synthesized for proteomic scale kinase profiling, quantitative measurement of kinase kinetic activities, and drug discovery research.
Known Kinases
Identify specific phosphorylation peptide substrates.
Characterize kinase kinetics and determine relative reaction rates.
Assay kinase inhibitors on an array of hundreds of peptide substrates for development of kinase regulatory agents.
Profile large sets of kinases with an array of signature “known” peptide substrates.
Make quantitative measurements for comparison of normal and mutant kinases reactivities.
Study signaling pathway proteins and mechanisms of disease.
Unknown Kinases
Identify substrate phosphorylation patterns and provide PK family assignments.
Large Scale Epitope Mapping LC Sciences provides a comprehensive epitope peptide microarray assay service to make both qualitative and quantitative measurements of antibody/epitope binding. Screening on a peptide microarray offers the opportunity to study thousands (up to thousands of peptides/chip) of potential epitopes in a single experiment utilizing only sub-µg quantity of protein. Using a tiling method, we can systematically map the binding sites on a pathogen/protein at single amino acid resolution.
Immunological Studies
Quantitate and optimize antibody binding affinity.
Optimize of phage-display lead peptides.
Identify immunodominant regions in antigens.
Screen antibody-targeting therapeutic peptides.
Vaccine Development
Screen vaccine peptides.
Develop specific antibodies by prescreening cross-reactivity.
Biomarker Screening
Detect autoimmune-response antibodies.
Develop biosensor arrays
Phosphopeptide-Binding Protein Studies LC Sciences provides a comprehensive phosphopeptide-binding protein assay service for profiling SH2-containing proteins in complex biological samples by an array of phosphopeptides which are carefully curated from literature.
Screen effective SH2 binding inhibitors and measure inhibitory activities.
Screen signature phosphopeptides for protein capture as a tool for signaling pathway characterization.
Optimize phosphopeptide domain binding.
Quantitative Peptide Microarray Applications
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Discovery - Screening - Profiling - Detection
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Multiplex Protein Kinase Assays
LC Sciences Standard Kinase Array Content
Covers the entire human kinome with substrates representative of all PK families.
Contains over a thousand unique peptide substrates.
Also contains corresponding negative controls (Ser/Thr/Tyr substituted by Ala) and
Replicates of each sequence.
Custom Content Kinase Arrays
Microfluidic platform and in situ synthesis permit total customization of sequence
content.
Thousands of customer defined unique peptide substrates are synthesized per
array. No minimum limit on the number of unique arrays synthesized.
LC Sciences can assist with sequence design.
Ser/Thr kinases
Group Family # of pepitdes
1 AGC AKT 20
2 AGC DMPK 1
3 AGC GRK 13
4 AGC NDR 1
5 AGC PKA 34
6 AGC PKC 46
7 AGC RSK 4
8 AGC SGK 1
9 Atypical PIKK 25
10 CAMK CAMKL 17
11 CAMK MAPKAPK 6
12 CAMK PKD 1
13 CAMK RAD53 1
14 CMGC CDK 56
15 CMGC CLK 1
16 CMGC DYRK 1
17 CMGC GSK 6
18 CMGC MAPK 45
19 Other AUR 5
20 Other BUB 4
21 Other CK2 44
22 Other IKK 7
23 Other NEK 1
24 Other PEK 2
25 Other PLK 8
26 STE STE11 1
27 STE STE20 7
28 STE STE7 15
29 STE STE-Unique 1
Subtotal 374
Tyr kinases Group Family # of pepitdes
1 TK Abl 17
2 TK Ack 1
3 TK Axl 3
4 TK BCR 2
5 TK Csk 3
6 TK EGFR 32
7 TK Eph 3
8 TK ErbB2 3
9 TK Fak 2
10 TK Fer 9
11 TK FGFR 9
12 TK IGF-R 1
13 TK InsR 12
14 TK JakA 24
15 TK Met 2
16 TK PDGFR 13
17 TK Ret 5
18 TK Src 44
19 TK STKR 3
20 TK Syk 12
21 TK Tec 6
22 TK Tie 2
23 TK Trk 2
24 TK Tyk 2
25 TK VEGFR 14
26 TKL IRAK 1
27 TKL RAF 1
28 TKL MLK 2
29 TKL STKR 1
Subtotal 231
Total 605
Characterization of a Novel Protein Kinase The preferred binding pattern of an unknown kinase revealed it is a serine/threonine kinase and belongs to PKA family.
