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UnknowntimsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery.
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S-EPMC10913052 | biostudies-literature
ProteomicstimsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Cancer cohort dataset)
Mass spectrometry (MS) has emerged as a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide range of plasma protein concentrations along with technical and biological variabilities, continue to present significant challenges for deep and reproducible protein qu...
ORGANISM(S): Homo sapiens (Human) 
2024-01-16 | PXD047839 | Pride
Plasma Liquid chromatography Mass spectrometry Timstof Proteomics Biomarkers 
ProteomicstimsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Loading curve dataset)
Mass spectrometry (MS) has emerged as a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide range of plasma protein concentrations along with technical and biological variabilities, continue to present significant challenges for deep and reproducible protein qu...
ORGANISM(S): Homo sapiens (Human) 
2024-01-16 | PXD047854 | Pride
Plasma Liquid chromatography Mass spectrometry Timstof Proteomics Biomarkers 
ProteomicsPhosphoproteomics of Natural Killer (NK) Cells Stimulated with Fibrin and IL-15
Phosphoproteomic analysis of fibrin or IL-15 treated NK cells with timsTOF HT
ORGANISM(S): Homo sapiens (Human) 
2024-06-26 | PXD049692 | Pride
Timstof ht Nk cells Phoshoproteomics 
ProteomicstimsTOF HT improves protein identification and quantitative reproducibility for deep unbiased plasma protein biomarker discovery (Cancer cohort dataset)
Mass spectrometry (MS) has emerged as a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide range of plasma protein concentrations along with technical and biological variabilities, continue to present significant challenges for deep and reproducible protein qu...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2025-04-11 | MSV000097608 | MassIVE
ProteomicsSpectral Libraries in proteomics
evaluated approaches for building a spectral library in plasma proteomics on a timsTOF HT system. Furthermore, the relationship between measurement time, library depth and number of protein and peptide identification for semi-high throughput plasma proteomics applications was assessed.
ORGANISM(S): Homo sapiens (Human) 
2025-11-17 | PXD058337 | Pride
Timstof ht Plasma proteomics Spectral library Data independent acquisition 
ProteomicsLabel-free mass spectrometry-based proteomics of lung cancer FFPE glass slides
Formalin-fixed, paraffin-embedded (FFPE) is the most common method for preserving tissue material in the clinic with millions of specimens stored in biobanks around the world. However, FFPE samples present challenges for molecular profiling, including proteomics. Nonetheless, optimized sample prepar...
ORGANISM(S): Homo sapiens (Human) 
2026-05-26 | PXD072014 | Pride
Dia Ffpe Label-free proteomics Tumor Lung cancer Lc-ms/ms 
Proteomics260119_The bacterial phosphotransferase system-mediated rifampicin phosphorylation- ancestral links to rifampicin-inactivating enzyme2
Invitro reactions, supernatants and lysates analysed on TimsTOF HT for presence of phosphorylated Rif_2
ORGANISM(S): Bacillus Subtilis (ncbitaxon:1423) 
2026-01-19 | MSV000100512 | MassIVE
ProteomicsProteomics and phosphoproteomics analysis primary human airway epithelial cells exposed to unflavored electronic cigarette smoke
Phosphoproteomics analysis following unflavored e-cigarette exposed donor-derived primary lung epithelial cells from one donor and 3 technical replicates condition using a Bruker timsTOF HT mass spectrometer paired to a ThermoScientific Vaquish Neo HPLC. Conditions were room air (“Air”) or vape (“Va...
ORGANISM(S): Homo sapiens (Human) 
2025-07-14 | PXD059015 | Pride
Phosphoproteomics Primary lung cells Cigarette exposure 
ProteomicsHow blood matrices and sample preparation can influence blood marker discovery
While plasma and serum are increasingly being studied by using high throughput proteomics, it remains largely unexplored how different types of blood materials collected in the routine clinical diagnostics laboratories influence protein marker discovery. We compared the LC-MS/MS proteomic profiles o...
ORGANISM(S): Homo sapiens (Human) 
2026-01-12 | PXD066304 | Pride
Plasma Speed Mass spectrometry Enrich-ist Serum Lc−ms Ist R package mpwr Data-independent acquisition Perca Mag-net 
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