FAIMS Pro Duo Interface

Overview

Overcome background interference to improve the analytical performance of your LC-MS methods with the Thermo Scientific FAIMS Pro Duo interface. Introduce high field asymmetric ion mobility spectrometry (FAIMS) into your existing workflows to leverage orthogonal selectivity to increase sample coverage, extend quantitative dynamic range, and expand research opportunities, quickly and easily.

Highlights

Maximum usability and selectivity for a broad range of mass spectrometry workflows

The FAIMS Pro Duo interface extends differential ion mobility to a wide range of applications from small molecules to intact proteins analyzed by direct infusion or with chromatographic separation using 100 nL/min to 1 mL/min flow rates. The FAIMS Pro Duo interface can be operated using the Thermo Scientific TSQ and TSQ Plus; Thermo Scientific Orbitrap Exploris; and Thermo Scientific Orbitrap Tribrid mass spectrometers. The impact that the FAIMS Pro and FAIMS Pro Duo interfaces have had on research can be summarized by contributing to over 1000 journal publications covering over 26 different applications.

The FAIMS Pro Duo interface integrated with the Thermo Scientific Orbitrap Ascend Tribrid mass spectrometer

Precursor ions of interest formed at the ionization source and introduced into the FAIMS Pro Duo interface are selectively transmitted through the interface to the ion transfer tube and into the mass spectrometer, based on the Compensation Voltage (CV) setting, while other ions are attenuated or filtered out.

Streamlined instrument software simplifies experimental settings for optimal FAIMS selectivity

Instrument control software facilitates quick and accurate determination of optimal Compensation Voltage (CV) settings for the FAIMS Pro Duo interface. Easy-to-use methods can be performed using direct infusion of purified standards or large-scale optimization of endogenous compounds following online separation. Either approach provides methods to cover a wide range of CV settings to determine optimum settings for targeted compounds or general settings for compound classes.

Increases the depth of analysis without the extra work

Minimize the time, expense, and variability of offline fraction, protein extraction or enrichment by leveraging online gas-phase fractionation prior to ion introduction into the mass spectrometer. Leveraging CV settings as well as electrode temperature can modify ion transmission through the FAIMS Pro Duo interface to reach experimental objectives.

Improve workflow robustness through the novel electrode geometry

The optimized cylindrical geometry substantially increases ion transmission to the mass spectrometer with short residence times, allowing multiple CV settings per data acquisition method. The positioning of the center electrode blocks the direct line of sight for ions formed in the source to the entrance of the mass spectrometer, blocking neutrals and unwanted ions to increase workflow robustness in the presence of complex samples.

Easy to install, use, and maintain

One-way assembly and installation can be performed without breaking the instrument vacuum, which makes cleaning the FAIMS Pro Duo interface or moving between Thermo Scientific mass spectrometers seamless. A simple and uniform calibration routine ensures ultimate usability to acquire high-quality data for users of all skill levels.

Webinars

Balancing key proteome profiling objectives

Maximizing proteome coverage with quantitative accuracy while driving sample throughput.

Increasing proteome coverage and confidence in proteome profiling

Using FAIMS selectivity to improve method sensitivity and comprehensiveness.

Driving improved LOQ measurements

Leveraging orthogonal selectivity to reduce background interference.

Expanding single-cell proteomics performance

New developments in MS-based single-cell proteomics.

Novel top-down protein imaging

FAIMS selectivity supporting liquid extraction surface analysis (LESA) for imaging protein distributions.

Balancing key profiling objectives

Balancing key proteome profiling objectives

Maximizing proteome coverage with quantitative accuracy while driving sample throughput.

Extending global proteome profiling

Increasing proteome coverage and confidence in proteome profiling

Using FAIMS selectivity to improve method sensitivity and comprehensiveness.

Driving improved LOQ measurements

Driving improved LOQ measurements

Leveraging orthogonal selectivity to reduce background interference.

Expanding single-cell proteomics performance

Expanding single-cell proteomics performance

New developments in MS-based single-cell proteomics.

Novel top-down protein imaging

Novel top-down protein imaging

FAIMS selectivity supporting liquid extraction surface analysis (LESA) for imaging protein distributions.

Ordering information

Resources

To expand your LC-MS workflow capabilities without expanding large amounts of resources, you can introduce orthogonal selectivity to reach your goals.

Instructional video: See how FAIMS selectivity works

The FAIMS Pro Duo interface utilizes differential ion mobility to introduce spatial ion selectivity, increasing the LC-MS peak capacity. This instructional video shows how ions enter and move through the interface towards the entrance of the mass spectrometer using a novel cylindrical electrode assembly.

Instructional video: How to care for your FAIMS Pro Duo interface

The unique design of the FAIMS Pro Duo interface not only boosts productivity through the introduction of differential ion mobility but presents operational simplicity. This video demonstrates simple maintenance routines with the calibration procedures.

Expanding bottom-up proteomics applications based on FAIMS selectivity

Leveraging surrogate peptides to characterize proteomes for differential protein analysis remains a key research approach. Inclusion of the FAIMS Pro interface in 2018 demonstrated increased proteome coverage through orthogonal selectivity. Recent research has focused on developing expanded applications using the FAIMS Pro Duo interface for not only discovery applications, but library building and quantitation. Suppression of background ions increases the dynamic range for normal loading amounts as well as low sample loading amounts to perform single-cell proteomics.

