Peptides and Arrays - JPT Peptide Technologies GmbHpeptidomimetics for T-cell epitope and peptide lead discovery and characte-rization on proteome wide levels. PepStar™ Proprietary

Innovative Peptide Solutions

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Peptides and Arrays> Flexible Peptide Libraries

> Reliable Peptide Arrays

> Validated Peptide Pools

> Custom Peptide, Peptidomimetic & Organic Synthesis

> Peptide Discovery & Optimization Services

HistoryJPT Peptide Technologies is an innovative service provider and partner for peptide-based tools and R&D collaborations. JPT is located in Berlin, Germany and has achieved world-wide credibility for its commit-ment to rigorous quality standards and a reputation for developing and implementing innovative peptide- based services and research tools for various applications.

Together with its US-subsidiary in Boston, Massachusetts, JPT serves a worldwide clientele in the pharmaceutical and biotechnology industries as well as researchers in universities, governmental and non-profit organizations.

Technology & ApplicationOver the past decade, JPT has developed a portfolio of proprietary technologies and a series of unique products and services, which support research efforts in proteomics and in all developmental phases of novel vaccines against infectious and autoimmune diseases as well as against allergies and cancer.

In addition, JPT’s technologies find application in areas where peptide screening is needed. Typical examples are: screening for proteoptypic peptides, enzymatic activities (proteases, kinases, phosphatases, methyltransferases), or systematic optimization of peptide lead structures.

Quality AssuranceJPT is DIN EN ISO 9001:2008 certified and GCLP audited.

JPT’s proprietary key technologies are:

SPOT

High throughput peptide synthesis and screening technology for peptides & peptidomimetics for T-cell epitope and peptide lead discovery and characte-rization on proteome wide levels.

PepStar™

Proprietary technology platform providing peptide microarrays used to screen for humoral immune responses, immune monitoring and enzyme substrate identification or optimization among other applications.

PepMix™

Defined antigen spanning peptide pools to stimulate CD4+ and CD8+ T-cell responses.

PepTrack™

Peptide libraries of individual peptides offering various specifications and optimization for different types of assays.

SpikeTides™

Small scale, light or heavily labeled proteotypic peptides for proteomics.

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nts02 / Peptide Libraries

02 / Applications & Specifications

04 / Select Your Peptide Library Platform

12 / Peptide Arrays 12 / Applications

13 / Specifications

14 / Choose Your Optimal Array Format

20 / Peptide Pools 20 / Applications & Specifications

21 / Select Your Peptide Pool

22 / Peptide, Peptidomimetic & Organic Synthesis 23 / Capabilities

23 / Options & Specialties

23 / Our Support

24 / Peptide Discovery & Optimization Services 24 / Our Know-How

25 / Available Services

25 / Service Specifications

25 / Applications

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Applications & Specifications

Assay DevelopmentPeptide libraries find widespread application in a large variety of biomedical assays. Depending on the assay, different peptide modifications, sequence lengths, purities and amounts must be applied. JPT’s longterm experience and background in biological assay princi-ples and peptide chemistry enable the provision of peptides and peptidomimetics that fit to the specific requirements of your assay. A selection of formats sup-ported by JPT’s tailor-made libraries is shown in the table on the right.

High Content Screening & DiscoveryJPT is able to synthesize hundreds of thousands of pep-tides for ultra high-throughput screening such as pro-teome wide B- and T-cell epitope discovery projects, proteotypic peptide libraries throughout entire species, random peptide libraries covering large parts of the diversity space, peptide substrate collections for enzyme profiling and many more.

Our scientists will be happy to discuss the require-ments for your peptide library in detail.

JPT produces tens of thousands of high quality peptides per year.

Peptide LibrariesJPT is the leading provider of flexible peptide libraries worldwide. We offer a wide variety of modifications and specifications tailored to comply with all popular assay formats in applied immunology, proteomics and drug discovery. Our production runs in accordance with DIN ISO 9001:2008 regulations and in compliance with Good Clinical Laboratory Practices (GCLP).

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Lead OptimizationThe ability to adjust chemistries, scales and purities of our diverse library formats to a large extent together with a strong background in bio- and cheminformatics qualifies JPT to help you optimizing peptide-based lead structures. Our previous successful projects were focused on optimizing parameters including binding affinity, immune response stimulation, molecular weight & peptide length, substrate sensitivity & selec-tivity, stability towards enzymatic degradation, in vivo pharmacokinetics, rigidity or solubility.

Peptide Validation JPT is well known for assembling highly purified and qualified peptides for applications in clinical T-cell assays and validation of screening results. The scale of these peptides ranges from 1 mg to 20 grams per peptide. They are supplied as individual freeze dried aliquots and / or as peptide pools mixed on the basis of a validated pooling procedure.

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Assay Development

Screening & Discovery

Hit & Lead Optimization

Validation

FRET peptides, biotinylated peptides, phosphopeptides, modified peptides, heavy peptides, dye labeled peptides ...

Random peptides, proteotypic peptides, peptide scans, designed & predicted sequences, biologically

active peptides, epitope collections ...

Substitution and truncation analysis, D-amino-acid-, alanine, and cyclo-scans

Highly pure and qualified peptides

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Selection of peptide specifications for different assay types.

Workflow from assay development to lead optimization.

Assay Type Peptide Specification JPT's Library Platform

Cell-Based Assays (ELISPOT, ICS, etc.)

Purified peptides with and without posttranslational modifications (glycosylation, methylation, phosphorylation, acetylation and more)

PepTrack™

Binding Assays (Biacore, ILB, Microarrays, etc.)

