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ProteomicsAn omics-based metabolic model of methane-driven denitrification by aerobic methanotrophic bacteria
Methylomonas denitrificans is the first characterized organism that couples methane oxidation to nitrate reduction in pure culture without a partner. The aim of this study is to develop a metabolic model of methane driven nitrate respiration using a multi-level omics approach. Samples of M. denitrif...
ORGANISM(S): Methylomonas denitrificans 
2025-09-17 | PXD004041 | Pride
Methane Denitrification Omics Hypoxic Methylomonas Respiration Methanotroph Nitrous oxide Nitrate 
ProteomicsB-cell-specific MYD88 L252P expression causes a premalignant gammopathy resembling IgM MGUS
A highly recurrent, somatic L265P mutation in the TIR domain of the signaling adapter MYD88 constitutively activates NF-kB. It occurs in nearly all human patients with Waldenström’s macroglobulinemia (WM), a B cell malignancy caused by IgM-expressing cells. Here we introduced an inducible leucine to...
ORGANISM(S): Mus musculus (Mouse) 
2020-11-06 | PXD017292 | Pride
Lymphoid neoplasia 
ProteomicsHigher-Throughput Proteome Profiling Enabled by Parallelized Pre-Accumulation and Optimized Ion Processing in the Orbitrap Astral Zoom Mass Spectrometer -Tritation Injection time-Astral-zoom
High-throughput proteomics is critical for understanding biological processes, enabling large-scale studies such as biomarker discovery and systems biology. However, current mass spectrometry technologies face limitations in speed, sensitivity, and scalability for analyzing large sample cohorts. The...
ORGANISM(S): Homo sapiens (Human) 
2026-02-16 | PXD066924 | Pride
Dia 300 spd Injection time 
ProteomicsAnother layer of complexity in Staphylococcus aureus methionine biosynthesis control: Unusual RNase III-driven T-box riboswitch cleavage determines met operon mRNA stability and decay
In Staphylococcus aureus, de novo methionine biosynthesis is regulated by a unique hierarchical pathway involving stringent-response controlled CodY repression in combination with a T-box riboswitch and RNA decay. The T-box riboswitch residing in the 5' untranslated region (met leader RNA) of the S....
ORGANISM(S): Staphylococcus aureus (strain Newman) 
2021-08-10 | PXD020619 | Pride
Methionine biosynthesis Staphylococcus aureus Rna decay T-box riboswitch 
ProteomicsConsequences of Cyp2c44 deletion in the polyoma middle T (PyMT) breast cancer tumor proteome
Comparison of the proteome of intact primary breast cancer tumors from PyMT mice versus PyMTxCyp2c44-/- mice.
ORGANISM(S): Mus musculus (Mouse) 
2020-03-03 | PXD017336 | Pride
Breast cancer Macrophage Wdfy1 Lymphangiogenesis Lc-msms Metastasis 
ProteomicsAntisense affinity selection of the lncRNA NTRAS in HeLa lysate
Biochemical characterization of the hypoxia-induced long non coding RNA NTRAS. NTRAS was found to regulate cell cycle progression, in vitro sprouting angiogenesis, and the paracellular permeability in human umbilical vein endothelial cells (HUVECs). Using desthiobiotinylated 2’O-Me-RNA probes, we pu...
ORGANISM(S): Homo sapiens (Human) 
2022-04-25 | PXD030620 | Pride
Rna-protein-interaction Antisense affinity selection Lncrna 
ProteomicsConsequences of sEH deletion in the polyoma middle T (PyMT) breast cancer tumor proteome
The aim of this investigation was to study the consequences of interfering with soluble epoxide hydrolase (sEH) expression on tumor growth and metastasis in genetically modified animals that spontaneously generate tumors without the exogenous application of high concentrations of epoxide mediators o...
ORGANISM(S): Mus musculus (Mouse) 
2021-09-14 | PXD026214 | Pride
Breast cancer Macrophage Lymphangiogenesis Lc-msms Metastasis 
ProteomicsHigher-Throughput Proteome Profiling Enabled by Parallelized Pre-Accumulation and Optimized Ion Processing in the Orbitrap Astral Zoom Mass Spectrometer-300-500 SPD
High-throughput proteomics is critical for understanding biological processes, enabling large-scale studies such as biomarker discovery and systems biology. However, current mass spectrometry technologies face limitations in speed, sensitivity, and scalability for analyzing large sample cohorts. The...
ORGANISM(S): Homo sapiens (Human) 
2026-02-16 | PXD066718 | Pride
300spd 500spd 
ProteomicsOff-line high pH reversed-phase fractionation for in-depth phosphoproteomics
In this study we provide a detailed analysis of the physicochemical characteristics of phosphopeptides, which have been fractionated by off-line high pH chromatography (HpH) before subsequent titanium dioxide (TiO2) enrichment and LC-MS/MS analysis. Our results demonstrate that HpH is superior to st...
ORGANISM(S): Mus musculus (Mouse) 
2014-10-23 | PXD001404 | Pride
Phosphoproteomics  high ph reversed-phase  phosphorylation  peptides  enrichment  fractionation  titanium dioxide  orbitrap 
ProteomicsProteomics of NGF-TrkA signaling dynamics in neuroblastoma cells
We used quantitative mass spectrometry-based proteomics to unravel global nerve growth factor (NGF)-induced TrkA signaling dynamics at the interactome, phosphoproteome and proteome level. A tetracycline-inducible system for TrkA expression was generated in the human neuroblastoma cell line, SH-SY5Y....
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-31 | MSV000080834 | MassIVE
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