0
10
20
30
RRRAISEA
RLRPLSFP
RGRLESAQ
RAREASGA
KQFLISPP
DIEQFSAV
RQLAFSAV
FQRRASDD
RGVRLSLP
AAARLSLA
VRRRQSVE
LERNLSFE
PPRKISAE
GMDFRSCI
RHARDSEA
RKVSAEGA
QARANSFV
EKKAFSFC
LMRRNSVA
EILNRSPR
MKKGPSGF
QNLMQSVK
QPAPGSVK
AGVGQSWK
DFEGFSFV
FGKENSAD
DIKNDSNF
AGLFKSQR
LAQVGSIL
GARRVSFA
PVQQPSAF
LKLGVSQQ
LIIEDSQP
QLFFISQP
PAGQLDSD
EILGDSQH
IGMHLSQA
LRKAASEP
AFVMASVD
AQRQNSAP
GLHIASPP
EGRPPSPP
ANNKGSAA
LARQASIE
HEGECSAV
EREPQSLA
QRFAFSPG
ERVAKSPG
IVPGKSPA
FIKENSPC
DAPPLSPF
QPMPASPG
VIDVPSAG
VPAPSPLG
KGKDQSGE
DDRHDSGL
VEDNRSQV
DGGAVSQE
GWIPASFL
REKEISDD
ARVLGSEG
LQPNASLN
KIRLESEE
FPRPASVP
ARKLLSRE
LRDGPSAP
MECRNSPV
DCAMESPP
NVLLMSPP
KVEPASPP
AGPALSPV
QAKVGSLD
DMKRLSME
RMVQLSPP
PEPFASPP
EVKEDSAF
DRPFISEG
EFCNKSKQ
AGPAPSPM
LFQFASAD
AALDWSWL
VLGEESPL
LCQAFSDV
FLKDESGF
Akt
Grk
PKA
PKC
RSK
PIK
K
CAM
K
MAPKAPK
AGC CAMK
Phosp
hory
latio
n S
ignal
CD
K
CK2
CMGC
Partial Plot of Results
P
P
% Phosphorylation = (Signal - Signal A)/Signal
P = PK catalyzed phosphorylation
Protein Kinase Assay
Dye detection
A=Ala Y=Tyr
A Y P A P P P P
Quantitative Detection of PK Catalyzed Phosphorylation Measuring the relative binding of built-in controls on the array enables us to make accurate quantitative measurements of protein binding.