Biotinylated peptides (e.g. for immobilization to streptavidin coated beads, membranes, microarrays) BioTides™

Kinase Assays Peptides containing known or random phosphorylation sites Kinase Substrate Sets

Protease Cleavage Assays (FRET assays, etc.) FRET peptides, fluorescently labeled peptides Protease Substrate Sets

or ProteaseSpots™

Phosphatase Assays Phosphorylated peptides Phosphatase Substrate Set

SRM/MRM Assays Proteotypic peptides unlabeled or heavy isotope- labeled with or without quantitation SpikeTides™

Fluorescence Based Assays

Peptides labeled with fluorescence dyes of varying absorption and emission wavelengths PepTrack™

High-Throughput Screening Large numbers of small scale peptides at low cost Micro-Scale Peptides

Your Assay Requirement Discuss your specific requirements with JPT’s peptide experts

Our Peptide LibrarySolution

JPT’s PepTrack™ Libraries are delivered in 96-well plates (Fast Track) or in 96-tube racks (Research, Discovery and Trial Track) and with detailed documentation on CD.

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Select Your Peptide Library Platform

JPT’s peptide libraries range from economic small scale libraries consisting of unpurified peptides to specific and complex collections of purified peptides. They vary in amounts, QC/QA measures as well as peptide modifications including phosphorylation, alkylation, glycosylation and many more.

PepTrack™ – Peptide Libraries for Cell-Based Assays

PepTrack™ peptide libraries were specifically designed to perform in cell-based assays such as ELISPOT, ICS, CFC and others. Four different options serve the requirements of your individual assay. Synthesis protocols are optimized to minimize toxic as well as peptidic contaminations.

For all four PepTrack™ options we offer a variety of posttranslational modifications. Among these are phosphorylation, glycosylation, acylation and alkylation. In addition, we are able to provide your pep-tide library biotinylated or fluorescently labeled.

> Fast Track peptide libraries represent the most inexpensive source of peptides worldwide. They are synthesized by JPT’s proprietary high-throughput method SPOT.

Purity QA / QC* Length Scale Delivery Price / peptide

Unpurified –no purity guarantee

5% LC-MS 5-15aa 50 -

200 nmol

2 weeks (for up to 10 000 peptides)

From 7$/€

* additional QC available upon request Delivery Format: 96-well plate format

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> Research Track peptide libraries are designed for applications requiring large numbers of fully analyzed peptides in quantities of 1-5 mg. All peptides are analyzed for identity and purity by LC-MS.

Purity QA / QC Length Scale** Delivery Price / peptide

Unpurified – no purity guarantee LC-MS 7-15aa 1-5 mg 2 weeks From 25$/€

Unpurified/purifiedmain product= target peptide

LC-MS 7-15aa 1-5 mg 2 weeks please inquire

** for larger amounts, please inquireDelivery Format: 96-array tube format (standard)

> Discovery Track peptide libraries have a guaranteed minimum purity for each peptide and are used for applications requiring similar and specified purities of all peptides (i.e. immune monitoring). All peptides will be QC’d by LC-MS.

Purity QA / QC Length Scale** Delivery Price / peptide

>70% LC-MS 7-15aa 1-5 mg 3 weeks From 45$/€


> Trial Track peptide libraries were designed to provide a reliable source of highly purified peptides and peptide pools for application as monitoring tools in clinical vaccination trials.

Purity QA / QC* Length Scale** Delivery Price / peptide

>80% LC-MS 7-15aa 1-5 mg 3 weeks From 69$/€

>90% LC-MS 7-15aa 1-5 mg 3 weeks please inquire



* full analytical coverage including amino acids analysis, capillary electrophoresis, peptide content determination, determination of residual solvents etc. is available upon request


Selected References> "Functional Characterization of Aquaporin-4 Specific T Cells: Towards a Model for Neuromyelitis Optica" Kalluri et al., PLoS ONE (2011)

> "Phase I Safety and Immunogenicity Evaluation of MVA-CMDR, a Multigenic, Recombinant Modified Vaccinia Ankara-HIV-1 Vaccine Candidate"

Currier et al., PLoS ONE (2010)

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BioTides™ – Small Scale Biotinylated Peptides

BioTides™ are designed for your binding assays using streptavidin coated beads, membranes, glass slides or ELISA plates. BioTides™ are synthesized by JPT’s high-throughput synthesis method SPOT and represent the most economic source of biotinylated peptides.

load beads for affinity

purifications

add enzyme

immobilize onto microtiter plates

print microarray

JPT’s BioTides™ are delivered in 96-well plates with detailed documentation.

Immobilization of BioTides™ for binding assays.

Applications• Identification and optimization of kinase-, phos-

phatase-, acetyltransferase- and histone deacetyla-se-substrates via standard screening systems (AlphaScreen, FlashPlates, SPA-Beads etc.)

• Mapping of protein/protein interaction sites (ELISA-like assays, precipitation of interacting proteins)

• Production of peptide microarrays• Loading of columns for affinity chromatography

Product Specifications• Amount of 50-200 nmol per peptide• Peptide length: 6-20mers• N-terminally biotinylated via a hydrophilic flexible

linker, ensuring proper presentation of peptides• Unpurified but capped after each synthesis step

for removal of deletion and truncation sequences during re-immobilization to streptavidine matrices

• Incorporation of non-standard amino acids and other modifications possible

Benefits• Highly parallel synthesis approach• Turnaround: > 10 000 peptides / week• Ready-to-use freeze dried peptides in 96-well

microtiter plates• Low cost source for small scale biotinylated

peptides

Selected References> "Extensive Phosphorylation with Overlapping

Specificity by Mycobacterium tuberculosis Serine/Threonine Protein Kinases"

Prisic et al., PNAS (2010)

> "GP4 of Porcine Reproductive and Respiratory Syndrome Virus Contains a Neutralizing Epitope That is Susceptible to Immuno-Selection in vitro"

Costers et al., Arch Virol. (2010)

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Micro-Scale Peptides are synthesized by SPOT technology and delivered in microtiter plates with documentation on CD.

