+ All Categories
Home > Documents > Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX...

Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX...

Date post: 17-Jun-2020
Category:
Upload: others
View: 4 times
Download: 0 times
Share this document with a friend
16
www.lcsciences.com 1-888-528-8818 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 V MAX , K M , and K I . 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 K d (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.
Transcript
Page 1: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

www.lcsciences.com 1-888-528-8818

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.

Page 2: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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.

30-10B-02

www.lcsciences.com 1-888-528-8818 30-10B-02

Page 3: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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.

30-10B-03

www.lcsciences.com 1-888-528-8818 www.lcsciences.com 1-888-528-8818 30-10B-03

Page 4: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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

30-10B-04

www.lcsciences.com 1-888-528-8818 30-10B-04

Page 5: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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

30-10B-05

www.lcsciences.com 1-888-528-8818 www.lcsciences.com 1-888-528-8818 30-10B-05

Page 6: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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

30-10B-06

www.lcsciences.com 1-888-528-8818 30-10B-06

Page 7: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

Discovery - Screening - Profiling - Detection

www.lcsciences.com 1-888-528-8818 www.lcsciences.com 1-888-528-8818 30-10B-07

Page 8: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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.

www.lcsciences.com 1-888-528-8818 30-10B-08

Page 9: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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

www.lcsciences.com 1-888-528-8818 www.lcsciences.com 1-888-528-8818 30-10B-09

Page 10: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

www.lcsciences.com 1-888-528-8818

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

30-10B-10

Page 11: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

www.lcsciences.com 1-888-528-8818

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

www.lcsciences.com 1-888-528-8818 30-10B-11

Page 12: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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

30-10B-12

www.lcsciences.com 1-888-528-8818

Page 13: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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://

30-10B-13

www.lcsciences.com 1-888-528-8818 www.lcsciences.com 1-888-528-8818

Page 14: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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.

30-10B-14

www.lcsciences.com 1-888-528-8818

Page 15: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

Real Time Data Collection

30-10B-15

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

Page 16: Custom Peptide Microarray Service - LC Sciences LLC · Custom Peptide Microarray Service MULTIPLEX PROTEIN KINASE ASSAYS Perform protein kinase reactions on arrays of comprehensive

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].

30-10B-16

www.lcsciences.com 1-888-528-8818 30-10B-16

@LCSciencesLLC @LCSciences LC Sciences LLC


Recommended