Application notes

Journal articles

Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering. Woo et al. Cell Syst. 2022, 13(5), 426-434
The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies. Sweet, Steve et al. Sci. Rep. 2022, 12, 13876
Improved Sensitivity of Ultralow Flow LC–MS-Based Proteomic Profiling of Limited Samples Using Monolithic Capillary Columns and FAIMS Technology. Ivanov, Alexander, et al. Anal. Chem. 2020, 92(21), 14702
Getting more out of FLAG-Tag co-immunoprecipitation mass spectrometry experiments using FAIMS. Ang, Ching-Seng et al. J. Proteome. 2022, 254(15), 104473
A fully automated FAIMS-DIA proteomic pipeline for high-throughput characterization of iPSC-derived neurons. Reilly, Luke et al. bioRxiv. 2021, 11(24) 469921
Combination of FAIMS, Protein A Depletion, and Native Digest Conditions Enables Deep Proteomic Profiling of Host Cell Proteins in Monoclonal Antibodies. O’Brien, Reid et al. Anal. Chem. 2020, 92(15), 10478
Rapid targeted quantitation of protein over expression with direct infusion shotgun proteome analysis (DISPA-PRM). Trujillo, Edna A., et.al. Anal. Chem. 2022, 94(4), 195

Intact/top-down analysis of large biomolecules

Intact analysis of biomolecules presents significant challenges for mass spectral detection due to the expanded charge state envelops and higher charge states that dilute the corresponding mass spectral signal. In addition, performing the analysis in complex biological samples results in significant overlap of non-targeted charge state envelops and solvent ions prohibiting confident characterization. To overcome these challenges, substantial effort is devoted to development of sample enrichment and/or purification strategies requiring greater time and cost. Introducing the FAIMS Pro Duo interface into the existing mass spectral method can overcome these challenges through differential ion mobility. Due to the increased charge states formed during biomolecule ionization, greater differences in ion mobility can be realized between the target biomolecules and background ions reducing the need for additional sample preparation while improving qualitative and quantitative analysis. Initial studies have focused on intact/top-down protein and proteome analysis but has recently expanded coverage to include oligonucleotides.

Journal articles

Deeper protein identification using field asymmetric ion mobility spectrometry in top-down proteomics. Gerbasi, Vincent et al. Anal. Chem. 2021, 93(16), 6323
Comprehensive LESA Mass Spectrometry Imaging of Intact Proteins by Integration of Cylindrical FAIMS. Griffiths, Ryan L., et al. Anal. Chem. 2020, 92(4), 2885
Enhancing top-down proteomics of brain tissue with FAIMS. Fulcher, James M., et al. J. Proteome Res. 2021, 20(5), 2780
Expanding the epitrascriptomic RNA sequencing and modification mapping mass spectrometry toolbox with field asymmetric waveform ion mobility and electrochemical elution liquid chromatography. Lauman, Richard, et al. bioRxiv 2022 10.28.514273

Increasing the dynamic range of functional proteomics analysis using the FAIMS Pro Duo interface

Detection and quantification of proteins in samples can be used as putative biomarkers helping to define biological states or conditions. However, analysis of protein interactions through cross-linking or post-translational modifications (PTMs) analysis such as phosphorylation or glycosylation can provide additional details defining biological states. Detection of these peptides in the presence of complex biological samples becomes challenging due to relatively low copy numbers. Biological studies using the FAIMS Pro Duo interface demonstrate increased selectivity for these peptides resulting in expanded coverage as well as enhanced characterization and quantitation.

Journal articles

FAIMS enhances the detection of PTM crosstalk sites. Adoni, Kish R., et al. J Proteome Res. 2022, 21(4), 930
Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer. Muehlbauer, Laura K., et al. Anal Chem. 2020, 92(24), 15959
Leveraging Parameter Dependencies in High-Field Asymmetric Waveform Ion-Mobility Spectrometry and Size Exclusion Chromatography for Proteome-wide Cross-Linking Mass Spectrometry. Sinn, Ludwig R., et al. Anal Chem. 2022, 94(11) 4627
Mucinomics as the next frontier of mass spectrometry. Rangel-Angarita, Valentina and Malaker, Stacy A. ACS Chem. Biol. 2021, 16(10), 1866

Targeted research opportunities using the FAIMS Pro Duo interface: focusing on small molecules and clinical research analysis

While FAIMS selectivity has been primarily used to enhance sample coverage, orthogonal selectivity can also be optimized for target compound transmission increasing quantitative dynamic range in the presence of complex biological samples. Clinically relevant compounds are often small molecules that can present additional challenges for operation of the FAIMS Pro Duo interface due to the decreased difference in physicochemical properties of the target compounds and background ions requiring different strategies to optimize experimental parameters. The benefit of including the FAIMS Pro Duo interface not only improves signal-to-noise ratios for target compounds but substantially increases the robustness of the mass spectrometer.

Application notes

Technical notes

Journal articles

Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV2-coronavirus from clinical specimens. Renuse, Santosh et al. eBioMedicine 2021, 69, 103465
Improved Thyreostatic Drug Detection in Animal Tissues Using Liquid Chromatography–High-Field Asymmetric Waveform Ion Mobility Spectrometry–Mass Spectrometry. Purves, Randy W., et al. J. Agric. Food Chem. 2022, 70(16), 4785