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MetabolomicsIntegrating two chromatographies in a co-fractionation mass spectrometry approach improved protein-metabolite interactions (PMIs) mapping capabilities and revealed novel protein-ligand pairings in Escherichia coli.
The protein-metabolite interactome remains understudied. We previously developed a co-fractionation mass-spectrometry-based approach called PROMIS to address this gap. PROMIS relies on size separation chromatography of protein-metabolite complexes from lysates, followed by proteomics and metabolomic...
2025-04-25 | MTBLS9098 | MetaboLights
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 
ProteomicsIn-depth proteome analysis of human ascites using high-pH peptide fractionation
For in-depth profiling, ascites from patients with benign disease or gastric cancer were subjected to high-resolution mass spectromtery analysis. By high-pH peptide fractionation, 3481 protein groups were identified in 72 LC-MS/MS runs.
ORGANISM(S): Homo sapiens (Human) 
2018-04-16 | PXD003351 | Pride
Ascites High-ph peptide fractionation Gastric cancer 
Proteomicsmouse microglia using High-pH fractionation and LC-MS/MS
To build a reference proteome, we established a BV-2 microglial proteome to a depth of 5494 unique protein groups using a novel strategy that combined FASP, StageTip-based high pH fractionation, and high-resolution mass spectrometry quickly and cost-efficiently. By bioinformatics analysis, the BV-2 ...
ORGANISM(S): Mus musculus (Mouse) 
2013-09-11 | PXD000168 | Pride
Mouse High-ph fractionation Microglia Lc-ms/ms 
ProteomicsDevelopment of a high-pH reversed-phase well plate for peptide fractionation and deep proteome analysis of cells and exosomes
Development of a high-pH reversed-phase well plate for peptide fractionation and deep proteome analysis of cells and exosomes
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-07-21 | MSV000087860 | MassIVE
ProteomicsProteomic analysis of human dentin matrix extracts by peptide-level high-pH reverse-phase fractionation
Proteomics research has increasingly focused on human cells, tissues, and fluids; however, comprehensive data regarding dental tissues remain limited. Dentin, a mineralized component of the tooth, contains structural proteins and bioactive molecules that, upon release, can modulate pulp cell acti...
ORGANISM(S): Homo sapiens (Human) 
2026-03-23 | PXD070849 | Pride
Dentin  dentin matrix  proteomics  extracellular matrix  mass spectrometry  regenerative endodontics 
ProteomicsHuman follicular fluid proteomic and peptidomic composition quantitative studies by SWATH-MS methodology. Applicability of high pH RP-HPLC fractionation
Analysis of proteomic composition of human follicular fluid (hFF) has been proposed as a potential tool of oocyte quality evaluation. In order to develop an efficient method to investigate the hFF proteome and peptidome components, we applied a prefractionation scheme of hFF material consisting of ...
ORGANISM(S): Homo sapiens (Human) 
2018-03-19 | PXD008073 | Pride
Human Follicular fluid Fractionation Swath-ms 
ProteomicsComprehensive evaluation of different TiO2-based phosphopeptide enrichment and fractionation methods for phosphoproteomics
We performed a comprehensive evaluation of four different TiO2-based phosphopeptide enrichment methods using different non-phosphopeptide excluders. Then, two phosphopeptide fractionation methods, including the ammonia-based and the TEA based high pH reversed-phase fractionation, are also evaluated.
ORGANISM(S): Homo Sapiens 
2022-06-02 | PXD034264 |
ProteomicsComparison of fractionation proteomics for local SWATH library building
For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. Th...
ORGANISM(S): Homo sapiens (Human) 
2017-07-04 | PXD006190 | Pride
Library building Comparative study Swath-ms Fractionation proteomics Hesc 
ProteomicsMining Missing Membrane Proteins by High-pH Reverse Phase StageTip Fractionation and Validation by Multiple Reaction Monitoring Mass Spectrometry
Several significant efforts have been made in the past decade to map all human proteome. However, more than 3000 proteins are grouped as missing having no evidence of translation. Membrane protein annotation of the current missing proteins list showed 34%to be missing membrane proteins, which are ch...
ORGANISM(S): Homo sapiens (Human) 
2015-07-27 | PXD002224 | Pride
High-ph reverse phase Stagetip Missing proteins Lung cancer 
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