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Applications• Proteome spanning peptide libraries• Systematic biomarker screening• Peptide microarray production• Optimization of peptide lead structures• Screening assays for biological activity• GPCR deorphanization

Product Specifications• Amount of 50-200 nmol per peptide• Peptide length: 6-20mers• Incorporation of non-standard amino

acids possible• Applicable posttranslational modifcations:

phosphorylation, glycosylation, acetylation, methylation and others

• Fluorescence labeling available

Benefits• Highly parallel synthesis approach

(> 10 000 peptides / week)• Ready-to-use peptides in 96- or 384-well plates• Most economic source for small scale peptides

Selected References> "Screening of Predicted Secreted Antigens from

Mycobacterium bovis Identifies Potential Novel Differential Diagnostic Reagents"

Jones et al., Clin. Vaccine Immunol. (2010)

> "Extensive Major Histocompatibility Complex Class I Binding Promiscuity for Mycobacterium Tuberculosis TB10.4 Peptides and Immune Dominance of Human Leucocyte Antigen (HLA)-B*0702 and HLA-B*0801 Alleles in TB10.4 CD8+ T-cell Responses "

Axelsson-Robertson et al., Immunology (2009)

Micro-Scale Peptide Libraries

Micro-Scale peptides are small scale unpurified peptides for high-throughput screening. Our patented SPOT technology allows for synthesis of thousands of peptides on membrane supports. The resulting peptides are then transferred into microtiter plates and lyophilized. Therefore, JPT has the unique ability to produce huge peptide libraries made of up to 1 million single, individual peptides with rapid turnaround at unmatched pricing.

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SpikeTides™ and SpikeTides™_L are delivered in 96-well microtiter plates accompagnied by a CD.

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One approach for quantitative analysis of proteins in complex mixtures is the use of tandem mass spectro-metry to monitor proteotypic peptides by selected reaction monitoring (SRM) or by parallel analysis of many proteotypic peptides using multiple reaction monitoring (MRM). For absolute quantitation, stable isotope-labeled proteotypic peptides are used as inter-nal standards. These standards usually need to be puri-fied to enable subsequent peptide content determina-tion. This results in prices of several hundred US$ / € per peptide. JPT overcomes this situation by attaching a small chemical tag (Quanti-Tag) to the proteotypic pep-tide which allows our specialists cost efficient quantita-tion of the proteotypic peptide. When you digest your sample, spiked with the appropriate SpikeTides™, the protease will cleave the peptide-tag bond, releasing the desired proteotypic peptide for your measure-ments.

Selected References> "SpikeTides™– Proteotypic Peptides for Large-Scale

MS-based Proteomics" Reimer et al., Application Note in Nature Methods

(2011)

> "Synthetic Peptide Arrays for Pathway-Level Protein Monitoring by Liquid Chromatography-Tandem Mass Spectrometry"

Hewel et al., Mol. Cell. Proteomics (2010)

> "High-Throughput Generation of Selected Reaction-Monitoring Assays for Proteins and Proteomes"

Picotti et al., Nature Methods (2009)

All SpikeTides™ are also available as larger scale Maxi SpikeTides™ !

SpikeTides™ – Synthetic Proteotypic Peptides:light – heavy – quantified

JPT has developed a synthesis technology that enables ultra-fast, highly parallel and inexpensive synthesis of small scale isotopically labeled peptides that are ideally suited for proteome wide profiling using SRM /MRM proteomic assays. In addition, these peptides can be delivered absolutely quantified in a most reliable and economic way.

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Available SpikeTides™ Options:

SpikeTides™ – light

Small scale, unpurified, unlabeled proteotypic peptides with C-terminal Arg or Lys for optimization and validation of multiplexed SRM assays.

Purity QA / QC Scale Delivery Price / peptide

Unpurified 5% LC-MS 50 nmol 2 weeks From 9$/8€

Delivery format: Freeze dried in 96-well plates

SpikeTides™_L – heavy

Isotopically labeled, small scale, unpurified proteotypic peptides with C-terminal heavy Arg or Lys for development of SRM assays and relative quantitation of proteins using a single product.


Unpurified 5% LC-MS 10 nmol 3 weeks From 19$/17€

Delivery format: Freeze dried in 96-well plates

SpikeTides™_TQ – light and quantified

Quantified, small scale, unlabeled proteotypic peptides. Each peptide carries a Quanti-Tag that will be cleaved by trypsin digestion.


Unpurified / Purified 100% LC-MS 5 x 1 nmol (target peptide) 3 weeks From 59$/52€

Delivery format: Freeze dried in 96-tube racks (5 aliquots per peptide)

SpikeTides™_TQL – heavy and quantified

Quantified & heavily labeled, small scale, proteotypic peptides. Each peptide carries a Quanti-Tag that will be cleaved by trypsin digestion.

Purity QA / QC Scale Delivery Price/peptide

Unpurified / Purified 100% LC-MS 5 x 1 nmol (target peptide) 3 weeks From 89$/78€

Delivery format: Freeze dried in 96-tube racks (5 aliquots per peptide)

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Our Enzyme Substrate Sets present an efficient way to screen many substrates in parallel.

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Kinase Substrate SetsJPT’s Kinase Substrate Sets come in 384-well micro-titer plates containing 250 pmol peptide substrate per well. After incubation with target kinase and radio-actively labeled ATP, the incorporated phosphate can be detected using strepavidine coated membranes, Flash-Plates or SPA-beads.

Three different sets are available: > General Kinase Substrate Set – 2 x 360 peptides

containing at least one phosphorylation site > Tyrosine Kinase Substrate Set – 145 peptides

containing at least one tyrosine residue (Subset of General Kinase Substrate Set)

> Proline-directed Kinase Substrate Set – 207 peptide sequences containing at least one Ser-Pro or Thr-Pro motif (Subset of General Kinase Substrate Set)

Phosphatase Substrate SetsOur Phosphatase Substrate Sets each include a 384-well microtiter plate containing 360 phosphopeptides (250 pmol per well) derived from human phosphoryla-tion sites together with 10 calibration standards. Subsequent to incubation with target phosphatase, the released phosphate ions can be detected by phosphate-binding dyes.

