Ion Torrent Proton System

Proton System is a sequencer released by Thermo Fisher Scientific in June 2012. It is based on Ion Torrent Semiconductor Sequencing.

Ion Torrent Proton System
Image of Proton: by ThermoFisher Scientific


Manufacturer Thermo Fisher Scientific
Technology Ion Torrent Semiconductor Sequencing
Release date June 2012
Price [2] $149,000
MSRP as of release date
Type Benchtop
Weight 59 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ, SFF, BAM and VCF
Read length Ion Torrent Proton I Chip: Up to 200bp
Run time Ion Torrent Proton I Chip: 2.5 hours
Reagent cost per Gb [1] Ion Torrent Proton I Chip: Unavailable
Data quality [3] Ion Torrent Proton I Chip:
Maximum output per run (Gb)[4] Ion Torrent Proton I Chip: 15.00
Primary error type [5] Indels
Notes about the specifications

  1. Cost per Gb: The cost per Gb is calculated by dividing the costs of sequencing reagents by the manufacturer’s maximum output per run. For these runs, the manufacturer may have included their own controls and used specific library preparation kits. Actual performance may vary based on sample and library type and quality, loading concentration, and other experimental factors. The sequencing reagent costs used for calculations do not include any other costs associated with preparing the samples or running the instrument, including reagents used for extraction, quality control or library preparation, labor, electricity, lab consumables, storage, etc. Performance metrics and prices are subject to change.
  2. Price: The final price may be different depending on the supplier, the region and any discounts provided through bulk orders or negotiation. Other factors that may influence the final price are warranty options, maintenance contracts, possible trade-ins of older instruments, and any financing arrangements chosen.
  3. Data quality: This is the maximum data quality that the instrument can offer based on manufacturer’s specifications and optimizations. The quality of a specific run will depend on multiple factors, including sample quality, sample quantity, library prep protocol, run conditions, etc.
  4. Maximum output: This is the maximum output of a full instrument run. This number is based on manufacturer’s specifications and optimizations.
  5. Primary error type: This is the most common type of error that may occur due to sequencing. Other types of error may occur as well.

More about the Proton System

The Proton System, manufactured by Thermo Fisher Scientific and released in 2012, was a benchtop sequencer targeted towards mid-throughput, targeted sequencing applications. It was positioned as a successor to smaller Sanger sequencing machines and a more affordable alternative to high-throughput sequencers like the Illumina HiSeq. However, it has since been discontinued and has been replaced by newer sequencing technologies.

While no longer commercially available, the Proton System offers valuable insights into the evolution of sequencing instruments and can be a helpful option for researchers with existing systems. Let's delve into its key features and considerations.

Key Innovations

The Proton System boasted several innovations aimed at improving ease of use and accessibility for targeted sequencing workflows. These included:

  • Ion Torrent Chip technology: The Proton System utilized the Ion PI Chip, which electronically detected base incorporation without fluorescence and was thus able to eliminate the need for an optical detection system. This allowed for a fast sequencing time of 2.5 hours.
  • Proprietary emulsion PCR: The system employed a unique emulsion PCR process for library amplification, which aimed to improve library uniformity and reduce PCR bias.

Features and Technologies

  • Read Length: The Proton System offered read lengths of up to 200 base pairs (bp), suitable for amplicon-based resequencing applications.
  • Accuracy: The system achieved base call accuracy exceeding Q20 (99% accuracy) for high-quality reads.
  • Throughput: A single run could generate millions of reads, sufficient for targeted resequencing of a small number of genes or amplicons.

Intended Uses and Specific Applications

The Proton System was primarily designed for:

  • Targeted resequencing of known genetic variants: This included applications like validation of single nucleotide polymorphisms (SNPs) identified through genome-wide association studies (GWAS) or targeted panels for disease diagnosis. Ion AmpliSeq panels would be suitable here.
  • Amplicon resequencing: The platform was well-suited for resequencing specific regions of interest like exomes or candidate genes. Using the Ion AmpliSeq Designer would be appropriate here.

Comparison with Competing Instruments

  • Ion Torrent GeneStudio S5: Similar to the Proton System, the GeneStudio S5 is a benchtop sequencer targeting mid-throughput applications. It offers longer read lengths (up to 600 bp) and a variety of available Chips and outputs with the max output being higher than the max offered by the Proton. However, the GeneStudio has longer run times.
  • Illumina MiSeq: The MiSeq offers higher read lengths and paired end reads along with comparable max output. It can also offer a variety of output based on the sequencing reagents. However, the run times are significantly longer than the Proton.

Special Considerations

While no longer commercially available and replacement parts and technical support may be hard to come by, the Proton System offers some advantages to consider:

  • Lower cost compared to high-throughput sequencers, especially if a lab has already bought one.
  • Ease of use due to its simple workflow and chip technology.
  • Faster speed compared to platforms with similar out, allowing researchers to perform a sequencing runs multiple times a day and adjusting their protocols accordingly.

Need sequencing done on a Ion Torrent Proton System or a specific instrument? Tell us about your project here, and we'll connect you with a qualified provider.

This information on this page is up-to-date as of May 9, 2024 and based on the spec sheets published by the manufacturer.