Custom Peptide Array

Build screening-ready peptide arrays and multi-peptide libraries for epitope mapping, antibody specificity, and protein interaction studies— with flexible design options (overlaps, scanning, PTMs) and configurable analytics/QC.

Overlapping libraries
Alanine scanning
Mutation panels
PTM arrays
HPLC/MS QC

Need single sequences instead? See Custom Peptide Synthesis. For ready-made options, browse Catalog Peptides.

Custom Peptide Array Synthesis Services

Bio-Synthesis, Inc. delivers custom peptide array synthesis that turns your target protein into a screening-ready library—so you can pinpoint linear epitopes, test antibody specificity across variants, and map interaction hotspots in a single experiment. Compared to generic peptide libraries, custom peptide arrays give you precise control over coverage, overlap/step size, and modifications (PTMs) to match your assay and budget. Send a FASTA or sequence list and we’ll help you choose peptide length/overlap, scanning or variant panels, and the right QC level.

1) Design review

Confirm target regions, peptide length/overlap, controls, variants, and PTMs.

2) Synthesis & QC

Produce peptides to spec with configurable analytics (HPLC/MS) and documentation.

3) Delivery & mapping

Receive arrays or plates/tubes with clear IDs/plate maps for fast screening and follow-up.

Quick Specs (Typical)
  • Peptide length: 5–30 amino acids
  • Overlap / step size: 1–29 amino acids (custom)
  • Library types: overlapping, alanine scan, mutation panels, truncations
  • PTMs: phospho (S/T/Y), acetylation, methylation, biotinylation + custom
  • QC options: MS, HPLC purity (as requested)
Fastest Quote Checklist
  • Target protein/FASTA or sequence list (one per line)
  • Peptide length + overlap/step size
  • Mutations/variants (alanine scan, substitutions, truncations)
  • Modifications/PTMs + positions
  • Preferred format (array vs plates/tubes) + QC needs

Use the quote request form or contact section to send details.

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Overlapping peptide libraries

Tiling designs for epitope mapping and domain coverage.

  • Custom peptide length and overlap
  • Full-protein or region-of-interest coverage
  • Optional controls (scrambled/negative)
Scanning & variant panels

Fine mapping and specificity testing.

  • Alanine scanning arrays
  • Single-point mutation libraries
  • Truncations and deletions
PTM peptide arrays

Probe regulation and signaling with modified peptides.

  • Phospho (Ser/Thr/Tyr)
  • Acetylation and methylation
  • Biotinylation and custom requests

Prefer to start from ready-made materials? We also offer a wide selection of on-demand Catalog Peptides that can complement custom array projects.

Request a Quote Speak to a Scientist

Specifications That Define Your Peptide Array

Sequences & Coverage
  • Target protein (FASTA/accession) or explicit sequence list
  • Regions of interest (domains, motifs, epitopes)
  • Include controls if needed (scrambled/negative/positive)
Peptide Length & Overlap
  • Typical peptide length: 5–30 aa (custom)
  • Overlap/step size: 1–29 aa (custom)
  • Tiling density can be tuned for fine mapping
Quantity, Format, and Delivery
  • Delivered as immobilized arrays or as peptides in plates/tubes
  • Lyophilized or solution (application-dependent)
  • Standardized labeling and plate maps for libraries
Modifications & Labels
  • Phosphorylation, acetylation, methylation
  • Biotin, fluorophores, linkers/spacers (as required)
  • Custom PTMs and special residues upon request

Explore Peptide Modifications →

Tip: If you’re doing epitope mapping, include antibody/sera type and detection method so we can recommend an efficient design.

Peptide Array Design Options

Choose from common library strategies or combine approaches in one project. We can help you define a design that balances coverage, interpretability, and budget.

Design Options Checklist
  • Overlapping tiling for full coverage epitope mapping
  • Alanine scanning to identify critical residues
  • Mutation/variant panels for specificity and cross-reactivity
  • Truncation/deletion series to define minimal epitopes
  • PTM-matched pairs (modified + unmodified controls)

The designs below illustrate the most common peptide array and peptide library strategies used for epitope mapping, antibody specificity testing, and protein interaction studies.

Peptide library and array design strategies including overlapping peptide libraries, truncation series, alanine scanning, T-cell peptide libraries, PTM peptide arrays, and mutation panels

Common peptide library and array designs: overlapping tiling, truncation series, alanine scanning, T-cell peptide libraries, PTM-matched arrays, and mutation panels.