Two sets are available:> Phosphatase Substrate Set> Tyrosine Phosphatase Substrate Set

Protease Substrate Sets The Protease Substrate Sets are comprised of inter-nally quenched (Dabcyl /EDANS) peptides derived from proteolytic cleavage sites (from P4 to P4’position). The peptides come in a 384-well microtiter plate (75 pmol per well). After incubation with target protease, change of fluorescence intensity is measured with standard ELISA readers.

Two sets are available:> Protease Substrate Set (360 peptides)> Caspase Substrate Set (4 x 88 peptides, Subset

of the above)

Selected References> "Proteolytic Cleavage of Covalently Linked Cell Wall

Proteins by Candida Albicans Sap9 and Sap10" Schild et al., Eukaryot. Cell (2010)

> "Protein-tyrosine Phosphatase H1 Controls Growth Hormone. Receptor Signaling and Systemic Growth"

Pilecka et al., J. Biol. Chem. (2007)

The detailed sequence lists and plate layouts are available at www.jpt.com.Please inquire for information about the production of customized Substrate Sets!

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Enzyme Substrate Sets

The most efficient way to study enzyme activity and substrate specificity is incubating the enzyme of interest with multiple substrates in parallel. JPT offers ready-to-screen or customized Enzyme Substrate Sets that are assembled from human phosphorylation or cleavage sites or present specially designed sequences.

Obtain semi-quantitative data using JPT's ProteaseSpots™.

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ProteaseSpots™

ProteaseSpots™ are low cost custom protease substrate collections. They are fluorescently labeled and immobilized on cellulose discs that are delivered in microtiter plates and can be incubated directly with your protease. You can take several fluorescent measurements at different timepoints.

add protease cleavage

30min 1st measurement

2h 2nd measurement

6h 3rd measurement

Applications• Detection of protein cleavage sites utilizing

peptide scans through proteins• Identification of novel substrates with

de novo libraries• Measurement of protease activities with

known substrates• Characterization of cleavage sites through

substitutional analyses

Product Specifications• Amount: 50 nmol per peptide• Peptide length: 6-20mers• N-terminally fluorescently labeled• Ready-to-use peptides in 96-well plates

immobilized on cellulose discs

Benefits• Screen large numbers of substrates economically• You specify the individual substrate sequences• Obtain semi-kinetic data• Choose your fluorophore (Abz, FAM, TAMRA

or others)

Selected References> "Identification of Candidate Substrates for

Ectodomain Shedding by the Metalloprotease-Disintegrin ADAM8"

Naus et al., Biol. Chem. (2006)

> "Screening a Combinatorial Peptide Library to Develop a Human Glandular Kallikrein-2 Activated Prodrug as Targeted Therapy for Prostate Cancer"

Janssen et al, Mol. Cancer Ther. (2004)

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Assay Type Peptide Origin JPT’s Array Platform

Immune Monitoring Overlapping peptide libraries through antigens or antigen domains, epitope collections and more PepStar™ or RepliTope™

Seromarker Discovery Overlapping peptide libraries through whole proteomes or random peptides PepStar™ or RepliTope™

Epitope Mapping, Validation and Optimization

Overlapping peptide scans through antigens, alanine-scans, substitutional or truncation analyses of identified epitopes

PepSpots™

Antibody Signature Profiling

Overlapping peptide libraries through antigens or whole proteomes PepStar™

Phosphatase Profiling Annotated phosphatase substrates as phosphorylated peptides

Annotated PhosphoSites-Tyrosine

Phosphosite Detection Overlapping peptide scans through known kinase substrate proteins

Phosphorylation Site Detectors

Kinase Profiling Annotated kinase substrates or selected random sequences Kinase Microarrays

Protease Profiling Annotated protease substrates or random peptides Protease Profiler (incl. full service)

Your Assay Requirement Let us know which experiment you are planning Our Peptide Array Solution

Peptide Arrays

JPT uses its proprietary PepStarTM technology for the validated production of peptide microarrays. Each microarray batch passes rigorous quality control ensuring high batch-to-batch reproducibility for reliable results.

Peptide arrays display individual peptides immobilized onto planar surfaces such as cellulose membranes or glass slides. They can be used for incubation with patient sera, purified antibodies, proteins or enzymes, cell lysates and other biologics. Our peptide arrays display from small numbers of peptides to several thousand peptides per array. These peptide collections can represent either overlapping peptides of a single protein, a whole proteome, biased peptide libraries, random sequences and more. In addition, we also provide our arrays with full service including incubation with your samples, readout, data analyses by our experts and delivery of a comprehensive report.

Applications Peptide arrays are used for a variety of research areas such as immune monitoring, seromarker discovery and vali-dation, patient stratification, protein-protein interaction studies, antibody signature profiling, quality control of therapeutic biologics and protein fingerprinting. Below you will find some example applications and our corres-ponding array platforms.

Our scientists will be happy to discuss provision of your peptide array in detail.

Selection of JPT's array platforms and their applications.

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Specifications

JPT has developed two different unique peptide array platforms:

> PepSpots™ are customized peptide arrays on cellulose membranes that are used for incubation with purified proteins and chemiluminescence readout. They present an easy-to-handle and economic tool if you plan a limited number of incubations with purified analytes such as antibodies.

> Our customized PepStar™ and premade RepliTope™ or Enzyme Substrate Microarrays are peptide microarrays based on glass slides. They hold up to 7 000 purified peptides in triplicate and thousands of identical copies can be produced. As readout is performed via fluorescence, signal-to-noise ratio is high. Even unpurified samples (serum, cell lysates...) can be used for incubation.

