ArticleJournal of the American Society for Mass Spectrometry2024
Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP.
Article in Journal of the American Society for Mass Spectrometry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
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- JUMPlion improves quantitative DIA proteomics through ion-level recovery of missing values.bioRxiv : the preprint server for biology · 2026Article
- Lipidome and proteome of astrocyte and microglia ApoE lipoprotein reveal differences based on cell type and ApoE isoform.Journal of lipid research · 2026Article
- Cell type-resolved proteomics reveals intra- and intercellular signaling in Alzheimer's disease.bioRxiv : the preprint server for biology · 2026Article
- Single Plaque Proteomics Reveals the Composition and Dynamics of the Amyloid Microenvironment in Alzheimer's Disease.bioRxiv : the preprint server for biology · 2026Article
- Wastewater metaproteomics: tracking microbial and human protein biomarkers.ISME communications · 2026Article
- Ectopic engraftment of nociceptive neurons derived from hPSCs for pain relief and joint homeostasis.bioRxiv : the preprint server for biology · 2025Article
- SLB-msSIM: A Spectral Library-Based Multiplex Segmented SIM Platform for Single-Cell Proteomic Analysis.Proteomics · 2025Article
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Authors and funding
12 authors.
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Abstract
Accurate and precise quantification is crucial in modern proteomics, particularly in the context of exploring low-amount samples. While the innovative 4D-data-independent acquisition (DIA) quantitative proteomics facilitated by timsTOF mass spectrometers gives enhanced sensitivity and selectivity for protein identification, the diaPASEF (parallel accumulation-serial fragmentation combined with data-independent acquisition) parameters have not been systematically optimized, and a comprehensive evaluation of the quantification is currently lacking. In this study, we conducted a thorough optimization of key parameters on a timsTOF SCP instrument, including sample loading amount (50 ng), ramp/accumulation time (140 ms), isolation window width (20
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