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Multiplex Protein Kinase Assays
0
10
20
30
RRRAISEA
RLRPLSFP
RGRLESAQ
RAREASGA
KQFLISPP
DIEQFSAV
RQLAFSAV
FQRRASDD
RGVRLSLP
AAARLSLA
VRRRQSVE
LERNLSFE
PPRKISAE
GMDFRSCI
RHARDSEA
RKVSAEGA
QARANSFV
EKKAFSFC
LMRRNSVA
EILNRSPR
MKKGPSGF
QNLMQSVK
QPAPGSVK
AGVGQSWK
DFEGFSFV
FGKENSAD
DIKNDSNF
AGLFKSQR
LAQVGSIL
GARRVSFA
PVQQPSAF
LKLGVSQQ
LIIEDSQP
QLFFISQP
PAGQLDSD
EILGDSQH
IGMHLSQA
LRKAASEP
AFVMASVD
AQRQNSAP
GLHIASPP
EGRPPSPP
ANNKGSAA
LARQASIE
HEGECSAV
EREPQSLA
QRFAFSPG
ERVAKSPG
IVPGKSPA
FIKENSPC
DAPPLSPF
QPMPASPG
VIDVPSAG
VPAPSPLG
KGKDQSGE
DDRHDSGL
VEDNRSQV
DGGAVSQE
GWIPASFL
REKEISDD
ARVLGSEG
LQPNASLN
KIRLESEE
FPRPASVP
ARKLLSRE
LRDGPSAP
MECRNSPV
DCAMESPP
NVLLMSPP
KVEPASPP
AGPALSPV
QAKVGSLD
DMKRLSME
RMVQLSPP
PEPFASPP
EVKEDSAF
DRPFISEG
EFCNKSKQ
AGPAPSPM
LFQFASAD
AALDWSWL
VLGEESPL
LCQAFSDV
FLKDESGF
CMGC
Measurement of Kinase Inhibition Curves A powerful tool for protein kinase inhibitor screen assays - A Single array assay measures multiple inhibitory constants on various PK substrate peptides, allowing comparison of specificity of PK inhibition and identification of potential major and off-site phosphorylation sites. (D1, D2, D3 - peptide surface density)
[Staurosphorine] (M)
-3 -2 -1 0 1 2 3
% A
ctivity
0
20
40
60
80
100
120
EIYEDLMR-D1
EIYEDLMR-D2
EIYEDLMR-D3
0.98 1.83 EIYDELMR-D3
0.97 1.36 EIYDELMR-D2
0.95 0.97 EIYDELMR-D1
R2IC50 (µM)Substrate
0.98 1.83 EIYDELMR-D3
0.97 1.36 EIYDELMR-D2
0.95 0.97 EIYDELMR-D1
R2IC50 (µM)Substrate
[Src Kinase I Inhibitor] (M)
-3 -2 -1 0 1 2 3
% A
ctivity
0
20
40
60
80
100
120
EIYEDLMR-D1
EIYEDLMR-D2
EIYEDLMR-D3
0.93 4.17 EIYDELMR-D3
0.96 1.86 EIYDELMR-D2
0.99 0.71 EIYDELMR-D1
R2IC50 (µM)Substrate
0.93 4.17 EIYDELMR-D3
0.96 1.86 EIYDELMR-D2
0.99 0.71 EIYDELMR-D1
R2IC50 (µM)Substrate
Kinetic Studies of PKA Reaction Parallel measurements of reaction curve as a function of time and substrate concentration. These measurements lead to derivation of VMAX and KM. Pico-liter titer plate arrays enable simultaneous measurement of hundreds of such curves increasing workflow efficiency 40x.
[Substrate]
(µM)
0
20
40
60
v(µ
mol/m
in/m
g)
0
1
2
3
4
5
6
LRRGSLG
LRRMSLG
LRRYSLG
LRRSSLG
LRRASLG
1/[S] 0.0 0.1 0.2 0.3 0.4 0.5 0.6
1/v (m
in*m
g/
m mol)
0 1 2 3 4 5
Time (min)
0 10 20 30 40 50 60 70
Ph
osp
ho
ryla
tio
n S
ign
al (A
.U.)
0
10000
20000
30000
40000
50000
0.1 uM
0.2 uM
0.5 uM
1 uM
2 uM
4 uM
8 uM
16 uM
32 uM
64 uM
LRRASLG
Real-time Measurements Microarray Titer Plate Measurements
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Large Scale Epitope Mapping
Epitope Discovery Measure relative binding affinity to epitope sequence variants (N-truncation, C-truncation, Ala scan, tiling). Achieve single amino acid resolution for the binding core.
Antibody: anti-HA
Epitope (known): YPYDVPDYA
Chip #1: HA and flag epitope and variant sequences
Chip #2: HA, c-myc, VSVG, and flag epitope and other peptide sequences
Assay solution: 200 ml TBS (pH 6.8)
Temperature: 4 ˚C
Experimental Time: 1 hour
Detection: Cy5-IgG
Results: HA epitope is a hexapeptide DVPDYA. Three amino acids (D4, D6 and Y7) are essential.
