Combinatorial Peptide Library Synthesis

Positional scanning • Alanine & substitution libraries • Focused motif sets • High-throughput peptide panels • OEM/private-label supply • Backed by 45+ years of peptide manufacturing expertise

Overview: combinatorial peptide libraries

Combinatorial peptide libraries are designed collections of related peptides that systematically explore sequence diversity to map binding requirements, identify active motifs, or optimize lead candidates. Unlike single custom peptides, libraries must maintain coverage (the members you planned are actually present), consistency (members behave similarly lot-to-lot), and traceability (what was made and how it was verified).

Bio-Synthesis provides combinatorial peptide library synthesis using a manufacturing-first approach: library design review, sequence-aware synthesis strategy, purification planning, and QC aligned to screening versus validation. We support high-throughput peptide panels and OEM/private-label supply for qualified partners, backed by more than 45 years of peptide manufacturing expertise.

Library design support High-throughput panels OEM supply available ISO 9001:2015/ISO 13485:2016 45+ Years of Expertise U.S. Facilities - Texas
Why choose Bio-Synthesis
  • 45+ years of peptide and modified-peptide manufacturing expertise
  • High-throughput workflows for panels and library programs
  • Process discipline for coverage, reproducibility, and resupply
  • Difficult sequence capability for hydrophobic/aggregation-prone members
  • OEM/private-label supply for qualified partners (confidential)
Light vs heavy: what changes

The goal is not just “a library once” — it’s repeatable supply as your program tightens specs.

  • Coverage controls: identify high-risk motifs early
  • Fit-for-purpose specs: screening vs confirmation tiers
  • Documentation: panel naming, IDs, and COA traceability
  • Resupply planning: consistent workflows for repeat orders
Combinatorial peptide library synthesis concept showing split-and-mix diversity generation, peptide libraries, QC, and screening workflow

Figure: Combinatorial peptide library synthesis concept illustrating split-and-mix diversity generation, library assembly, QC, and screening workflows

Best fit: epitope mapping, binder discovery, SAR/lead optimization, motif exploration, and platform screening programs that require consistent panel resupply.

Related: Peptide Arrays, Peptide Libraries, Difficult Peptide Synthesis, Peptide Modifications.

Tools: Peptide Library Screening Tool

Capabilities at a glance

Fast-scanning matrix for buyers and partners. For design help, see library types and quote specs.

Need What we offer Best fit for Notes
Positional scanning
One position varied Defined alphabets Panelized output
Motif discovery, binding rules Designed to expose position-specific contributions.
Alanine / substitution sets
Single substitutions Conservative variants WT comparators
Epitope mapping, SAR Clean comparisons require consistent specs.
Focused motif libraries
Motif exploration Constraint options Follow-up sets
Lead optimization Built for iterative rounds and resupply.
High-throughput panels
100s–1000s members Consistent documentation Repeatable workflows
Screening platforms Panel naming/IDs and resupply planning available.
Difficult members
Hydrophobic sequences Aggregation control Recovery planning
Real-world targets Sequence-aware strategy reduces dropouts.
OEM/private label
Confidential supply Partner SKUs Spec alignment
Reagent providers Qualified partner onboarding under confidentiality.

Need an addressable format for screening? Consider a peptide array approach in addition to soluble panels.

Why combinatorial libraries fail (and how to prevent it)

Sequence bias

Certain residues and motifs couple less efficiently, skewing diversity or creating “dropouts.” We identify risk drivers early and adapt strategy to protect coverage.

Close impurities

Libraries can generate closely related impurities that confound screening. We align purification and analytics to your screen vs validation needs.

Resupply inconsistency

Programs often fail when the second run doesn’t match the first. We design workflows for repeatable manufacturing and documentation from day one.

Manufacturing-first controls
  • Design review: define alphabets, positions varied, and comparators
  • Risk mapping: flag hydrophobic/aggregation-prone members
  • Tiered specs: screening vs confirmation sets
  • Purification planning: methods selected for library purpose
  • QC alignment: representative vs member-level identity checks
  • Traceability: naming/IDs + COA reporting for resupply

Library types we synthesize

Positional scanning librariesmotif discovery
  • Systematically vary one position (or a defined subset) while holding others constant
  • Define residue alphabets (e.g., 19/20 amino acids, conservative sets, or custom alphabets)
  • Outputs as addressable peptide panels for straightforward screening
Alanine scanning & single-position substitution setsepitope mapping
  • Alanine scan to identify critical residues
  • Conservative substitutions to explore tolerance and SAR
  • WT comparators included for clean interpretation
Focused motif librarieslead optimization
  • Explore a defined motif with targeted diversity around key positions
  • Iterative rounds supported with resupply planning and documentation
  • Optional modifications/handles (project-dependent)
Variant panels (WT vs mutant, truncation series, length scans)validation
  • Matched WT/mutant or truncation series for mechanism and specificity
  • Length scans for binding and activity windows
  • Designed for confirmation after screening hits
Library formats & controls (commonly requested)screen-ready design
  • Overlapping peptide libraries: epitope mapping with defined length and offset
  • Truncation series: N- or C-terminal truncations to identify minimal active cores
  • Scrambled / negative controls: controls to benchmark assay specificity
  • Length scans: windowed peptides around a motif or hotspot region
  • WT vs mutant pairs: paired designs for specificity, SAR, and confirmation

If you already have a protein region of interest, we can help choose fragment length/offset to balance cost vs data resolution.

