Automated Peptide/Protein Sequencers

Edman degradation is a process for protein sequencing first discovered by the Swedish biochemist Pehr Victor Edman in 1950. The technique is characterized by cycles. In a full cycle, the N-terminus of a given peptide is labeled with the reagent phenylisothiocyanate, forming a cyclic compound. Under acidic conditions, the labeled amino acid is cleaved from the peptide and further treated in acid to form a more stable phenylthiohydantoin (PTH)-amino acid derivative, which is then identified using HPLC. The Edman degradation cycle is performed repeatedly to the sequential amino acids of the shortened peptide to identify the remaining sequence.

In 1982, Applied Biosystems introduced the first commercial automated peptide sequencer, which proved to be reliable and robust. In fact, with only a handful of enhancements over the decades, these automated peptide sequencers continue to be the gold standard. However, tandem MS has become an increasingly important tool for peptide sequencing. MS, particularly tandem TOF-TOF and QTOF instruments, allow for performing the task faster with low quantities of samples.

The obvious advantage of automated Edman degradation over MS includes accuracy from proven chemistries and significantly lower initial system costs. However, its drawbacks include longer analysis times and a limited number of sequences, typically ranging from 20 to 50 amino acids. MS, on the other hand, is ideal if the peptide quantity is in low abundance, the N-terminal is inaccessible or if the time of analysis is an issue. However, MS comes with a heftier price tag and has trouble distinguishing isobaric amino acids.

Applied Biosystems dominated the automated peptide sequencer market, but discontinued the product line in 2008, after the market for systems softened. Given the gap in the market, Shimadzu introduced its PPSQ automated peptide sequencer in North America at Pittcon 2009. The PPSQ has been used in Japan for more than 20 years. Thermo Fisher Scientific indicated last summer the possibility of entering the market, but has not announced any further plans.

Advancements in MS for protein sequencing remain strong. For top-down protein sequencing, Bruker Daltonics introduced at Pittcon 2009 the Edmass Micro, based on the company’s microFlex LT MALDI-TOF system, and the Edmass Ultra, based on the ultraFlex III 200 Hz MALDI TOF-TOF system. Both systems are designed for peptide chemists who do not have MS experience.

The market for automated peptide sequencers is the strongest at academic core facilities, but growth has been stagnant over the last several years, particularly due to the accessibility of MS. However, as automated peptide sequencers age, devoted Edman Degradation users are looking to purchase new systems. Service, accessories, consumables and reagents are expected to drive the automated peptide sequencer market in the short term.

Peptide Sequencers at a Glance:

Leading Suppliers

• Applied Biosystems

• Shimadzu

• Bruker Daltonics

Largest Markets

• Academia

• Government

• Biotechnology

Instrument Cost

• $80,000–$200,000

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