Peptide Library & Pool Design

JPT has been designing and synthesizing peptide libraries and peptide pools  for more than 15 years. Each design facilitates  answering specific scientifc questions. 

We are happy to provide recommendations to choose the most efficient peptide library or pool design for your specific application. 

Common Peptide Library & Pool Designs

Positional Scanning Library

A Positional Scanning Library is used to

  • Increase activity of enzyme substrates
  • Enhance antibody epitopes
  • Improve T-cell epitopes
  • Optimize peptide binding sites 
Positional Scanning Libraries are generated by systematically replacing one or more selected residues within a peptide sequence by all other natural (or non-natural) amino acids. Amino acids that increase activity or binding can be identified by using a positional scanning library and a sequence with improved properties is designed. 
In combinatorial positional scanning libraries 2 or more residues at different positions are varied in each peptide taking effects of multiple positions on the biological activity of a peptide sequence into account. 

Use our free and easy-to-use PepSequencer for generation of positional scanning libraries! 

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Overlapping Peptide Library

Overlapping peptide libraries as designed by an overlapping peptide scan are used to

  • Scan an antigen sequence for epitopes (epitope mapping)
  • Screen a protein for a substrate
  • Search for other binding sites within a given protein
  • Identify a T-cell epitope
  • Stimulate T-cells in T-cell assays
  • Map antibody epitopes
Overlapping peptide libraries are generated by dividing the original protein or peptide sequence into many overlapping peptides of the same length. The overlapping peptides are defined by peptide length and peptide offset. The optimal peptide length for epitope mapping is 8 to 20 amino acids with an offset of 2-4 amino acids. 

Use our free and easy-to-use PepSequencer for generation of overlapping peptide sequences!

Neo-Epitope Library

Neo-epitope libraries are used for neo-epitope prioritization. Neo-epitopes identified from patient samples (e.g. cancer patients) by methods such as NGS have to be prioritized to be used for immunotherapy. 
Therefore, a new neo-epitope library is needed for each patient, making fast production the key feature of a neo-epitope library.For a neo-epitope library, each neo-epitope is used to create an overlapping peptide scan to identify the most immunogenic epitope.

Use our free and easy-to-use PepSequencer for generation of overlapping peptide sequences from neo-epitopes or contact us!

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Peptide Modifications & Specialty Peptides
SpotMix Antigen Discovery Pools
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Cyclization Library

Peptide cyclization libraries consisting of cyclic peptides (cyclized peptides) are used for

  • Development of peptides with enhanced bio stability
  • Mimicking secondary protein structures (e.g. protein loops)
  • Optimizing peptides (e.g. peptide ligands with increased binding potency/selectivity and enhanced protease stability)
For a cyclization library cyclic peptides can be synthesized by different methods, e.g. head-to-tail cyclization, side-chain-to-side-chain, head-to-side-chain, and side-chain-to-tail cyclization. 

Contact us for the generation of cyclization libraries!
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Antigen Discovery Pool

Antigen Discovery Pools are used for

  • Epitope discovery
  • Screening projects
  • Target discovery

Antibody discovery pools  consist of overlapping peptides synthesized by our proprietary ultra high-throughput SPOT technology. 
SPOT peptides are synthesized fully automated on a membrane. Therefore we are able to provide SpotMix Pools very quick and inexpensive. They are optimal for proteome spanning antigen target discovery, deep T-cell epitope discovery and biological screening. 
Learn more about SpotMix Antigen Discovery Pools
Use our free and easy-to-use PepSequencer.

Matrix Pools

Matrix Pools have a specialized layout that enables fast and minimal material consuming identification of epitopes within an antigen. From a given antigen overlapping peptides are generated and pooled into many subpools.

Each peptide is present in exactly two subpools according to a layout that we design for each antigen.

In the example shown below 64 peptides are pooled into 16 Matrix Pools. Pools V and XIII elicit a positive T-cell response. Only peptide 37 is present in both pools and therefore is the peptide containing the epitope.

Matrix Pools are also the main component of Epitope Mapping Peptide Sets (EMPS).

Contact us for further information!

ULTRA Library & Pools

ULTRA libraries and pools are used to represent sequence diversity with the least possible number of peptides for

  • Immune monitoring of T- and B-cell response
  • T-cell stimulation in immunotherapy
  • Biomarker discovery
  • Development of vaccines

We generate ULTRA libraries with our proprietary algorithm to reflect the full spectrum of sequence variation within a virus or type of cancer with one comprehensive peptide library. This saves precious time and resources.

Our algorithm creates all possible peptide variations and scores these according to their frequency of occurrence across all sequences. We can then define the optimal overlap required to provide homogeneous overall coverage.

Sequence Diversity in Viruses

  • Hallmark in many pathogenic viruses including HIV, HBV, Influenza and SARS-CoV-2
  • Most sequence diversity found in viral envelope proteins, due to their important role in eliciting host immune recognition
  • Sequence diversity has to be taken into account in the design of antigen-based products, intended for immune monitoring and vaccination

Sequence Diversity in Tumors

  • 10 000 to 12 000 sites with coding mutations have been identified per individual, translating into a sequence alteration in one of every two genes
  • Somatic mutations cause sequence heterogeneity within individuals which are of special significance in the pathological mechanisms of cancer
  • 767 germline and 29881 somatic mutations have been identified for TP53, one of the most important tumor driver genes

Selected Epitope Pool

Selected Epitope Pools consist of a number of peptides representing key immunodominant epitopes from antigens or pathogens. Peptides are selected from pre-identified epitopes with respect to HLA restrictions.

Well known examples are our CEFX Ultra SuperStim and CEF control pools that contain epitopes from different organisms and the Pan Select Pools containing all immunodominant epitopes from one virus each. 

The benefits of selected epitope pools are

  • Well characterized epitopes provide a representative picture of the T cell response
  • Smart selection of epitopes creates powerful controls for T-cell standardization
  • Individual peptide responses can be mapped more easily
  • Efficient and cost effective method for classifying T cell response

Request a price for your customized peptide pool.

Truncation Library

A truncation library is used to

  • Determine the minimum length of an epitope (minimal epitope)
  • Map the minimal binding site of a protein that is required for proper binding

Truncation libraries are generated by reducing the peptide length (truncation) amino acid per amino acid from each terminus creating a set of truncated peptides with different lengths. If the key residues have already been identified using an alanine scanning library , truncation can be stopped at the key residues position.

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Alanine Scanning Library

Alanine scanning libraries are used to

  • Identify key residues in epitopes
  • Search binding parameters of enzymes
  • Study binding sites of proteins

Creating an alanine scanning library, alanine systematically substitutes the residues at each amino acid position of the original peptide i.e. identified epitope (= alanine walk). Substitution of an important or essential amino acid by alanine results in less or no binding or activity.

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Random Library

A random library is used for peptide sequence optimization. To generate random peptide libraries selected residues of a peptide sequences (wobbles) are randomly and simultaneously substituted with all or some of the 20 natural amino acids via a shotgun approach. Alternatively, a random library with specific physico-chemical properties can be designed by computer scientists resulting in random peptide libraries of defined size and properties for target identification and drug discovery.

Contact us for the generation of random libraries!

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Scrambled Library

Scrambled Libraries are used for screening proteins of interest, e.g. antibodies or enzymes with the permutations of a peptide for sequence optimization. A scrambled library is generated by permutation of the original peptide sequence and represents all alternative peptides with the same amino acid composition. Scrambled peptides or scrambled peptide libraries are also used as negative controls.

Contact us for the generation of scrambled libraries!

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