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Custom MHC Peptide Synthesis (HLA Class I & II)

Tetramer-ready epitopes • Neoantigen & viral panels • Immunopeptidomics validation peptides • High-throughput production • OEM/private-label supply • Backed by 45+ years of peptide manufacturing expertise

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Overview Capabilities at a glance Why quality matters What we make Workflow Quote specs QC High-throughput & OEM Contact

Overview: custom MHC peptide synthesis

MHC (HLA) peptides are short peptides presented by MHC molecules for T-cell recognition. In practice, Class I epitopes are commonly 8–11 amino acids, while Class II peptides are typically longer (13–20+) with a binding core embedded within the sequence. Synthetic MHC peptides are used to validate immunopeptidomics discoveries, build tetramers, perform T-cell stimulation assays, and screen neoantigen/viral epitope panels.

Bio-Synthesis manufactures custom HLA-restricted peptides with a manufacturing-first mindset—route selection, purification strategy, and analytical controls aligned to the downstream use. We also support high-throughput MHC peptide production and OEM/private-label supply for qualified partners, delivering consistent quality and batch reproducibility backed by 45+ years of peptide manufacturing expertise.

Class I (8–11 mer) Class II (13–20+) 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 capability for panels and screening workflows
  • Manufacturing discipline for difficult epitopes and tight impurity control
  • Confidential OEM supply for qualified vendors
  • COA + chromatograms with each lot; documentation options available
What “assay-ready” means in practice

Most downstream failures are not “biology problems” — they trace back to peptide quality and behavior.

  • Sequence fidelity: reduce truncations/deletions that can impact loading
  • Oxidation control: manage Cys/Met states when relevant
  • Solubility planning: select salt/form and handling notes to prevent loss
  • QC aligned to use: tetramers, MS validation, or stimulation assays
Custom MHC peptide synthesis showing HLA Class I and Class II peptides, high-throughput production, and QC workflow
Figure: Custom MHC peptide synthesis workflow for HLA Class I & II epitopes, high-throughput panels, and assay-ready QC
Best fit: immunopeptidomics validation, tetramer generation, T-cell assays, neoantigen discovery, and high-throughput epitope screening.

Related: Peptide Modifications, Peptide Arrays, Difficult Peptide Synthesis, Isotope-Labeled Peptides.

Capabilities at a glance

Fast-scanning matrix for buyers and partners. If you’re selecting peptides for tetramers or functional assays, see quality drivers.

Need What we offer Best fit for Notes
Class I peptides
8–11 mer epitopes Anchor-optimized variants N/C caps (optional)
Tetramers, T-cell assays, validation Length and identity control; QC aligned to downstream use.
Class II peptides
13–20+ mer Core-focused designs Flanking variants
CD4 assays, antigen mapping Longer peptides may require solubility/workup planning.
Neoantigen panels
WT vs mutant pairs Tiered purity options High-throughput production
Screening, validation, prioritization Panel consistency, controlled specs, batch reproducibility.
Difficult epitopes
Hydrophobic sequences Aggregation control Purification strategy
Challenging viral/tumor epitopes Route and purification tuned to reduce losses and close impurities.
MS validation
Identity-confirmed peptides Optional heavy labels QC-ready reporting
Immunopeptidomics confirmation Use labeled pairs when quantitation/confirmation requires it.
OEM/private label
Confidential supply Partner specs & SKUs Repeatable workflows
Reagent providers, platforms Qualified partner onboarding; consistent lots and documentation.

Need MHC tetramers? We can supply tetramer-ready peptides and QC data aligned to your workflow.

Why MHC peptide quality matters

Loading & presentation

Truncations, deletions, or close variants can compete during loading and complicate interpretation—especially in tetramer workflows and sensitive assays.

Oxidation state

Cys and Met can introduce multiple chemical states. We manage oxidation expectations and QC so you know what you are using.

