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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 
UnknowntimsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery.
Not available
S-EPMC10913052 | biostudies-literature
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
ProteomicsABPP-HT* - Deep meets fast for activity-based profiling of deubiquitylating enzymes using advanced DIA mass spectrometry methodsABPP-HT* - Deep meets fast for activity-based profiling of deubiquitylating enzymes using advanced DIA mass spectrometry methods
Activity-based protein profiling (ABPP) uses a combination of activity-based chemical probes with mass spectrometry (MS) to selectively characterise a particular enzyme or enzyme class. ABPP has proven invaluable for profiling enzymatic inhibitors in drug discovery. When applied to cell extracts and...
ORGANISM(S): Homo sapiens (Human) 
2022-04-04 | PXD031848 | Pride
Data-independent acquisition mass spectrometry (dia) Drug discovery Proteomics Activitomics Mass spectrometry Chemical biology Deubiquitylating enzymes Ubiquitin Activity-based probes 
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 
ProteomicsABPP-HT - high-throughput activity-based profiling of deubiquitylating enzyme inhibitors in a cellular context
The potency and selectivity of a small molecule inhibitor are key parameters to assess during the early stages of drug discovery. In particular, it is very informative for characterizing compounds in a relevant cellular context in order to reveal potential off-target effects and drug efficacy. Activ...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) 
2021-02-24 | PXD023036 | Pride
Drug discovery Pharmacology Activitomics Deubiquitylating enzymes Ubiquitin Automation Activity-based probes 
ProteomicsExpanding glycopeptide identification with Match-Between-Glycans (MBG) in FragPipe
Glycosylation is one of the most important, but also most complex, post-translational modifications of proteins. Mass spectrometry-based glycoproteomics analysis offers a powerful approach to explore the fundamental roles of glycosylation, but achieving sufficient fragmentation for glycopeptide assi...
ORGANISM(S): Candida albicans (Yeast) Mus musculus (Mouse) Homo sapiens (Human) 
2026-09-01 | PXD074575 | Pride
Human plasma  glycoproteomics  n-glycopeptides  pasef  timstof  msfragger-glyco  fragpipe  ion mobility 
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 
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