Anti-HA Epitope Binding Array Cy5-IgG Staining
Results of epitope high resolution mapping are consistent with published data by protein crystallography method.
(Science 1992, 255:959; Curr Opin Immunol 1999, 11:193-202)
0
3
6
9
12
YP
YD
VP
DY
A
AP
YD
VP
DY
A
YA
YD
VP
DY
A
YP
AD
VP
DY
A
YP
YA
VP
DY
A
YP
YD
AP
DY
A
YP
YD
VA
DY
A
YP
YD
VP
AY
A
YP
YD
VP
DA
A
YP
YD
VP
DY
A
Bin
din
g S
ignal (n
orm
aliz
ed)
x 1,000
0
3
6
9
12
YP
YD
VP
DY
A
P
YD
VP
DY
A
Y
DV
PD
YA
D
VP
DY
A
V
PD
YA
P
DY
A
D
YA
Y
A
YP
YD
VP
DY
Y
PY
DV
PD
Y
PY
DV
P
Y
PY
DV
Y
PY
D
Y
PY
Y
P
PY
DV
PD
Y
Y
DV
PD
D
VP
Chip #1 Chip #2
Sig
nal (A
U)
x 1,000
C-truncation
N-truncation
Ala-scanning
YPYDVPDYA red: important residues
N,C-truncation
YPYDVPDYA blue: residues dispensable from both ends
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Large Scale Epitope Mapping
Measurement of Association Constants Make high-throughput quantitative measurements of antibody binding curves and calculate association constants.
Association curves measured with protein concentration titration on an epitope peptide microarray
Microfluidic design enables multiple concentration bindings on the same chip to generate not only a single titration curve for
the known epitope but also titration curves for all the epitope variants.
Anti-HA varied from 0.1 to 60,000 ng/ml, signal intensities acquired at different scanning gains were scaled according to a
calibration curve, curve fitting used Origin (Origin Lab).
Kd values measured are in the range of 2-4 ug/ml.
Association curves measured with peptide concentration (density) variation on an epitope peptide microarray
Unique synthesis chemistry makes it possible to vary the substrate density across the array. “Pico-titer” plate.
Thousands of binding curves can be measured simultaneously by one assay incubation. Equivalent to 40 microtiter plates.
In situ synthesis and innovative chemistry can provide more than 25-fold change in peptide density on the surface.
Measured a 31-fold change in anti-HA binding for highest density vs regular peptide density.
X Data
1e-2 1e-1 1e+0 1e+1 1e+2 1e+3 1e+4 1e+5 1e+6
Y D
ata
0
2e+5
4e+5
6e+5
8e+5
1e+6
YA
D YA
PD YA
VPD YA
D VPD YA
YD VPD YA
PYD VPD YA
YPYD VPD YA
one s ite saturation + nonspecific
[anti HA]
Sig
nal (A
U)
X Da ta
1e-2 1e-1 1e+0 1e+1 1e+2 1e+3 1e+4 1e+5 1e+6
Y D
ata
0
2e+5
4e+5
6e+5
8e+5 YPYDV PDYA YPYDV PDY
YPYDV PD
YPYDV P YPYDV
YPYD
YPY YP
one site saturation + nonspecif ic
Sig
nal (A
U)
[anti HA]
Quantitation of Epitope Binding Epitope mapping of SmBB' with purified anti-PPPGMRPP sample from patient sera on a tiling array.
