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Peptide library design guide

Peptide libraries have quickly become an invaluable tool for a variety of research applications, including protein binding studies, cancer immunotherapy and proteomics. By screening hundreds of peptide combinations simultaneously, identifying important, bioactive peptides is cheaper and easier; however, choosing the right peptide library design can make a big difference in your results. Prior to purchasing your peptide library, consider this design guide to ensure you choose the best options for your research application.


Proteomics   T cell immunotherapy
Cancer research   Antibody and T cell epitope mapping
Vaccine Development   Biological Assays

Proteomics

Peptide libraries have been used for a variety of proteomics applications, such as for proteolytic peptide screening or immune monitoring. These libraries are commonly combined with mass spectrometry (MS) to study reaction progress, to screen for important biomarkers, or to identify post-translational modifications (Picotti, 2012, Nature Methods).

Design recommendations:

Service Micro-scale peptide library
Design Overlapping library design
Purity Crude
Design details 10 AA peptides, 2-4 AA overlap

Cancer research

Designing targeted therapeutics is critical for effective elimination of cancer cells, and peptide libraries are commonly used to quickly identify important biomarkers on cancer cells. Peptides corresponding to tumor associated antigens (TAA) are displayed in a library format and bioactive peptides are screened. Once identified, highly specific antibodies can be designed for cancer immunotherapy or cancer vaccines.

Design recommendations:

Service Standard peptide library
Design Overlapping library design
Purity Crude or >70% purity

Vaccine Development

Peptide libraries are commonly used to identify immunogenic epitopes and also evaluate vaccine effectiveness. Since libraries can span an entire protein sequence, no important epitopes will be missed. In addition, while vaccines should ideally be tested first, this is not recommended for certain highly infectious diseases (Chen, ACS Chem Biol, 2014). In this case, peptide libraries are ideal for in vitro immune monitoring. To find out more about how peptide libraries accelerate vaccine development, click here.

Design recommendations:

Service Standard peptide library
Design Overlapping library or Alanine scanning library
Purity High purities recommended (>90%)

T cell immunotherapy

Engineering T cells to target and eliminate viruses and cancer cells has become a very important research field. By engineering the receptor to identify specific TAAs or viral epitopes (Franzoni, Clin Vaccine Immunol, 2013), immunotherapy becomes much more efficient and effective. Chimeric antigen receptor (CAR) T cells are examples of such cells, and peptide libraries are invaluable for identifying the antigenic sequences against which to design the T cell receptor.

Design recommendations:

Service Micro-scale peptide library or Standard peptide library
Design Overlapping library design and Truncated library design
Purity Crude or >70% purity
Design details Overlapping library: 10-15 AA peptides, 2-4 AA overlap
Truncated library: 8-12 AA peptides

Antibody and T cell epitope mapping

Identifying the antigens that stimulate antibody and T cell binding is an important first step in immunotherapy development. Potential antigens are sequenced and separated into overlapping peptides. When positive T cell or antibody binding is confirmed, these peptide sequences can then be used to design targeted therapeutics. For more information on how peptide libraries have accelerated antibody and T cell epitope mapping, click here.

Design recommendations:

Service Standard peptide library
Design

Overlapping library, positional scanning library, or truncation library design

Purity Crude or >70% purity

Biological assays

Individually aliquoted peptide sequences that comprise a larger protein can be ideal for a variety of biological assays. These libraries can be used to identify peptides that have antimicrobial activity, direct stem cell differentiation, or even monitor pharmacologic activity.

Design recommendations:

Service

Micro-scale peptide library or Standard peptide library

Design

Overlapping library or scrambled peptide library design

Purity >70% purity or higher

References

Picotti P and Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nature Methods. 2012 May 30;9(6):555-66. doi: 10.1038/nmeth.2015.

Chen G et al. Synthetic antibodies with a human framework that protect mice from lethal Sudan ebolavirus challenge. ACS Chem Biol. 2014 Oct 17;9(10):2263-73. doi: 10.1021/cb5006454.

Franzoni G et al. Assessment of the phenotype and functionality of porcine CD8 T cell responses following vaccination with live attenuated classical swine fever virus (CSFV) and virulent CSFV challenge. Clin Vaccine Immunol. 2013 Oct;20(10):1604-16. doi: 10.1128/CVI.00415-13.

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