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Thermo Fisher Scientific, Ion Proton System

Thermo Fisher Scientific, Ion Proton System

Next-generation sequencing instruments, December 2017

Contact Information

Thermo Fisher Scientific
5791 Van Allen Way
Carlsbad, CA 92008

Name of instrument Ion Proton System
Name of model/Model has been upgraded —/no
Country where designed/Manufactured/FDA cleared or approved U.S./U.S./no
First year sold in U.S./Outside U.S./First year installed 2012/2012/2012
Dimensions in inches (H × W × D)/Footprint of all instrumentation and computing hardware 34.5 × 29 × 38/14 square feet
Equipment supplied with system/Automation for library preparation Torrent Suite Server, Ion OneTouch2, ES Station/yes
Necessary equipment not included with system and additional cost general laboratory supplies
Bioinformatics tools provided/For use by biologist or bioinformatician Torrent Suite software, Ion Reporter/biologist
Supplied with UPS/Entire workflow can occur in same lab no/yes
Clean room requirements/Electrical connection no/standard voltage
List price/Total list price for equipment needed to perform simplest and fastest workflow from amplification through variant calling (not typically found in lab) $225,000/—
Purchase options purchase or lease (financing available)
Warranties offered 1 year included, extended warranty available
Training included/Total time for standard install and basic training yes/<2 days
Training location/Follow-up training available on and off site/yes, extra charge
Instrument core performance:
Maximum No. of libraries amplified in single amplification event 96
Read length/Percent bases >Q30 200 bp/>70
Paired-end capability/Tag lengths/Spans
Fragment/Tag lengths/Spans yes/up to 200 bp/—
Mate-pair/Tag lengths/Spans yes/2 × 100 bp/up to 10 kb
Single-end/Tag lengths/Spans yes/up to 200 bp/—
RNA sequencing/Tag lengths/Spans yes/up to 200 bp/—
ChIP sequencing/Tag lengths/Spans yes/up to 200 bp/—
Bisulfite sequencing/Tag lengths/Spans no/—/—
Output per run >10 Gb
Total time from library construction to variant calling to achieve output per run/Technical bench time/Bioinformatics time <1 day/<4 hours/—
Sample preparation:
Total time for generating standard gDNA library <2 hours
• Paired-end
• Fragment <2 hours
• Mate-pair 2.5 days
• Single-end <2 hours
• RNA sequencing <6 hours
• ChIP sequencing customer demonstrated
• Bisulfite sequencing
Hands-on time each:
• Paired-end
• Fragment ~15 minutes
• Mate-pair ~8 hours
• Single-end ~15 minutes
• RNA sequencing <1 hour
• ChIP sequencing customer demonstrated
• Bisulfite sequencing
Equipment required for library construction standard laboratory equipment
Reagents and controls:
Cost per run varies based on application
Cost per sample* varies based on application
Reagent tracking method on instrument yes
Information contained in tracking method
Reagent shipping conditions/Storage conditions ambient, 8°–20°C/ambient, 20°C
Shelf life of amplification and sequencing reagents ≥6 months
Controls introduced during creation of library/Sequencing control avail. yes/yes
Capable of complete walkaway automation for amplification, sequencing, and variant calling yes
Remote system monitoring yes
Instrument control software and devices to start run/for data analysis 10 minutes/7 hours
Total time required for setup of amplification, sequencing, and variant calling steps <1 hour
Maximum No. of libraries sequenced in a single run 384
Types of maintenance plans available AB Assurance, AB Complete, AB Maintenance Plus, AB Maintenance Service
No. of field apps scientists and engineers based in U.S.
Weekly maintenance required/Monthly/Pre-run chlorite cleaning/none/automated cleaning of instrument after run
System offers secondary analysis software developed by instrument vendor yes
Variant report generated directly on instrument yes
Third-party analysis software available yes, Partek, DNAStar, NextGene, Ingenuity, more
Ability of software to detect mutations substitutions, indels, copy number changes
Total No. of peer-reviewed publications for this platform >845 based on RUO platform
Published applications in pathology-related research >195 based on RUO platform
Fastest published turnaround time from sample to analyzed result <15 hours based on RUO platform
Lowest published variant sensitivity level 25 percent
Distinguishing features of sequencer (supplied by company) fast exome capture workflow leverages the power and simplicity of AmpliSeq target enrichment technology; competitive pricing matched with capacity means economical exomes; custom and fixed panels enable targeted resequencing technology; low input requirements (as little as 10 ng DNA or 500 pg total RNA) are compatible with FFPE samples; users can design custom panels tailored to their own research interests using a simple Web application, order consortium-developed targeted gene panels, or purchase ready-to-use gene panels
*inclusive of sample prep, for multiple configurations, using 1 Mb and 30x average coverage per sample
Note: a dash in lieu of an answer means company did not answer question or question is not applicable
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