ArticleJournal of proteome research2024
timsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery.
Article in Journal of proteome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
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- Proteomic Stability and Ex Vivo Compatibility of a Processed Phospholipoproteic Secretome-Derived Formulation.Pharmaceutics · 2026Article
- dia-PASEF Enables Rapid Profiling of the Human Secretome for Deeper Insights Into Cellular Dynamics and Inflammatory Mechanisms.Molecular & cellular proteomics : MCP · 2026Article
- Systematic optimization and benchmarking of synchro-PASEF for high-throughput phosphoproteome profiling.bioRxiv : the preprint server for biology · 2026Article
- Full-DIA enables complete single-cell proteomics from diaPASEF using deep learning.Genome biology · 2026Article
- Impact of Variations in Commercial Standard Operating Procedure on Plasma Proteome Recovery.Journal of proteome research · 2026Article
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- Automated Mag-Net Enrichment Unlocks Deep and Cost-Effective LC-MS Plasma Proteomics.Journal of proteome research · 2026Article
- ProteoBoostR: an interactive framework for supervised machine learning in clinical proteomics.Clinical proteomics · 2026Article
- From cellular heterogeneity to precision medicine: single-cell multi-omics in CNS disease research.Frontiers in cellular neuroscience · 2026Review
- Wastewater metaproteomics: tracking microbial and human protein biomarkers.ISME communications · 2026Article
- Evaluation of Nanoparticle-Based Plasma Enrichment on Individuals with Primary and Metastatic Pancreatic Cancer.Cancers · 2025Article
- Considering Measurement Time and Depth in diaPASEF Plasma Proteomics.Journal of proteome research · 2025Article
- Comparative evaluation of Olink Explore 3072 and mass spectrometry with peptide fractionation for plasma proteomics.Communications chemistry · 2025Article
- Proteomic Profiling of GLP-1-Mediated Cardioprotection in a Large Animal Model of Chronic Coronary Artery Disease.Medical research archives · 2025Article
- Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep.Analytical chemistry · 2025Article
- Thin-diaPASEF: diaPASEF for maximizing proteome coverage in single-shot proteomics.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mass spectrometry (MS) is a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide-ranging plasma protein concentrations, along with technical and biological variabilities, present significant challenges for deep and reproducible protein quantitation. Here, we evaluated the qualitative and quantitative performance of timsTOF HT and timsTOF Pro 2 mass spectrometers for analysis of neat plasma samples (unfractionated) and plasma samples processed using the Proteograph Product Suite (Proteograph) that enables robust deep proteomics sampling prior to mass spectrometry. Samples were evaluated across a wide range of peptide loading masses and liquid chromatography (LC) gradients. We observed up to a 76% increase in total plasma peptide precursors identified and a >2-fold boost in quantifiable plasma peptide precursors (CV < 20%) with timsTOF HT compared to Pro 2. Additionally, approximately 4.5 fold more plasma peptide precursors were detected by both timsTOF HT and timsTOF Pro 2 in the Proteograph analyzed plasma vs neat plasma. In an exploratory analysis of 20 late-stage lung cancer and 20 control plasma samples with the Proteograph, which were expected to exhibit distinct proteomes, an approximate 50% increase in total and statistically significant plasma peptide precursors (
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