For both array formats, peptides are immobilized chemoselectively via a flexible linker. This is a major advantage over common protein arrays or other peptide arrays because it ensures proper presentation of binding sites present in the peptides. The table below gives you an overview of the properties of cellulose and glass arrays.

PepSpots™ PepStar™ / RepliTope™/ Enzyme Substrate Microarrays

Array material Cellulose Glass slides

Peptides attached via C-terminus N-terminus

Peptides purified No Yes

Readout via Chemiluminescence Fluorescence

Number of identical arrays per synthesis batch

1 1 000 – 2 000

Immobilization of full length protein controls possible

No Yes, up to 8 control proteins

Array size Depending on number of peptides 3 x 1 inch (2,54 x 7,62 cm)

Incubation volume Depending on number of peptides 200 – 300 µl

Usable with unpurified samples (serum etc.) No Yes

Properties of cellulose and glass slide based peptide arrays in comparison.

Thousands of identical microarrays can be printed from one synthesis

batch.

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On the following pages you will find detailed descriptions of our different types of customized and premade peptide arrays and microarrays as there are:

> Customized PepStar™ microarrays

> Catalog RepliTope™ microarrays

> Customized PepSpots™ arrays on cellulose

> Premade Enzyme Substrate microarrays for Kinase, Phosphatase and Protease

> Customized Enzyme Substrate microarrays

Our experts are constantly working on new products and evaluation of our exis-ting products. Examplarily, microarrays displaying substrates for glycosyltrans-ferases and acetyltransferases and histone peptide collections are under develop-ment. Please contact our customer support team for updated information.

We offer our unique all-in-one incubation

and analysis service for all our peptide

microarrays. For information on this service, please visit our

website on www.jpt.com

or contact our customer support

team!

22,66

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> Patented high-throughput synthesis of peptides warrants high batch-to-batch reproducibility

> Defined posttranslational modifications are possible

> All peptides purified

> Peptides are N-terminally attached to glass slides by directed and chemoselective immobilization

> Flexible co-immobilization of controls

> Cost effective provision of thousands of identical microarrays from a single synthesis batch

> Incubation can be performed with proteins, patient samples, cell lysates and others

> Low consumption of patient materials and proteins

> Validated incubation and readout protocols available

> High shelf stability

> High assay sensitivity

> Readout is achieved by fluorescence using standard protocols and equipment

Selected References> "Mapping Mouse IL-13 Binding Regions Using

Structure Modeling, Molecular Docking, and High-Density Peptide Microarray Analysis"

Madala et al., Proteins (2010)

> "Long-Lived Plasma Cells and Memory B Cells Produce Pathogenic Anti-GAD65 Autoantibodies in Stiff Person Syndrome"

Rizzi et al., PloSOne (2010)

> "Antibody Signatures Defined by High-Content Peptide Microarray Analysis"

Schutkowski et al., Application Note in Nature Methods (2009)

Left: Your PepStar™ microarrays are delivered with detailed QC / QA documentation and application protocol.

Below: Layout and dimensions of PepStar™ microarrays: Three identical subarrays displaying all peptides and controls are printed onto each microarray.

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Selection of available RepliTopes™

A full up-to-date list can be found on: www.jpt.com

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RepliTopes™ combine all the advantages of PepStar™ microarrays with the availability as catalog product.

> Premade microarrays display peptide scans through antigens, whole proteomes or random peptide libraries

> Each peptide is presented 2-4 times on each microarray to ensure reproducibility of results

> Fully compatible with standard ELISA protocols

> Economical access to many identical peptide microarrays

> Reliable epitope mapping using minimal amounts of antibody

> All-in-one service available (incubation, data analysis and a detailed report)

Selected References> "Epitope Mapping Using Randomly Generated Peptide Libraries" Bongartz et al., Methods in Molecular Biology, Epitope Mapping Protocols (2009)

> "Peptide Microarray – Based Identification of Mycobacterium Tuberculosis Epitope Binding to HLADRB1*0101, DRB1*1501 and DRB1*0401"

Gaseitsiwe et al., Clin. Vaccine Immunol. (2009)

Tumor Associated Antigens Infectious Diseases Antigen Collections

Breast/Prostate• Mammaglobin A• NY-ESO-1• PSA ...

Epithelia• CEA• Claudin-6 ...

Melanoma• MAGEA1, A3 and A4• Melan-A/MART-1• Prame/OIP4 ...

Vaccinia virus• MVA018L (Host range p. 2)• MVA093L (p53) ...

Wilms tumor1• WT33

Miscellaneous• Cyclin B1• Histone H1.2 and H4• P53_human ...

Adenovirus• Hexon and penton proteins

BKV• Capsid proteins (VP1, VP2, VP3)• Large and small T antigens

EBV• EBNA (1, 2, 3a, 3b, 3c, LP)• LMP1 and LMP2 ...

HCMVA• IE-1, IE-2, pp65,• UL28, UL32, UL40 ...

Influenza A• HA, MP1 and NC from different strains

RSV• Protein F, NC protein N

Miscellaneous• HBV (Large envelope protein)• HHV6 (U54)• Yellow fever (NS24B) ...