High-throughput peptide panelsplatform screening
  • Panel naming/ID schemes and documentation
  • Tiered purity and QC aligned to screen vs validation
  • Confidential OEM/private-label supply available for qualified partners

Workflow: design → manufacture → QC → resupply

1) Library design review
  • Confirm positions varied, alphabets, and member count
  • Define controls (WT, scrambled, or known binders)
  • Align format: individual vials, plates, or sets (project-dependent)
2) Synthesis strategy
  • Sequence-aware strategy for coverage and difficult motifs
  • Aggregation control for hydrophobic members
  • Purification plan matched to library purpose
3) QC & release
  • Analytical HPLC/UPLC (fit-for-purpose)
  • LC–MS identity checks (as appropriate to library type)
  • COA + traceable documentation
4) Resupply planning
  • Repeatable workflows to reduce drift
  • SKU/ID alignment for partner programs
  • Change control approach for program evolution

Quote specifications (copy/paste)

Required
  • Library design (positions varied, alphabet, length)
  • Number of members and quantity per member
  • Purity targets (screening vs validation)
  • Format needs (vials/aliquots/plates; project-dependent)
Recommended (speeds feasibility)
  • Intended use: screening, mapping, confirmation
  • Controls/comparators (WT, alanine scan, known binders)
  • Any sensitive motifs (Cys/Met states; modifications)
  • Resupply expectations and naming/ID scheme
Tip: If you plan follow-up rounds, tell us now. We can design documentation and workflows for repeat supply.

QC & typical deliverables

Screening libraries

Built for speed and coverage.

  • Fit-for-purpose purity targets
  • Representative QC strategy (project-dependent)
  • COA + documentation aligned to library IDs
Validation sets

Recommended for hit confirmation and SAR.

  • Higher purity / tighter impurity control
  • LC–MS identity confirmation
  • Chromatograms + COA per member (as scoped)
Partner/OEM programs

Built for repeat orders and consistency.

  • Standardized workflows
  • Partner spec/SKU alignment
  • Resupply planning and documentation

High-throughput libraries & OEM supply

High-throughput programs
  • Large panels with consistent specs and naming
  • Tiered purity for screening vs confirmation
  • Repeatable workflows to minimize drift
  • Optional modifications/handles (project-dependent)
OEM / private-label support
  • Confidential supply for qualified partners
  • Partner SKUs/specs and documentation alignment
  • Resupply planning and lot consistency controls
  • Packaging/format options (project-dependent)

We do not publicly disclose partner relationships. OEM support is available under confidentiality for qualified vendors.

FAQ

What is a combinatorial peptide library?

A combinatorial peptide library is a designed collection of related peptide sequences that systematically explores sequence diversity (e.g., substitutions at defined positions) to map binding/epitope requirements or optimize activity.

What is the difference between a peptide library and a peptide array?

A peptide library refers to the collection design (diversity and composition). A peptide array is a physical format where many peptides are synthesized or printed in an addressable layout (e.g., membrane, slide, plate) for screening.

Do you make positional scanning and substitution libraries?

Yes. We support positional scanning, single‑position substitution sets (including alanine scanning), and focused motif libraries. Share your target motif and constraints and we’ll recommend a design.

Can you produce high-throughput peptide panels for screening?

Yes. We manufacture high-throughput peptide panels with consistent specifications and documentation to support screening and resupply.

Do you provide OEM/private-label library manufacturing?

Yes. OEM and private-label manufacturing support is available for qualified partners, including confidential supply and consistent specifications.

What purity should I request for a screening library?

Many screens use fit‑for‑purpose purity targets to balance cost and speed, while confirmation sets typically use higher purity. Tell us your assay sensitivity and we’ll recommend targets for screening vs validation.

How do you reduce sequence bias and library “dropouts”?

We apply sequence-aware synthesis strategy, monitor difficult motifs early, and align purification and QC to the library purpose. For high-risk motifs, we recommend design variants or process controls to maintain coverage.

Can you make difficult or hydrophobic library members?

Yes. We use aggregation-aware SPPS strategies and solubility-aware purification to improve recovery for difficult sequences within a library.

What QC do you provide with libraries?

Typical deliverables include analytical HPLC/UPLC purity and LC–MS identity (as appropriate to the library type), plus a COA and chromatograms for representative or defined members. QC scope can be aligned to screening vs validation.

What do you need to quote a combinatorial library?

Provide the library design (positions varied, alphabet, length), number of members, quantity per member, target purity, and intended use (screening, mapping, validation). For panels, include naming/ID scheme and resupply needs.

Contact & quote request

Request a quote

Send your library design and intended assay workflow. We’ll recommend a synthesis + QC plan aligned to coverage, throughput, and resupply needs.

For OEM partners

Confidential OEM/private-label supply is available for qualified partners. We can align SKUs/specs, documentation, and resupply planning.


Combinatorial Peptide Library Synthesis

High-throughput combinatorial peptide libraries and panels with manufacturing-first design, QC/COA, and OEM/private-label supply—backed by 45+ years of peptide manufacturing expertise.

Get a quote

Quote request form
sales@biosyn.com
+1-972-420-8505

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 40+ years of delivering high quality, fast and scalable synthetic biology solutions.