Overlapping Tiling
  • Linear mapping across proteins/domains
  • Custom step sizes for resolution
  • Ideal for linear epitope mapping
Alanine scanning
  • Residue-by-residue contribution
  • Pinpoints critical contacts
  • Useful for antibody/receptor binding
Mutation & variant panels
  • Single-point mutants and SAR sets
  • SNP/strain/escape variant screens
  • Cross-reactivity assessment
Truncations & deletions
  • Define minimal epitopes/motifs
  • N-/C-terminal walking series
  • Deletion mapping for hotspots
PTM-focused libraries
  • Phospho-site mapping (Ser/Thr/Tyr)
  • Acetyl/methyl variants for regulation
  • Matched unmodified controls

Helpful tool: Peptide Library Design Tool →

Formats Available

Immobilized peptide arrays
  • Designed for high-throughput screening workflows
  • Custom layouts and controls (as requested)
  • Share platform requirements and detection method
Peptides supplied in plates/tubes
  • One peptide per well/tube with mapping
  • Lyophilized or in solution (custom)
  • Custom concentration/buffer when required

If you’re not sure which format fits your assay, share your workflow and we’ll recommend the best option.

Common Applications

Immunology & antibody workflows
  • Linear epitope mapping
  • Antibody specificity and cross-reactivity
  • Serology profiling across variants
  • Vaccine antigen discovery support
Protein interactions & enzymology
  • Binding motif discovery
  • Protein–protein interaction mapping
  • Kinase/enzyme substrate profiling
  • Variant impact screens

Need peptides quickly for assay setup? Browse ready-made options: Catalog Peptides.

Analytics & Quality Control

Analytics confirm identity and purity and should match your application (screening vs quantitative assays vs regulated work). QC is configurable based on library size and design.

Standard analytics (common)
  • HPLC purity profiling (where applicable)
  • Mass spectrometry (MS) identity confirmation
  • Certificate of analysis (COA) per spec
Optional add-ons (upon request)
  • Endotoxin testing (application-dependent)
  • Residual solvent/chemical analysis
  • Water content / additional characterization

Explore Peptide Analytics & QC →

How to Request a Quote (Fastest)

To get the most accurate quote quickly, include the details below. If you’re not sure, send your target protein/FASTA and goal (epitope mapping, antibody specificity, PTM mapping, etc.) and we’ll propose a recommended design.

Include in your request
  • Target protein/FASTA or sequence list (one per line)
  • Peptide length and overlap/step size
  • Mutation plan (alanine scan, variants, truncations)
  • Modifications/PTMs and positions
  • Preferred format (array vs plate/tube)
Helpful optional details
  • Detection method and assay platform
  • Controls you want included
  • QC needs (MS/HPLC/add-ons)
  • Timeline and shipping constraints

Request a Quote Contact a Scientist

FAQ

What is a peptide array?

peptide array is a structured collection of peptides designed for parallel screening—commonly used to measure antibody binding, receptor interactions, enzyme preferences, or immune recognition across many sequences at once. Arrays are often built as overlapping tiles across a protein, or as focused libraries such as alanine scanningmutation panels, and PTM variants.

If you already have sequences, send them as one sequence per line (or a spreadsheet). If you only have a target protein, share the accession/FASTA and your goal; we’ll recommend a design.

Can I include modified peptides in the same array?

Yes. Modified and unmodified peptides can be combined within one project (e.g., phospho, acetyl, methyl, biotinylated), including matched unmodified controls.

Do you help with peptide array design?

Yes. If you share the target protein/region and your goal, we can recommend peptide length, overlap/step size, controls, and whether scanning/variant panels will improve resolution.

What format should I choose: immobilized array or peptides in plates?

It depends on your assay platform and detection method. Immobilized arrays simplify parallel screening, while plate/tube formats integrate well with custom workflows and secondary validation. Share your workflow and we’ll recommend the best option.

What do you need for a quote?

Provide sequences/FASTA, peptide length and overlap, number of peptides, any mutation/PTM plan, delivery format, and QC requirements. If you only have a target protein, we can propose a recommended design.

Can you combine array work with bioconjugation?

Yes. If your project requires conjugation (e.g., linkers/labels), tell us up front so we can align synthesis and QC. See Peptide Biocunjugation.

CONTACT US

Speak to a Peptide Scientist

Share your target protein/sequence list, peptide length/overlap, mutation/PTM plan, format preference, and QC needs. We’ll recommend practical specifications and provide a quote.

Tip: If you’re mapping epitopes, include antibody/sera type, target species/strain, and detection method to speed design.

Why Choose Bio-Synthesis

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