HCMV whole proteome = over 17 000 peptides

M. tuberculosiswhole proteome =over 100 000 peptides

C. pneumoniaepartial proteome = over 5 000 peptides

B. Pertussispartial proteome =over 3 000 peptides

Random Peptide Libraryover 50 000 random peptidessorted acc. to hydrophobicity

PepSpots™

More than 200 scientific publications describe the application of PepSpots™ as the method of choice for fast and reliable antibody epitope mapping.> Peptides are C-terminally attached to a cellulose

membrane via a flexible linker

> Membrane can be used directly for incubation with antibodies or other proteins

> Readout via chemiluminescence by standard equipment

> Rapid, economical, and accurate synthesis using robotics

> Hydrophilic cellulose membranes minimize unspecific interactions

> Detection of low affinity interactions

> Easy detection using standard ELISA protocols

Selected References> "A Robust Protocol to Map Binding Sites of the 14-3-3 Interactome: Cdc25C Requires

Phosphorylation of Both S216 and S263 to bind 14-3-3" Chan et al., Mol. Cell. Proteomics. (2011)

> "Biological Effects and Use of PrPSc- and PrP-Specific Antibodies Generated by Immunizing with Purified Full Length Native Mouse Prions"

Petsch et al., J. Virol. (2011)

Above: Automated synthesis of PepSpots™ membranes.

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Right: Your PepSpots™ package includes: PepSpots™ membrane, data CD

and application protocol.

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Kinase ProfilingJPT Peptide Technologies has compiled a database of human phosphorylation sites and overlapping peptide scan libraries through known proteins. Subsequent to incubation with target kinase or cell lysate in the pre-sence of radioactive ATP, incorporated phosphate can be detected by autoradiography or phosphorimaging. Alternatively, phospho-specific antibody-based fluo-rescence readout is applicable for phosphopeptide detection.

The following kinase microarrays are available:> Annotated Phosphosites-K displays 720 peptides

derived from human phosphosites sites distributed on two microarrays. It allows both kinase sub-strate identification and consensus sequence determination. Each identified in vitro substrate peptide corresponds to a known protein, which represents a potential in vivo target of the studied kinase.

> Random Library Tyrosine-K consists of one microarray displaying 1 536 peptides containing one tyrosine residue in the center position. Screening of the complete or partial library results in the identification of peptidic substrates of the target tyrosine kinase.

> Random Library Threonine-K consists of one microarray displaying 1 536 peptides containing one threonine residue in the center position. Screening of the complete or partial library results in the identification of peptidic substrates of the target serine/threonine kinase.

> Random Library Serine-K consists of one micro-array displaying 1 536 peptides containing one serine residue in the center position. Screening of the complete or partial library results in the identification of peptidic substrates of the target serine/threonine kinase.

> Over 50 different Phosphorylation Site Detectors display overlapping peptide scans through a variety of mostly human proteins. Among them are Beta-Casein, C-Jun, Histone H1, MBP, p53, Pin1 and Tau protein.

For a full list, please visit our website!

We offer a variety of premade enzyme substrate microarrays. Sequences were selected from commonly used databases or designed by our computational scientists. All enzyme substrate microarrays display each peptide in triplicate (three subarrays) and are available within days. Tailor-made enzyme substrate microarrays are also easily available. Please contact us for further information.

Enzyme Substrate Microarrays

We offer our unique all-in-one incubation and analysis service for all our peptide microarrays.

For information on this service, please visit our website on www.jpt.com or contact our customer support team!

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Phosphatase ProfilingJPT's database of human phosphorylation sites is re-presented as collection of phosphopeptides on micro-arrays. Readout is performed with phospho-specific antibodies.

The following phosphatase microarray is available:> Annotated PhosphoSites-Tyrosine displays over

6 000 human phosphorylation sites as phospho-tyrosine containing peptides displayed on one peptide microarray. The phosphatase profiling will result in identification of both peptidic sub-strates and potential in vivo substrates of the target tyrosine phosphatase.

Protease ProfilingOur Protease Profiler microarray is offered in combina-tion with JPT’s full service only, including incubation with target protease, imaging, spot recognition and data evaluation followed by statistical analysis of the results. Images and results will be delivered as PDF-file. The sequence information for identified substrates is included.

> Protease Profiler Microarray displays 1989 anno-tated 8meric cleavage sites and 1536 randomly generated 15meric peptide substrates. All pep-tides are distally tagged with phosphotyrosine. Readout is performed via fluorescence by treat-ment with anti-phosphotyrosine antibody (diffe-rential measurement).

Selected References> "Identification of New Substrates of the Protein

Tyrosine Phosphatase PTP1B by Bayesian Integration of Proteome Evidence"

Ferrari et al., J. Biol. Chem. (2011)

> "Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors"

Whisenant et al, PLoS Computational Biology (2010)

JPT's various catalog as well as customized peptide arrays will satisfy your requirements.

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JPT's PepMixes™ are synthetic peptide pools containing overlapping peptide scans through antigens or selected MHC restricted epitopes. Each peptide is analyzed to meet the requirements of T-cell assays. Peptides are pooled according to our proprietary validated protocol ensuring presence of all peptides in the pool.

Applications & SpecificationsFor reliable and validated T-cell assays such as ELISPOT, appropriate positive and negative controls are essential to confirm proper functionality of the assay and viability of the cells. Compared to commonly used controls like PHA, ConA or full length antigens, synthetic peptide pools offer the advantage of a high batch-to-batch reproducibility, applicability of reliable chemical and biochemical QC/QA measures, longer shelf stability and extremely efficient immunostimulation.

ApplicationsEfficient in vitro stimulation of antigen-specific CD4+ and CD8+ T-cells • For optimization and/or validation of T-cell assays• For monitoring of cellular immune responses • For vaccine efficacy testing• As positive and negative controls• For T-cell epitope mapping

Specifications• Length / Overlap: 15 / 11 aa

(for pooled peptide scans)• Purity: 70% / 90% (LC-MS)• Amount: 25 tests / vial

Selected References> "Polyomavirus BK Large T-antigen Derived Peptide

Elicits a HLA-DR Promiscuous and Polyfunctional CD4+ T-cell Response"

Ramaswami et al., Clin. Vaccine Immunol (2011)

> "Induction of Complete and Molecular Remissions in Acute Myeloid Leukemia by Wilms’ Tumor 1 Antigen-Targeted Dendritic Cell Vaccination"

Tendeloo et al., PNAS (2010)

Validated pooling and aliquoting is performed in an environment

regulated by ISO 9001:2008 and GCLP.

