Enhancement of mass spectrometry performance for proteomic analyses using high‐field asymmetric waveform ion mobility spectrometry (FAIMS)

Abstract

Remarkable advances in mass spectrometry sensitivity and resolution have been accomplished over the past two decades to enhance the depth and coverage of proteome analyses. As these technological developments expanded the detection capability of mass spectrometers, they also revealed an increasing complexity of low abundance peptides, solvent clusters and sample contaminants that can confound protein identification. Separation techniques that are complementary and can be used in combination with liquid chromatography are often sought to improve mass spectrometry sensitivity for proteomics applications. In this context, high-field asymmetric waveform ion mobility spectrometry (FAIMS), a form of ion mobility that exploits ion separation at low and high electric fields, has shown significant advantages by focusing and separating multiply charged peptide ions from singly charged interferences. This paper examines the analytical benefits of FAIMS in proteomics to separate co-eluting peptide isomers and to enhance peptide detection and quantitative measurements of protein digests via native peptides (label-free) or isotopically labeled peptides from metabolic labeling or chemical tagging experiments.

A Novel Differential Ion Mobility Device Expands the Depth of Proteome Coverage and the Sensitivity of Multiplex Proteomic Measurements

“…The ability of FAIMS to reduce spectral complexity and precursor co-selection was advantageously exploited on previous generations of Orbitrap mass spectrometers to improve the accuracy and precision of quantitative measurements in proteomic analyses (55,56). In the present study, we compared the analytical benefits of FAIMS for multiplex proteomics using isobaric labeling with that of the synchronous precursor selection SPS-MS3 method which is commonly used to reduce peptide co-fragmentation and distorted reporter ion ratios (57,58).…”

“…Finally, FAIMS ion transit time is typically less than 50 ms and can be parallelized with 7 the LC-MS duty cycle. Previous studies have reported the benefits of FAIMS to improve proteome coverage and to reduce the extent of co-fragmentation that impedes the identification of low-abundance peptide ions (28)(29)(30)(31)(32)(33). The separation capability of FAIMS also facilitates the resolution of isomeric peptides, including histone variants and isomeric phosphopeptides (34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44).…”

Coupling Front-End Separations, Ion Mobility Spectrometry, and Mass Spectrometry For Enhanced Multidimensional Biological and Environmental Analyses

“…Both DTIMS and FAIMS have shown great potential in enhancing biological analyses when coupled with MS platforms by reducing chemical noise and detecting low-abundance analytes in complex biological matrices (126). DTIMS and FAIMS are also appealing because they offer analysis speeds that exceed condensed-phase separations by two to three orders of magnitude for rapid proteomic (127–129), lipidomic (130, 131), and other molecular analyses (109, 132). …”

Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13 m Serpentine Path Length Structures for Lossless Ion Manipulations Module

“…1,2 IMS applications at present include the detection of chemical warfare agents, 3–5 illicit drugs, 6–8 and explosives 9–13 and more recently have been combined with mass spectrometry (i.e., ion mobility (IM)-MS) for the detection, separation, and characterization of biomolecules, e.g., in metabolomics, 14–18 glyco-mics, 19–22 and proteomics applications. 23–36 A constraint of contemporary IMS technology is its limited ability to resolve species with similar mobilities (<2%) in a mixture, particularly in conjunction with achieving high sensitivity. 37,38 In drift tube IMS, the resolving power ( R ) is often defined by…”