PurePep® Blog

5 factors to consider when choosing a peptide synthesizer

Choosing a peptide synthesizer to meet your specific needs can be a daunting task. Here are some key factors to consider to be able to synthesize high quality peptides in the number and scale that matches your applications.

1. The question of throughput and parallel synthesis

Different applications and phases of research require different numbers of peptides. A peptide drug discovery program may involve screening hundreds (or even thousands) of peptides to find hits, followed by optimizing structure-activity relationships (SAR) with focused libraries to identify a single candidate that can be advanced to the clinic. The key to success is therefore to choose a synthesizer that has reaction vessels that can deliver the level of parallel synthesis you need to match your application1.

2. Synthesis scale

Different stages of the R&D process will also require different amounts of peptide material. For example, the quantities needed increase as peptide therapeutics move through early screening to lead optimization and pre-clinical development. The right peptide synthesizer will meet current needs for scale and may even offer some flexibility for scale up to match requirements further down the line.1

3. Sequence difficulty and peptide length

Synthesizing peptides can present many sequence-based challenges, such as aggregation or secondary structure formation caused by certain residue combinations. Overcoming these challenges involves choosing a peptide synthesizer that can help you to optimize synthesis. Seeking the highest possible purity includes optimizing many parameters, such as reaction times, choice of coupling reagent, concentrations, resin type, temperature, and placement of structure-breaking residues.2, 3
Multi-channel instruments are ideal for testing different parameters in parallel.

Heating accelerates chemistry and improves purity for many difficult sequences, which means that an instrument with optional heating capabilities could be the system of choice. For example, induction heating enables the temperature in multiple reaction vessels to be set independently, providing maximum flexibility when searching for optimal synthesis conditions.4, 5

One way to minimize trial-and-error when synthesizing difficult peptides is the use of real-time UV monitoring instead of monitoring the waste stream as most commercially available instruments do. Synthesizers that monitor the reaction solution while it is mixing provide in-process control of reaction times, which greatly improves yield and purity.6

If you are synthesizing long peptides then it is crucial that reaction efficiency is maximized at every step, as even small inefficiencies and side reactions will escalate to dramatically reduce purity and yield. To improve synthesis efficiency, some instruments have a fluidic system that ensures zero dead volumes and no cross-contamination between reaction steps, which minimizes additions, deletions, and other common side reactions of solid phase peptide synthesis.

4. The need for special chemistry

Will you just be synthesizing standard linear peptides, or will you be making cyclic peptides, peptoids or other peptidomimetics? Will you be working with PNAs, PMOs, or oligos? The synthesis of cyclic peptides will often involve the use of specially protected amino acid derivatives and reaction steps for orthogonal deprotection and cyclization. The synthesis of peptoids and other types of peptidomimetics, as well as PNAs, oligos, and oligomimetics all require unique monomers and reagents. Preparing these types of molecules will demand an instrument that offers maximum flexibility in terms of protocol and bottle positions. This is why some instruments use up to 40 amino acids or other monomers during a synthesis, rather than being restricted to 20 positions for the natural amino acids. Many of the monomers and reagents used for these special chemistries can be expensive or precious, so some synthesizers also offer prime-free ‘Single-Shot’ additions from any amino acid/monomer bottle position to ensure that nothing is wasted.

In some cases, air- or moisture-sensitive catalysts may be used for special steps, necessitating that chemistry is performed in a closed system under inert nitrogen or argon. While most SPPS today utilizes Fmoc-protected amino acids, some groups continue to use Boc chemistry, and instruments in that environment must be compatible with concentrated trifluoroacetic acid (TFA) solutions. The key is therefore to select a peptide synthesizer that can deliver the flexibility you need to handle the special chemistries used in your lab.7, 8, 9, 10

5. Find a partner that can provide a cost-effective future-proof solution to meet your peptide synthesis needs

For most laboratories and production facilities, the purchase of a peptide synthesizer is a significant expenditure that will require justification based on the return on investment. The instrument is expected to provide many years of worry-free operation and should enhance the productivity of the team. Ideally, an instrument will have the flexibility to meet both current and anticipated future needs. If the current budget is limited, or the needs of the group change, it should be possible to upgrade or provide trade-in value towards a system with added features or capacity. All along, your instrumentation partner should provide support to ensure that you can achieve your goals.

