ArticleCell systems2022
Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering.
Article in Cell systems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 91 citations in OpenAlex.
- Optimization of trap column properties and loading conditions for proteome profiling of single-cell-level sample inputs.Analytical and bioanalytical chemistry · 2026Article
- Reproducible-by-design: Romics Processor, a FAIR ecosystem for multi-omics and spatial-omics analysis.bioRxiv : the preprint server for biology · 2026Article
- A 3D spatial proteomic map of the human pancreatic islet microenvironment.Research square · 2026Article
- Multi-Tiered µDicer Enables Protein-Preserving Microdissection at 10 µm Resolution.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Single-cell proteomics of Arabidopsis leaf mesophyll reveals dynamic protein responses to water-deficit stress.Genome biology · 2026Article
- A Spatial Proteomics Approach to Isolate and Analyze Amyloid Proteins Using Laser Capture Microdissection and Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The pursuit of ultrasensitive phosphoproteomics to unravel signalling in rare cells.Communications biology · 2025Review
- High-Throughput Label-free Single-Cell Proteomics Enabled by Multicolumn NanoLC with a 5-min Cycle Time.Research square · 2025Article
- Single-Islet Proteomics Maps Pseudo-Temporal Islet Immune Responses and Dysfunction in Stage 1 Type 1 Diabetes.bioRxiv : the preprint server for biology · 2025Article
- SLB-msSIM: A Spectral Library-Based Multiplex Segmented SIM Platform for Single-Cell Proteomic Analysis.Proteomics · 2025Article
- Single-cell proteomics using mass spectrometry.Cell genomics · 2025Review
- scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data.Genome biology · 2025Article
- Data-Independent Acquisition Shortens the Analytical Window of Single-Cell Proteomics to Fifteen Minutes in Capillary Electrophoresis Mass Spectrometry.Journal of proteome research · 2025Article
- Trends in Mass Spectrometry-Based Single-Cell Proteomics.Analytical chemistry · 2025Review
- Advancements in Single-Cell Proteomics and Mass Spectrometry-Based Techniques for Unmasking Cellular Diversity in Triple Negative Breast Cancer.Proteomics. Clinical applications · 2025Review
- Review
- Spatial Proteomics towards cellular Resolution.Expert review of proteomics · 2024Article
- Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.Journal of proteome research · 2024Review
- Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting.Nature communications · 2024Article
- Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements.Trends in molecular medicine · 2024Review
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
Single-cell proteomics (scProteomics) promises to advance our understanding of cell functions within complex biological systems. However, a major challenge of current methods is their inability to identify and provide accurate quantitative information for low-abundance proteins. Herein, we describe an ion-mobility-enhanced mass spectrometry acquisition and peptide identification method, transferring identification based on FAIMS filtering (TIFF), to improve the sensitivity and accuracy of label-free scProteomics. TIFF extends the ion accumulation times for peptide ions by filtering out singly charged ions. The peptide identities are assigned by a three-dimensional MS1 feature matching approach (retention time, accurate mass, and FAIMS compensation voltage). The TIFF method enabled unbiased proteome analysis to a depth of >1,700 proteins in single HeLa cells, with >1,100 proteins consistently identified. As a demonstration, we applied the TIFF method to obtain temporal proteome profiles of >150 single murine macrophage cells during lipopolysaccharide stimulation and identified time-dependent proteome changes. A record of this paper's transparent peer review process is included in the supplemental information.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.