Pathogen
Custom Microarray
Single AA Tiled Peptide Sequences
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
PPPGMMGP
PPGMMGPP
PGMMGPPP
GMMGPPPG
MMGPPPGM
MGPPPGMR
GPPPGMRP
PPPGMRPP
PPGMRPPM
PGMRPPMG
GMRPPMGP
MRPPMGPP
RPPMGPPM
PPMGPPMG
PMGPPMGI
MGPPMGIP
GPPMGIPP
PPMGIPPG
PMGIPPGR
MGIPPGRG
GIPPG
RGT
IPPGRGTP
PPGRG
TPM
PGRGTPMG
GRGTPMGM
RGTPMGMP
GTPMGMPP
TPMGMPPP
PMGMPPPG
MGMPPPGM
GMPPPGMR
MPPPGMRP
PPPGMRPP
PPGMRPPP
PGMRPPPP
GMRPPPPG
MRPPPPGM
RPPPPG
MR
PPPPGMRG
PPPGMRGP
PPGMRGPP
PGMRGPPP
GMRGPPPP
MRGPPPPG
RGPPPPGM
GPPPPGMR
PPPPGMRP
PPPGMRPP
PPGMRPPR
PGMRPPRP
Series1SmBB’ Tiling Sequences
An
ti-h
um
an
Ig
G C
y5 C
on
jug
ate
Sig
nal
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0
2,000
4,000
6,000
8,000
10,000
12,000
PTPN6-1261
PTPN6-1259
PTPN6-1245
PTPN6-1231
PTPN6-1222
PTPN6-1221
PTPN6-1220
PTPN6-1217
PTPN6-1211
PTPN11-1194
PTPN11-1190
PTPN11-1178
PTPN11-1163
PTPN11-1157
PTPN11-1147
PTPN11-1146
PTPN11-1134
PTPN11-1133
PTPN11-1123
PTPN11-1122
PTPN11-1121
PTP_N5637
PTP_N0153
PTP_N0123
CagA
A1
CagA
B1
CagA
C1
CagA
D1
STAT5B
-1682STA
T5B-1681
STAT5B
-1680STA
T5B-1679
STAT5B
-1678STA
T5B-1677
STAT3-1628
STAT3-1627
STAT3-1626
STAT3-1620
STAT3-1618
STAT1-1599
SRC-1595
SRC-1593
SRC-1590
SRC-1589
SRC-1588
SRC-1585
SRC-1575
SRC-1567
SRC-1565
SRC-1564
SRC-1562
SRC-1561
SRC-1556
SRC-1554
SRC-1551
SRC-1547
SRC-1543
SRC-1535
SRC_N5392
SRC_N0066
PLCG1-1077
PIK3R2-0985
LCK-0732
INPP5D
-0656GRB2-0609
GRB2-0569
FYN-0415
EPHA3-0339
SOCS3-1522
SOCS1-1502
SHC1-1456
SHC1-1407
SHC1-1383
SH2D
1A-1334
SH2B1-1319
RASA
1-1272
p85alpha-CSH2 SHP2-NSH2
SHP1 SHP2 CagA STAT SRC Other
Predicted non
SHP-2 binding
0
2,000
4,000
6,000
8,000
10,000
12,000
PTPN6-1261
PTPN6-1259
PTPN6-1245
PTPN6-1231
PTPN6-1222
PTPN6-1221
PTPN6-1220
PTPN6-1217
PTPN6-1211
PTPN11-1194
PTPN11-1190
PTPN11-1178
PTPN11-1163
PTPN11-1157
PTPN11-1147
PTPN11-1146
PTPN11-1134
PTPN11-1133
PTPN11-1123
PTPN11-1122
PTPN11-1121
PTP_N5637
PTP_N0153
PTP_N0123
CagA
A1
CagA
B1
CagA
C1
CagA
D1
STAT5B
-1682STA
T5B-1681
STAT5B
-1680STA
T5B-1679
STAT5B
-1678STA
T5B-1677
STAT3-1628
STAT3-1627
STAT3-1626
STAT3-1620
STAT3-1618
STAT1-1599
SRC-1595
SRC-1593
SRC-1590
SRC-1589
SRC-1588
SRC-1585
SRC-1575
SRC-1567
SRC-1565
SRC-1564
SRC-1562
SRC-1561
SRC-1556
SRC-1554
SRC-1551
SRC-1547
SRC-1543
SRC-1535
SRC_N5392
SRC_N0066
PLCG1-1077
PIK3R2-0985
LCK-0732
INPP5D
-0656GRB2-0609
GRB2-0569
FYN-0415
EPHA3-0339
SOCS3-1522
SOCS1-1502
SHC1-1456
SHC1-1407
SHC1-1383
SH2D
1A-1334
SH2B1-1319
RASA
1-1272
p85alpha-CSH2 SHP2-NSH2
SHP1 SHP2 CagA STAT SRC Other
Predicted non
SHP-2 binding
Predicted non SHP2 binding
SHP2-NSH2 XSH2
SHP1 SHP2 CagA STAT SRC Other
Phosphopeptide-Binding Protein Studies
LC Sciences Standard Profiling Array Content Phosphoprotein binding proteins (PPBP) contain domains which binds to phosphorylation sites in phosphoprotein or phosphopeptide (PPEP).
