ArticleCell reports methods2023
A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline.
Article in Cell reports methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Profiling of Aggregated Amyloid β42-induced Proteomic Alterations in KOLF2.1J Induced Pluripotent Stem Cell-derived Neurons.bioRxiv : the preprint server for biology · 2026Article
- APOE genotypes differentially remodel the astrocytic lipid droplet proteome to shape lipid droplet dynamics.Nature communications · 2026Article
- Endothelial Cell Proteins as Biomarkers in Susac Syndrome.Annals of clinical and translational neurology · 2026Article
- SenCat: Cataloging human cell senescence through multi-omic profiling of multiple senescent primary cell types.Molecular cell · 2026Article
- A One Health Framework for Proteomics Across the Tree of Life to Advance Food Security, Animal Health, and Ecosystem Resilience.Proteomes · 2026Review
- Circulating cell type senescence signatures track distinct dimensions of health status and trajectories in human longitudinal cohorts.Cell reports · 2026Article
- Tuning Secretomes for Regenerative Medicine.Biology · 2026Review
- Microtubules in the axon are GDP bound but adopt a stable GTP-like expanded state.Nature structural & molecular biology · 2026Article
- Circulating Cell Type Senescence Signatures Reveal High-Resolution Health Status and Trajectories in Human Longitudinal Studies.medRxiv : the preprint server for health sciences · 2026Article
- SenCat: Cataloging human cell senescence through multiomic profiling of multiple senescent primary cell types.bioRxiv : the preprint server for biology · 2026Article
- Integrated Structural and Glycoproteomic Profiling Reveals Protein Conformational Remodeling and Biomarkers Across Alzheimer's Disease Progression.ACS central science · 2026Article
- Data-Independent Acquisition Enhancement of a Competitive Activity-Based Protein Profiling Platform for Kinase Inhibitor Screening.Journal of mass spectrometry : JMS · 2026Article
- In-depth analysis of data characteristics and comparative evaluation of dda and dia accuracy in label-free quantitative proteomics of biological samples.Clinical proteomics · 2025Article
- Multiplexed Data-Independent Acquisition-Based Proteomics Enabled by TMTpro Complementary Ions.Analytical chemistry · 2025Article
- Lysosomal proteomics reveals mechanisms of neuronal APOE4-associated lysosomal dysfunction.Autophagy · 2025Article
- Article
- Liquid Chromatographic and Mass Spectrometric Methods for Quantitative Proteomic Analysis from Single-Cell and Nanogram-Level Samples.Analytical chemistry · 2025Article
- Quantitative decoding of coupled carbon and energy metabolism in Pseudomonas putida for lignin carbon utilization.Communications biology · 2025Article
- Altered mRNA transport and local translation in i3Neurons with RNA-binding protein knockdown.Nucleic acids research · 2025Article
- TDP-43 pathology induces CD8bioRxiv : the preprint server for biology · 2025Article
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17 authors.
Funding
Abstract
Here, we present a standardized, "off-the-shelf" proteomics pipeline working in a single 96-well plate to achieve deep coverage of cellular proteomes with high throughput and scalability. This integrated pipeline streamlines a fully automated sample preparation platform, a data-independent acquisition (DIA) coupled with high-field asymmetric waveform ion mobility spectrometer (FAIMS) interface, and an optimized library-free DIA database search strategy. Our systematic evaluation of FAIMS-DIA showing single compensation voltage (CV) at -35 V not only yields the deepest proteome coverage but also best correlates with DIA without FAIMS. Our in-depth comparison of direct-DIA database search engines shows that Spectronaut outperforms others, providing the highest quantifiable proteins. Next, we apply three common DIA strategies in characterizing human induced pluripotent stem cell (iPSC)-derived neurons and show single-shot mass spectrometry (MS) using single-CV (-35 V)-FAIMS-DIA results in >9,000 quantifiable proteins with <10% missing values, as well as superior reproducibility and accuracy compared with other existing DIA methods.
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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.