Solubility & handling

Many epitopes are “sticky” or hydrophobic. We plan salt/form and provide handling notes to reduce adsorption and loss.

Common failure modes (and how we prevent them)
  • Aggregation during synthesis: optimized chemistry and sequence-aware strategy
  • Low recovery: behavior-first workups and purification planning
  • Close impurity profiles: method selection aligned to resolution needs
  • Oxidation variability: define acceptable states; verify by MS
  • Assay inconsistency: lot-to-lot controls and documentation options
  • Panel drift: standardized workflows for high-throughput panels

What we make

Class I epitope peptides (HLA-A/B/C) 8–11 mer
  • Standard epitopes and variant libraries (anchor scans, alanine scans, conservative substitutions)
  • Tetramer-ready peptides with QC aligned to your workflow
  • Optional terminal modifications (acetylation/amidation) when required by design
Class II peptides (HLA-DR/DP/DQ) 13–20+ mer
  • Core-focused and flanking-variant designs for mapping
  • Long peptides with solubility-aware purification and handling recommendations
  • Optional biotin/handles for downstream workflows (project-dependent)
Neoantigen peptides (WT vs mutant pairs) screening → validation
  • Matched WT/mutant pairs with consistent spec across the panel
  • Tiered purity options for screening vs confirmation
  • Repeatable workflows for large panels
Immunopeptidomics validation peptides LC–MS confirmation
  • Identity-confirmed peptides for discovery confirmation
  • Optional stable-isotope labeled versions (light/heavy pairs) for targeted MS workflows
  • Documentation aligned to lab reproducibility and panel integrity

Workflow: request → manufacture → QC → delivery

1) Design & feasibility review
  • Confirm HLA class, target length, and any variant strategy
  • Identify risk drivers (hydrophobicity, aggregation, oxidation)
  • Align purity/QC to tetramers, assays, or MS validation
2) Synthesis & purification strategy
  • Route selected for reproducibility (especially for panels)
  • Purification planned to resolve close variants when needed
  • Solubility-aware workups to maximize recovery
3) QC & release
  • Analytical HPLC/UPLC purity profile
  • LC–MS identity confirmation (HRMS as needed)
  • COA + chromatograms for each lot
4) Packaging & delivery
  • Aliquoting and plate formats (project-dependent)
  • Handling notes for difficult epitopes
  • Repeat supply planning for panels and OEM partners

Quote specifications (copy/paste)

Required
  • Peptide list (sequence, length, class I vs II)
  • Quantity per peptide
  • Purity target (screening vs tetramer/functional)
  • Salt/form preference (or ask us to recommend)
Recommended (speeds feasibility)
  • Application: tetramer, T-cell assay, MS validation, screening
  • Any oxidation requirements (Cys/Met states)
  • Format needs: aliquots, plates, labeling
  • Panel scope and resupply expectations (high-throughput/OEM)
Tip: If you’re ordering a panel, include your preferred naming/ID scheme. We can align SKUs and documentation for repeat orders.

QC & typical deliverables

Standard (RUO)
  • Analytical HPLC/UPLC purity
  • LC–MS identity
  • COA + chromatograms
Assay-aligned

Recommended for tetramers and sensitive functional assays.

  • Tighter impurity control (project-dependent)
  • Oxidation-state expectations noted
  • Handling guidance for recovery
Panel / OEM support

Built for repeat orders and consistency.

  • Standardized workflows
  • Partner spec alignment
  • Documentation options for resupply

High-throughput MHC peptides & OEM supply

High-throughput production
  • Peptide panels with consistent specs and naming
  • Tiered purity for screening vs validation
  • Repeatable workflows to minimize panel-to-panel drift
  • Optional labeled peptides for MS validation
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

Do you synthesize both HLA Class I and Class II peptides?

Yes. We manufacture Class I epitopes (often 8–11 mer) and longer Class II peptides (commonly 13–20+), including panels and variant sets.

Can you make tetramer-ready peptides?