Through the use of high density arrays with addressable “signature” peptides for specific kinds of protein binding domains we can detect the presence or absence of these kinds of proteins in complex biological samples (cell lysate, human serum).
We have standard content phosphopeptide binding arrays with information from literature incorporated into the standard array design. Important signaling protein binding domains are represented on the array.
Drug development studies can be performed by measuring differential binding affinity to compare various phosphoprotein binding proteins or to quantitatively measure inhibitor effect.
Quantitative Analysis of Phosphopeptide-Binding on a Profiling Array Binding specificity of SHP2-N-terminal SH2 versus an alternate domain (XSH2) to PPEP
Standard SH2 Profiling Array SH2 is an example of PPBD which recognizes phosphorylated tyrosine (pY).
Total 1122 unique signature phosphopeptides from 87 phosphopeptide binding domains with 2 replicates and one set of negative controls (with phosphotyrosine substituted by alanine)
Measuring the relative binding of built-in controls on the array including natural Tyrosine, Phosphorylated Tyrosine, and Alanine (negative) enables us to make accurate quantitative measurements of protein binding and to minimize false positive signals due to non-specific phosphate binding.
= Phosphorylated Tyrosine P
A=Ala Y=Tyr
A Y P
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Phosphopeptide-Binding Protein Studies
Differential Binding Affinity Analysis Measure relative binding affinity to various recombinant phosphoprotein binding proteins.
Samples: GST-tagged recombinant fusion proteins: S01-SHP2 CSH2, S02-SHP2 NSH2, S03-SHP2 2SH2
Chip: LC Sciences standard SH2 profiling array. Detection: Anti-GST Ab Cy5 conjugate Data Processing: Global background subtraction and Z transformation, hierarchical clustering analysis. Plot Information: TMEV (9) image of the Z-values for relative binding affinity ranked for each SH2 protein. From red to green is stronger to weaker binding.
Quantitative Measurement of Inhibitor Effect Differential binding measurement in complex biological samples.
Sample 1: Normal Human Serum Sample 2: Treated Human Serum Treatment: Removal of Albumin and IgG Sample Size: 5ng/µl in 100 µl total volume.
Chip: LC Sciences standard SH2 profiling array. Detection: Anti-human IgG-Cy5 conjugate
IL6R4 (Negative) CagA-A CagA-B CTLA-4 IL6R3 EGFR-1173 IL4Ra1 IL6R4 EGFR-954 VEGFR-1
S01 -
Tre
ate
d S
eru
m
S02 -
Norm
al Seru
m
-3.0 0.0 3.0
CagA-E Gab1-659 IRS-1 AFAP110-3 Gab-3 FRS2-392 PDGFRB_Y1009 STAT3-1642 CagA-A Met2 SRC-1589 IL-6R-1
S01-C
SH
2
S02-N
SH
2
S03-2
SH
2
-3.0 0.0 3.0
Signature Peptide Sequences
Web-based tools are available to assist with experimental design. PepCyber - A searchable database of human protein–protein interactions mediated by phosphoprotein-binding domains (PPBDs).
http://
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Comprehensive Sample to Data Service
Sample QC Appropriate sample requirements are established for each particular array application. Integrity of the received customer sample is determined via a thorough analysis process. Samples that do not meet requirements are flagged and notification is sent with a recommendation not to proceed with the microarray assays.