Sub-Pool IV

MarkerPeptide

Sub-Pool I Sub-Pool II Sub-Pool III

MarkerPeptide

MarkerPeptide

MarkerPeptide

Individual Peptides

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6463626160595857XVI

5655545352515049XV

4847464544434241XIV

4039383736353433XIII

3231302928272625XII

2423222120191817XI

161514131211109X

87654321IX

VIIIVIIVIVIVIIIIIIPool No.

Select Your Peptide PoolJPT offers negative and positive control pools, as well as a variety of peptide pools through knownantigens of infectious organisms and through cancer related antigens. A selection of available PepMixes™ is listed below.

Tumor Associated Antigens Infectious Diseases Control Pools

Breast/Prostate• Mammaglobin A• NY-ESO-1• PSA ...

Epithelia• CEA• Claudin-6 ...

Melanoma• MAGEA1, A3 and A4• Melan-A/MART-1• Prame/OIP4 ...

Vaccinia virus• MVA018L (Host range p. 2)• MVA093L (p53) ...

Wilms tumor1• WT33

Miscellaneous• Cyclin B1• Histone H1.2 and H4• P53_human ....

Adenovirus• Hexon and penton proteins

BKV• Capsid proteins (VP1, VP2, VP3)• Large and small T antigens

EBV• EBNA (1, 2, 3a, 3b, 3c, LP)• LMP1 and LMP2 ...

HCMVA• IE-1, IE-2, pp65,• UL28, UL32, UL40 • PepMix™ Collection (Assembly of 20 different antigens)...

Influenza A• HA, MP1 and NC from different strains

RSV• Protein F, NC protein N

Miscellaneous• HBV (Large envelope protein)• HHV6 (U54)• Yellow fever (NS24B) ...

Positive control pools • HCMVA (pp65, IE-1, IE-2)• CEF Pool (standard)• CEF Pools (extended)• CEFT Pools

Negative control pools• Human Actin and MOG• HIV (Con B gag motif )

Master Pool contains all 64 peptides.Matrix Pool I contains peptides 1, 9, 17, 25, 33, 41, 49 and 57.Matrix Pool II contains peptides 2, 10, 18, 26, 34, 42, 50 and 58....Matrix Pool IX contains peptides 1, 2, 3, 4, 5, 6, 7 and 8.Matrix Pool X contains peptides 9, 10, 11, 12, 13, 14, 15 and 16.

Not found what you are looking for?

We produce customized PepMixes™ and matrix pools in ready-to-use and stable aliquots.

Please contact our customer support team for more information.

Below: Customized Matrix Pools enable the fast and minimal material consuming identifcation of the epitope(s) within an antigen. Each peptide is present in only two matrix pools. In the example shown, 64 peptides are pooled into 16 Matrix Pools. Pools V and XII elicit a T-cell response. Only peptide 37 is present in both pools and therefore is the peptide containing the epitope.

Your Pools are delivered in glass vials with screw cap (individual PepMixes™) or in 96-tube racks (PepMix™ Collection).

A full up-to-date list including the respective protein IDs can be found at www. jpt.com

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Peptide, Peptidomimetic & Organic Synthesis

JPT Peptide Technologies has substantial, long-standing expertise in providing custom peptides, peptidomimetics, and proteins to the global scientific community. Our highly skilled and committed scientific staff ensures that the most appropriate methods and techniques are selected for every synthesis project. These include state-of-the-art automated synthesis approaches, optimized solution phase procedures, scales ranging from 1 mg to several grams and chemistries involving a variety of protection schemes such as Fmoc and BOC approaches.

Most of JPT‘s specialty peptides are provided in the highest purity (> 95%), with a range of included and optional analyses such as LC-MS (trap and/or quad), MALDI-MS, HPLC, AAA, NMR, CE, as well as peptide content determination to confirm the identity and demonstrate the high quality of our peptides. The exceptional quality and reliability of this service has been appreciated by customers worldwide for many years.

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JPT is dedicated to synthesize even the most challenging peptides.

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Capabilities• Extended organic synthesis and medicinal

chemistry facilities• Solution and solid phase techniques • Experience in conjugating peptides to shuttle

molecules, biologicals, carbohydrates and adjuvants

• Track record in systematic optimization of physicochemical and biological properties

• Know-how in stabilizing biologically active conformations by: head-to-tail cyclizations, backbone cyclizations, disulfide and thioether bridges, incorporation of structures inducing mimetics, creation of stapled peptides and more

• Unusual modifications, peptide bond isosters, click chemistries (azido peptides, aldehyde chemistry, thiol anchoring and more)

Options & Specialties• Fluorogenic and chromogenic peptides

(AMC, etc.) as well as peptide esters• Internally quenched peptides

(Abz/nitroTyr, EDANS/DABCYL, MCA/DNP) without fluorescent impurities guaranteed

• Immunogenic peptides (MAPs, palmitinylation, Pam3Cys labeling, etc.)

• Phosphopeptides and peptidomimetics (amide bond isosters, non-standard amino acids, etc.)

• Non-commercial building blocks available

• Labeling using stable isotopes, chromophores, etc.• Site-directed conjugations with KLH, BSA,

ovalbumine or other carriers• Cyclic peptides

(disulfide bridges, stapled peptides, lactams, thioether-bridges, etc.)

• Long peptides (>70 amino acids)

Our Support Includes> Quick and personal consultation

with experienced scientists> Rapid order processing> Reliable quality control using

state-of-the-art techniques> Fast turnaround times> Competitive prices

Selected References> "Highly Specific Auto-antibodies against Claudin-18

Isoform 2 Induced by a Chimeric HBcAg Virus-like Particle Vaccine Kill Tumor Cells and Inhibit the Growth of Lung Metastases"

Klamp et al., Cancer Res. (2011)

> "Splice Variants of the Dual Specificity Tyrosine Phosphorylation-regulated Kinase 4 (DYRK4) Differ in Their Subcellular Localization and Catalytictivity"

Papadopoulos et al., J. Biol. Chem. (2011)

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State-of-the-art commercial and open source software packages are used for creative and efficient problem solutions.