Yes. We supply peptides suitable for tetramer workflows with QC/COA and handling notes aligned to your use. Share your workflow and we’ll recommend an appropriate purity and QC level.

What purity is best for MHC peptides?

Screening often uses ≥95% purity, while tetramers and sensitive assays may benefit from higher purity and tighter impurity control—especially when truncations or close variants could co-load. We’ll recommend a fit-for-purpose target.

Do you support high-throughput panels and libraries?

Yes. We manufacture high-throughput panels using controlled workflows and consistent specs to support screening and resupply.

Do you offer OEM/private-label supply?

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

Can you help with difficult or hydrophobic epitopes?

Yes. We apply aggregation-aware synthesis strategies and solubility-aware purification to improve recovery and reduce close-impurity issues for challenging epitopes.

Can you provide isotope-labeled peptides for immunopeptidomics confirmation?

Yes. We can provide optional stable isotope labeled versions (light/heavy pairs) for targeted MS workflows where confirmation or quantitation requires it.

How do you manage oxidation (Cys/Met)?

We plan synthesis and handling with oxidation in mind and verify identity by MS. If a specific oxidation state is required, include it in your request so QC expectations are aligned.

How do you control closely related impurities or isomers?

MHC peptides can produce closely related truncations or sequence variants that behave similarly. We align synthesis route, purification method, and analytics to resolve and monitor these species, and recommend fit-for-purpose specifications for tetramers or sensitive assays.

Can you make WT vs mutant neoantigen pairs and matched sets?

Yes. We manufacture matched WT/mutant pairs and panel sets with consistent specifications and documentation to support prioritization and follow-up studies.

Do you provide N- or C-terminal modifications (Ac/Am) if needed?

Yes. Optional N-terminal acetylation and/or C-terminal amidation can be provided when required by your design.

What peptide lengths do you recommend for Class II projects?

Many programs use 15-mers (or 13–20+) to cover a Class II binding core with flanking residues. If you have an epitope core, we can propose flanking variants to improve coverage.

Can you supply peptides in plates or aliquots for screening?

Packaging and formatting options (aliquots, plate layouts, labeling) are available on a project basis. Share your workflow and we’ll recommend a practical format.

How should I dissolve or handle hydrophobic MHC peptides?

We can recommend a suitable salt/form and provide handling notes to reduce adsorption and loss. For difficult peptides, small-volume pre-wetting and controlled dilution often improves recovery.

Can you synthesize peptides containing cysteine, methionine, or other sensitive residues?

Yes. We routinely manufacture peptides with oxidation-prone or sensitive residues and align QC reporting to the expected chemical state(s).

Do you support anchor scans, alanine scans, or variant libraries?

Yes. We can produce systematic variant sets for SAR/epitope mapping such as anchor substitutions, alanine scans, or conservative mutation panels.

What analytics do you provide with each peptide?

Typical deliverables include analytical HPLC/UPLC purity and LC–MS identity confirmation, plus a COA and chromatograms. Additional analytics can be discussed for specific needs.

What do you need to quote?

Send your peptide list (sequence/length/class), quantity per peptide, purity targets, and intended use. For panels, include naming/ID format and resupply expectations.

More FAQ'sAll FAQ's

Contact & quote request

Request a quote

Send your peptide list and intended workflow (tetramers, assays, MS validation, screening). We’ll recommend a synthesis + QC plan aligned to your goals, throughput, and resupply needs.

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For OEM partners

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

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Custom MHC Peptide Synthesis

High-throughput HLA-restricted peptide manufacturing for tetramers, T-cell assays, neoantigen screening, and immunopeptidomics validation—plus OEM/private-label supply—backed by 45+ years of peptide manufacturing expertise.

Related services

Difficult Peptide Synthesis
Peptide Modifications
Isotope-Labeled Peptides
Peptide Arrays

Get a quote

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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.

Greetings Researchers,

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