Chip Synthesis and Control Experiments A standard or custom peptide microarray is synthesized on a high density peptide µParaflo® microfluidic biochip.
Each chip contains multiple synthesis control sites optimized for rigorous quality analysis.
On-Chip Binding or Enzymatic Assays Multiplex assays are performed on a µParaFlo® microfluidics chip which ensures uniform flow of the protein samples through closed pico-liter chambers. The assay is controlled by optimized binding protocols and performed under temperature controlled conditions. Binding/Enzymatic experiments are monitored to achieve high quality and stringency.
Titer-Plate Binding or Enzymatic Assays Peptides on reaction sites are synthesized according to pre-determined surface densities as “concentration” variation sites. Parallel protein assays on these titer-plate reaction sites provide hundreds of curves for binding or enzymatic/inhibitory activity measurements with minimal systemic variations.
Time and Concentration Dependent Measurements Multiple measurements are performed to obtain variable plots using time or concentrations of protein, enzyme, inhibitor, or co-factor.
Microarray Scan and Data Extraction Microarray images are carefully scanned for a balanced view. Numerical intensities are extracted for control, background, reference and test peptides.
Data Analysis Basic data analysis includes background subtraction, control and reference signal guided data processing, list of detected signals and data averaging results. Optional in-depth analysis and comprehensive data processing services such as: consensus sequence analysis, statistical and pattern analysis, plot generation and kinetic/thermodynamic parameter calculation is available as requested based on your specific application . A summary of the analysis report is emailed. The complete data set is saved to a CD, which is shipped via overnight carrier.
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Real Time Data Collection
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Microfluidic Array Platform The microfluidic technology produces a uniform distribution of the sample solutions on the array, ensures efficient sample-peptide contact and enhances binding reactions and stringency wash processes. The microarray chip consists of thousands of three-dimensional chambers and is a closed system. Under these conditions multiplex protein assays are carried out in a way much like in thousands of pico-liter tubes, enclosure keeps the proteins in a stable environment, in solution and protected from air– oxidation/contamination. The miniaturized system provides automation, sample/reagent-savings and simplicity in operation.
Multiple-Time Repetitive Assays on the Same Chip Peptide microarrays can be used for time-, protein/antibody/enzyme concentration-, or co-factor/inhibitor-dependent measurements. The array can be used multiple times, each time assay is carried out and assay signals are collected by fluorescence scan. These assays generate a very large set of data for proteomic assays and valuable information which would take weeks and months to produce using a conventional single protein/antibody/enzyme assay kit.
Flow
Pump
Sample
Light Source
Cooling/Heating
CCD Camera
Substrate Concentration (µM)
Sig
nal I
nte
nsity
(A.U
.)
0 min
4 min
8 min
16 min
30 min
60 min
120 min
240 min
480 min
Kinetic Curve of PKA Reaction
LRRXSLG series of peptides. Parallel measurements of hundreds of reaction curves.
Kinetic curves on time courses at different concentration of substrate.
PKA kinase reaction was performed at 30oC, 0-480 min w/0.2 mM ATP, 0.5 µg/mL PKA.
Longer reaction time reaches higher product. At 120 min, reaction at all concentrations
reaches the highest product yield (signal plateau).
www.lcsciences.com 1-888-528-8818 www.lcsciences.com 1-888-528-8818
Custom Peptide Microarray Service
Kinase Profiling Customer Publications
1. Wang W, Woodbury NW. (2014) Unstructured interactions between peptides and proteins: Exploring the role of sequence
motifs in affinity and specificity. Acta Biomaterialia 11(88-95) [abstract].