Peptide Discovery & Optimization Services

JPT has a long standing expertise to escort biomedical screening and peptide lead optimization programs with its comprehensive bioinformatic and cheminformatic capabilities. We offer this unique know-how and expertise as part of our high content peptide microarray and library services or in R&D collaborations focusing on peptide hit discovery and optimization.

Our Know-How

Specialty Peptide, Organic Synthesis & MedChem Capabilities

• Extensive know-how for labeled, conjugated, conformationally restricted & modified peptides, mimetics and small organic molecules

• Skilled project team• High capacity in solid and solution phase synthesis,

analytics and purification• Extensive building block library available

Bio- & Cheminformatics • Peptide design & optimization, data mining,

evaluation, conversion and interpretation• Evaluation of microarray & screening experiments,

management and presentation of data• Support for compound logistics• Supply of compound data in any format

(sequence or structure)

Molecular Modeling• Docking, molecular mechanics & dynamics,

homology models, virtual screening, QSAR• Optimization of peptidic hit & lead structures

(size, affinity, physicochemical properties) • Ligand- and protein-based molecular modeling• Generation of homology models• Prediction and modeling of data• Scaffold design for native-like presentation

of peptides

Assay Development and Screening • Development of high throughput and/or optimiza-

tion assays with focus on binding assays, serological screening and enzymatic assays.

R&D Project Management • Professional project management backed

by ISO 9001:2008 and GCLP regulations.

PAT A1

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PAT B1

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PAT C1

PAT C2

PAT D1

PAT D2

PAT E1

PAT E2

PAT F1

PAT F2

PAT G1

PAT G2

PAT H1

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PAT I1

PAT I2

PAT K1

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PAT L1

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Immunology• Peptide seromarker discovery/validation • Autoantibody profiling • Genome wide identification and optimization

of epitopes • Development of peptide-based immune

monitoring tools

Drug Discovery• Peptide lead discovery• Peptide optimization / transformation to

small peptidomimetics• Peptide SAR studies

Diagnostics• Peptide design and modeling • Development of diagnostic content • Peptide ELISA development• Development of affinity purification kits • Peptide ligand identification & optimization

Proteomics• Protein-protein interactions • SRM/MRM assay development • Pathway specific protein quantification kits

Service Specifications> Discuss your project with our scientists to define

a suitable strategy based on scientific feasibility and experience

> Receive project proposal on how our expertise can support your project

> Obtain detailed and comprehensive service reports

> Benefit from JPT’s long term track record on the discovery and development of peptides in drug discovery and diagnostic development

> Make use of our state-of-the-art prediction, data interpretation and data mining algorithms and software paired with chemical and biological know-how

> Choose between fee-for-service or collaborative partnership

Capabilities• Design of peptide content for high-density

peptide microarrays and complex peptide libraries• Design of peptide libraries based on biological

pathways, literature data or complex database search strategies

• Generation of homology models and use of avai-lable structural information for peptide selection

• Optimization of hit and lead structures (affinity, physicochemical properties, ADME)

• Prediction and modeling of data• Scaffold design for native-like presentation of

peptides• Interpretation, management and integration

of data

Selected References> “Probing the Epitope Signatures of IgG Antibodies

in Human Serum from Patients with Autoimmune Disease”

Lorenz et al., Methods Mol. Biol. (2009)

> “Peptidomimetic C5a Receptor Antagonists with Hydrophobic Substitutions at the C-terminus: Increased Receptor Specificity and in vivo Activity.”

Schnatbaum et al., Bioorg. Med. Chem. Lett. (2006)

> “Translating Peptides into Small Molecules” Hummel et al, Book chapter in Mol. BioSyst. (2006)

Want to take notes?

!

< There’s a world of options under the flap.

Want to take notes?

!!!!!!!Call JPT’s customer support at 0049-30-6392-7878 (for USA/Canada at 1-888-578-2660)

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Selection of JPT’s Peptide Library Types

Overlapping Peptide Scan

Lenght: 13 aaOffset: 2 aa

An overlapping peptide scan is generated to identify epitopes, substrates or other binding sites within a given protein sequence. A free and easy-to-use tool for generation of overlapping peptide sequences can be found on our website (www. JPT.com, search for PepSequencer).

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Cyclization Library

The formation of different cycles within the peptide sequence mimics different loops within the corresponding protein.

Scrambled Library

The original peptide sequence is permutated to represent all possible alternative peptides.

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Alanine Scanning Analysis

Each residue is substituted for an alanine enabling identification of key residues in your peptide sequence.

Truncation Analysis

Truncation of the peptide sequence from both termini results in identification of the minimum epitope, substrate or binding motif.

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Positional Scanning Analysis

One or all residues within the peptide are replaced by all 20 natural amino acids (or modified ones, analoga and others) to identify motifs within consensus sequences.

Volmerstraße 5 (UTZ)12489 BerlinGermany

P. O. Box 2619Acton, MA 01720USA

USA/Canada T 1-888-578-2660F 1-888-578-2666

European Head Office T +49-30 - 6392-7878F +49-30 - 6392-7888

JPT Peptide Technologieswww.jpt.com | peptide@ jpt.com

We take pride in our competent service and swift response.Please do not hesitate to contact us for further information.We also very much welcome your feedback and comments.

Documents

Peptides and Arrays - JPT Peptide Technologies GmbHpeptidomimetics for T-cell epitope and peptide lead discovery and characte-rization on proteome wide levels. PepStar™ Proprietary