FAIMS Pro Duo interface - Enhanced selectivity, ultimate flexibility

Significance of the topic

The FAIMS Pro Duo interface extends differential ion mobility separation to mainstream high-performance mass spectrometry workflows. By adding an orthogonal gas‑phase separation step upstream of the mass analyzer, FAIMS enhances selectivity and signal‑to‑noise for complex mixtures while remaining compatible with a wide range of chromatographic flow rates. This capability is important for proteomics, lipidomics, targeted quantitative assays, and workflows requiring suppression of chemical background or isobaric interferences without sacrificing throughput.

Objectives and overview of the product

This product specification describes the Thermo Scientific FAIMS Pro Duo interface designed to integrate with next‑generation Thermo mass spectrometers. Key objectives are to improve analytical selectivity and sensitivity, enable rapid Compensation Voltage (CV) switching for targeted and multiplexed acquisition, maintain compatibility with both nanoflow and high‑flow LC, simplify installation and maintenance, and provide software tools for CV optimization and data processing.

Methodology and technical description

• Principle: Differential ion mobility (FAIMS) separates ions in an oscillating asymmetric electric field across an analytical gap; ions are transmitted by tuning a compensation voltage (CV) that offsets net ion drift.
• Optimized analytical gap: A 1.5 mm gap increases electric field strength compared with larger gaps, preserving separation efficiency while eliminating the requirement for helium as buffer gas.
• Ion transfer and CV switching: CV switching time depends on ion transfer tube geometry. Systems using a round bore ion transfer tube (ITT) have a maximum CV switching time of 40 ms; systems with a high capacity ion transfer tube (HCITT) achieve up to 25 ms. Faster switching supports targeted acquisition and small CV step methods (<2 V), beneficial for multiplexing strategies such as TMT.
• Gas and thermal control: The interface uses nitrogen as carrier/cooling gas to convey ions and control electrode temperature. Carrier gas ranges differ by ion transfer tube type (HCITT: 3.5–7.7 L/min, default 4.6 L/min; ITT: 0.7–4.3 L/min, default 1.2 L/min). Typical cooling flow: ~5 L/min for nanoflow and ~10 L/min for high‑flow conditions. FAIMS gas supply recommendation: 99.5% pure N2 at ≥20 L/min and 100 psi for installation.
• Mechanical and operational design: One‑way electrode assembly for simplified handling, quick install/uninstall without breaking vacuum, and easy disassembly for cleaning. Electrical requirements: 100–240 VAC, 50/60 Hz, 2.0 A. Environmental recommended operating range: functional 15–32 °C, optimal 18–27 °C.

Used instrumentation

The FAIMS Pro Duo is compatible with a broad set of Thermo mass spectrometers and chromatography systems, enabling seamless integration into existing platforms. Documented MS compatibility includes:

• Orbitrap Exploris series: 120, 240, 480
• Orbitrap Tribrid series: ID‑X, IQ‑X, Fusion, Fusion Lumos, Eclipse
• TSQ series: Altis, Quantis
• Vanquish UHPLC and general direct infusion setups; chromatographic flow compatibility 0.1 µL/min to 1000 µL/min

Software compatibility includes FreeStyle (for CV data handling and CV maxima extraction), Proteome Discoverer, Compound Discoverer, LipidSearch, TraceFinder, Biopharma Finder, and Chromeleon (with version requirements noted in vendor documentation) to support qualitative and quantitative processing and targeted method generation.

Main results and discussion (performance highlights)

• Improved selectivity and signal‑to‑noise: The FAIMS stage reduces chemical background and separates coeluting isobaric or chemically similar species, increasing detectability for low‑abundance analytes.
• Increased ion transmission: The curved electrode geometry and optimized gap improve transmission relative to traditional planar FAIMS designs, balancing sensitivity and resolving power.
• Wide flow‑rate compatibility: Supports nano‑ to high‑flow LC and direct infusion, enabling the same FAIMS device to be used across discovery proteomics, targeted quantification, and small‑molecule analyses.
• Rapid CV switching enables targeted multiplexed workflows: With CV switching as low as 25 ms on HCITT instruments, the interface supports on‑column CV scanning and integration with scheduled SRM/PRM routines and TMT workflows where fast alternation between CVs is beneficial.
• Automated CV optimization: Two workflows — an automated Tune routine for general CV optimization and an on‑line chromatographic CV optimization for targeted TSQ workflows — facilitate method development by extracting optimal CVs per analyte and importing them into instrument methods.

Benefits and practical applications

• Proteomics: Improved depth and confidence in peptide identifications, reduced chemical noise, and enhanced performance for multiplexed TMT experiments.
• Lipidomics and small molecules: Enhanced separation of isomeric/isobaric species and lower limits of detection through background suppression.
• Targeted quantitative analysis: Dynamic CV optimization and fast switching improve selectivity and throughput for SRM/PRM workflows on TSQ instruments.
• Operational advantages: Quick installation/uninstallation without venting the MS and straightforward cleaning minimize instrument downtime and laboratory maintenance burden.

Future trends and potential applications

• Deeper integration with real‑time acquisition strategies: Combining fast CV switching with data‑independent acquisition (DIA) or intelligent acquisition engines will permit richer, interference‑reduced datasets in a single run.
• Automated and AI‑assisted CV selection: Machine learning could predict optimal CVs for classes of analytes or routine samples, reducing method development time and improving reproducibility.
• Extended multiplexing and throughput gains: Continued reductions in switching latency and improved ion transmission may enable more complex multi‑CV acquisition schemes without loss of duty cycle—beneficial for high‑throughput clinical and QA/QC labs.
• Broader analyte classes and native/structural MS: Adaptations may expand applicability to intact protein complexes, post‑translational modification localization, and improved separation for conformational isomers.

Conclusion

The FAIMS Pro Duo interface is a flexible, high‑performance differential ion mobility device engineered to increase selectivity and sensitivity across diverse mass spectrometry applications. Key design choices—reduced analytical gap, curved electrode geometry, nitrogen cooling, rapid CV switching, and ease of service—enable better detection of low‑abundance analytes, compatibility with both low and high LC flows, and streamlined integration into Thermo Scientific software ecosystems. These attributes make FAIMS Pro Duo a practical option for labs seeking improved analytical depth and throughput without extensive changes to existing workflows.

Reference

• Thermo Fisher Scientific. FAIMS Pro Duo interface: Product specifications (PS66008‑EN), 2021.