2. González Burón H. (2014) The role of the Tousled Like Kinases in genome stability and mammalian development. [Epub
ahead of print] [abstract].
3. Jang J, Stella A, Boudou Fd, Levillain F, Darthuy E, Vaubourgeix J, Wang C, Bardou F, Puzo G, Gilleron M. (2010) Functional
characterization of the Mycobacterium tuberculosis serine/threonine kinase PknJ. Microbiology 156(6), 1619-1631 [abstract]
Epitope Mapping Customer Publications
4. Cai F, Dou Z, Bernstein SL, Leverenz R, Williams EB, Heinhorst S, Shively J, Cannon GC, Kerfeld CA. (2015) Advances in
Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component.
Life 5(2), 1141-1171 [abstract].
5. Aloisio GM, Nakada Y, Saatcioglu HD, Peña CG, Baker MD, Tarnawa ED, Mukherjee J, Manjunath H, Bugde A, Sengupta AL. (2014)
PAX7 expression defines germline stem cells in the adult testis. Journal of Clinical Investigation 124(9), 3929-3944 [abstract].
6. Assis DN, Leng L, Du X, Zhang CK, Grieb G, Merk M, Garcia AB, McCrann C, Chapiro J, Meinhardt A. (2013) The role of macrophage
migration inhibitory factor (MIF) in autoimmune liver disease. Hepatology [Epub before print] [abstract].
7. Reichmann D, Xu Y, Cremers CM, Ilbert M, Mittelman R, Fitzgerald MC, Jakob U. (2012) Order out of Disorder: Working Cycle of an
Intrinsically Unfolded Chaperone. Cell 148(5), 947-57 [abstract].
8. Butterfield K, Caplan M, Panitch A. (2010) Identification and Sequence Composition Characterization of Chondroitin Sulfate-
Binding Peptides through Peptide Array Screening. Biochemistry 49(7), 1549-55 [abstract].
9. Williams BA, Diehnelt CW, Belcher P, Greving M, Woodbury NW, Johnston SA, Chaput JC. (2009) Creating protein affinity reagents
by combining peptide ligands on synthetic DNA scaffolds. J Am Chem Soc 131(47), 17233-41 [abstract].
µParaflo® Peptide Microarray Synthesis Technology Articles
10. Zhu Q, Hong A, Sheng N, Zhang X, Matejko A, Jun K-Y, Srivannavit O, Gulari E, Gao X and Zhou X. (2007) µParaflo Biochip for
Nucleic Acid and Protein Analysis. Methods in Molecular Biology, 382, 287-312 [abstract].
11. Gao X, Pellois J P, Kim K, Na Y, Gulari E, and Zhou X. (2004) High density peptide microarrays. In situ synthesis and
applications. Molecular Diversity. 8, 177-187 [abstract].
12. Gao X.(2004) In situ parallel synthesis of addressable peptide microarrays - in Proceedings of the 7th China Peptide
Symposium. Peptides. Biology and Chemistry. Eds. Du, Y-C., Zhang, Y. S., and Tam, J. P. Shanghai Scientific & Technology Publishers.
pp. 29-33 [abstract].
13. Gulari E, Gao X, and Zhou X. (2003) Light directed massively parallel on-chip synthesis of peptide arrays with t-Boc
chemistry. Proteomics 3, 2135–2141 [abstract].
14. Pellois J P, Zhou X, Srivannavit O, Zhou T, Gulari E, and Gao X. (2002) Individually addressable parallel peptide synthesis on
microchips. Nat. Biotechnol. 20, 922-926 [abstract].
15. Pellois J P, Wang W and Gao X. (2000) Peptide synthesis based on t-Boc chemistry and solution photogenerated acids. J.
Comb. Chem. 2, 355-360 [abstract].
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@LCSciencesLLC @LCSciences LC Sciences LLC