Gyros Protein Technologies has been an innovator in automated SPPS since the 1980s, and today is the world’s leading provider of peptide synthesis instrumentation. All our instruments rely on the proprietary PurePepTM Pathway microfluidics technology to maximize purity and provide industry-leading reliability.

To accommodate different user needs, synthesizers from Gyros Protein Technologies offer different levels of throughput. For instance, Tribute® can synthesize one or two peptides at a time, while Prelude® X can be used to synthesize as many as six peptides in parallel, and Symphony® X can synthesize up to 24 peptides simultaneously. Libraries of short peptides and even long peptides synthesized with Symphony X using fast protocols can be prepared overnight, enabling the production of as many as 120 peptides in a week. Real-time UV monitoring using the IntellisynthTM system, as well as heating options are available on Prelude X, Tribute, and Symphony X.

All bench-scale instruments from Gyros Protein Technologies can be used to efficiently synthesize peptides at the low micromole scale, which could range from a couple of milligrams up to around 50 milligrams, depending on the length of the sequence. With these systems, the maximum scale for each reaction vessel is around 1 mmol, meaning a medium-length peptide can be synthesized on Tribute, Prelude X, and Symphony X at over 8 gram, 25 gram, and 100 gram scale, respectively. If you need hundreds of grams for animal studies then Sonata® XT can deliver a maximum scale of around 200 mmol.

Our employees have decades of experience in peptide chemistry, and take pride in our reputation for delivering a high level of customer service and technical support. With the longevity of our robust peptide synthesizers, our history of innovation, and the people who stand behind our products, Gyros Protein Technologies is your trusted partner for peptide synthesis solutions.



  1. Cyf Ramos-Colón, Daniel Martinez, Andrew Kennedy and James Cain. High-throughput parallel synthesis optimization of Glucagon-like Peptide 1 receptor agonists. Poster presented at EPS 2018
  2. Cyf Ramos-Colón, Daniel Martinez, Andrew Kennedy and James Cain. Turning up the heat on peptide purity. Chemistry Today – vol. 36(4) July/August 2018
  3. Daniel Martinez, Cyf Ramos-Colón, and James P Cain. Efficient synthesis of 84-mer human parathyroid hormone for the study of osteoporosis and hypoparathyroidism. Poster presented at APS 2017.
  4. James P. Cain, Daniel Martinez, and Cyf Ramos-Colón. Optimized crude purity of cyclic melanocortin receptor agonist Melanotan II using induction heating. Poster presented at German Peptide Symposium 2018
  5. Andrew Kennedy, Daniel Martinez, James Cain and Cyf Ramos-Colón. Fast solid phase peptide synthesis method development for the synthesis of complex peptides. Poster presented at German Peptide Symposium 2019
  6. Comparison of Alternative Deprotection Reagents to Piperidine for the Synthesis of a Poly-Alanine Peptide. Application Note #20
  7. Paramjit Arora and Ganesh Jedhe. Fully Automated Synthesis of Oxopiperazine Helix Mimics on Prelude® X. Application note #25
  8. Cyf Ramos-Colón, Daniel Martinez, and James P. Cain. Synthesis of [des-Arg7]-Dynorphin A peptoid analogue: faster methods using parallel automated synthesis and induction heat. Poster presented at Foldamers 2018
  9. James Cain, Daniel Martinez, Andrew Kennedy, and Cyf Ramos-Colón. Synthesis of therapeutic stapled peptides: Fully automated peptide cyclization via olefin metathesis, Poster presented at EPS 2018
  10. Cyf Ramos-Colón, Daniel Martinez, Andrew Kennedy, and James Cain. Parallel automated solid phase synthesis: efficient high-throughput optimization for therapeutic discovery and development of peptide nucleic acids. Poster presented at TIDES 2018