ArticleAnalytical chemistry2018
Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer.
Article in Analytical chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 papers.
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Who cites it
153 citing papers in PubMed.
- Proximity Proteomics Maps Candidate Cellular Uptake Pathways for Cell-Derived Nanovesicles.Small methods · 2026Article
- Chromatin remodeling coordinates chromosome compaction, synaptonemal complex architecture and meiotic crossing-over.Research square · 2026Article
- Toward simple, rapid, and deep plant proteome analysis with an in-cell proteomics strategy.Plant physiology · 2026Article
- Detecting protein higher-order structural changes using kinase as a phospho-labeler.Cell reports methods · 2026Article
- A Parallel Accumulation-Mobility Aligned Fragmentation Strategy Utilizing High-Resolution Ion Mobility for High-Performance Proteomics Analysis.Molecular & cellular proteomics : MCP · 2026Article
- MALDI-TOF Mass Spectrometry for Glioblastoma Secretome Biomarker Screening: A Review of Challenges and Perspectives.Current issues in molecular biology · 2026Review
- Advanced Phosphoproteomics Depth and Quantitative Performance Using an Integrated noFAIMS-FAIMS Approach.Rapid communications in mass spectrometry : RCM · 2026Article
- Single-Injection Multi-Omics Analysis by Direct Infusion Mass Spectrometry.Angewandte Chemie (International ed. in English) · 2026Article
- Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling.Nature communications · 2026Article
- Low-resolution FAIMS for increased peptide coverage in low-load and single-cell proteomics.Scientific reports · 2026Article
- In-Cell Proteomics Enables High-Resolution Spatial and Temporal Mapping of Early Xenopus tropicalis Embryos.Molecular & cellular proteomics : MCP · 2026Article
- Review
- Development and Modification of Ion Mobility Mass Spectrometry Instrumentation for Enhanced Analysis of Biological Molecules.Journal of the American Society for Mass Spectrometry · 2025Review
- Toward simple, rapid, and deep plant proteome analysis with an in-cell proteomics strategy.bioRxiv : the preprint server for biology · 2025Article
- Extracting informative glycan-specific ions from glycopeptide MS/MS spectra with GlyCounter.bioRxiv : the preprint server for biology · 2025Article
- Boosting Quantification of N-Glycans by an Enhanced Isobaric Multiplex Reagents for Carbonyl-Containing Compound (SUGAR) Tagging Strategy.Journal of the American Society for Mass Spectrometry · 2025Article
- Analysis of FAIMS for the study of affinity-purified protein complexes using the orbitrap ascend tribrid mass spectrometer.Molecular omics · 2025Article
- Characterization of Pharmaceutical Transformation Products by High-Field Asymmetric Waveform Ion Mobility and Infrared Ion Spectroscopy Coupled to Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2025Article
- Article
- Simple In-Cell Processing Enables Deep Proteome Analysis of Low-InputAnalytical chemistry · 2025Article
93 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Liquid chromatography (LC) prefractionation is often implemented to increase proteomic coverage; however, while effective, this approach is laborious, requires considerable sample amount, and can be cumbersome. We describe how interfacing a recently described high-field asymmetric waveform ion mobility spectrometry (FAIMS) device between a nanoelectrospray ionization (nanoESI) emitter and an Orbitrap hybrid mass spectrometer (MS) enables the collection of single-shot proteomic data with comparable depth to that of conventional two-dimensional LC approaches. This next generation FAIMS device incorporates improved ion sampling at the ESI-FAIMS interface, increased electric field strength, and a helium-free ion transport gas. With fast internal compensation voltage (CV) stepping (25 ms/transition), multiple unique gas-phase fractions may be analyzed simultaneously over the course of an MS analysis. We have comprehensively demonstrated how this device performs for bottom-up proteomics experiments as well as characterized the effects of peptide charge state, mass loading, analysis time, and additional variables. We also offer recommendations for the number of CVs and which CVs to use for different lengths of experiments. Internal CV stepping experiments increase protein identifications from a single-shot experiment to >8000, from over 100 000 peptide identifications in as little as 5 h. In single-shot 4 h label-free quantitation (LFQ) experiments of a human cell line, we quantified 7818 proteins with FAIMS using intra-analysis CV switching compared to 6809 without FAIMS. Single-shot FAIMS results also compare favorably with LC fractionation experiments. A 6 h single-shot FAIMS experiment generates 8007 protein identifications, while four fractions analyzed for 1.5 h each produce 7776 protein identifications.
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