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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
ProteomicsIn Situ Cross-linking Based Co-Fractionation Mass Spectrometry (XL-CoFrac-MS)
We developed an in situ cross-linking coupled reversed-phase liquid chromatography-based co-fractionation mass spectrometry (XL-CoFrac-MS) platform to analyze drug-induced protein complex changes. A software tool, ChromaQuant, was built to automate chromatographic peak quantification. Using RS4;11 l...
ORGANISM(S): Homo Sapiens 
2025-08-23 | PXD067673 |
ProteomicsBlue Native PAGE co-fractionation of purified human endosomes
EndoMAP aims to systematically dissect the human endosomal protein complexes. To purify endosomes from human cells, a modified Endo-IP protocol was developed to be compatible with complexomics methodologies and evaluated by DIA-MS. Three independent biological replicates of human endosomes purified ...
ORGANISM(S): Homo sapiens (Human) 
2025-03-29 | PXD054684 | Pride
Co-fractionation Human Endosomes Bn-page Endomap 
ProteomicsMultiplexed interactome analysis reveals the molecular architecture of the human prefoldin network
The majority of proteins are organized in protein complexes. Protein complexes represent an important cellular organizational layer, which regulate and catalyze most of the cellular processes. Within the field of proteomics several techniques such as Affinity Purification (AP) and co-fractionation (...
ORGANISM(S): Homo sapiens (Human) 
2024-03-11 | PXD035032 | Pride
Co-fractionation based profiling Dia Affinity purification coupled to mass spectrometry Size-based fractionation Protein complexes 
Proteomicsmini-Complexome Profiling, an FDR-controlled workflow for global targeted Detection of protein complexes (Heart Data)
Co-fractionation mass spectrometry experiments (CF-MS) using native-like protein separations such as Blue Native electrophoresis (BNE) or size exclusion chromatography (SEC) enable a global characterization of protein networks, and a better understanding of cellular functions. They do, however, pose...
ORGANISM(S): Mus musculus (Mouse) 
2024-07-25 | PXD049426 | Pride
Protein complexes Proteomics Blue native electrophoresis Protein-protein interactions Data-independent acquisition Systems biology 
Proteomicsmini-Complexome Profiling, an FDR-controlled workflow for global targeted Detection of protein complexes (Hek293 data)
Co-fractionation mass spectrometry experiments (CF-MS) using native-like protein separations such as Blue Native electrophoresis (BNE) or size exclusion chromatography (SEC) enable a global characterization of protein networks, and a better understanding of cellular functions. They do, however, pose...
ORGANISM(S): Homo sapiens (Human) 
2024-07-25 | PXD049340 | Pride
Protein complexes Proteomics Blue native electrophoresis Protein-protein interactions Data-independent acquisition Systems biology 
ProteomicsQuantative pTyr protein complex
Our current research focuses on the complex-centric quantification of pTyr protein complexes. We initially constructed a tri-functional probe based on pTyr superbinder (SH2-S) for the enrichment of pTyr protein complexes. The pTyr protein complexes were separated by ion exchange chromatography (IEC)...
ORGANISM(S): Homo Sapiens 
2024-05-31 | PXD052742 |
UnknownProteomic analysis of insulin secretory granules in INS-1 cells by protein correlation profiling.
Not available
S-EPMC6276070 | biostudies-literature
ProteomicsSEC-SWATH-MS HEK293 - Complex-centric proteome profiling by SEC-SWATH-MS
Increasingly, biochemical co-fractionation-based approaches are used to study interactomes and protein complexes at high throughput. The devised methods facilitate the qualitative assignment and prediction of hundreds of putative cellular assemblies in one experiment and without dependency on geneti...
ORGANISM(S): Homo sapiens (Human) 
2019-01-11 | PXD007038 | Pride
Size exclusion chromatography Mass spectrometry Swath Protein complexes 
ProteomicsExtensive Peptide Fractionation and y1 Ion-based Interference Detection Enable Accurate Quantification by Isobaric Labeling and Mass Spectrometry
Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from co-isolated ions, resulting in ratio compression. Here we report that the...
ORGANISM(S): Escherichia coli 
2022-02-28 | PXD005797 | Pride
Isobaric labeling Proteomics Tmt Mass spectrometry And ratio compression Itraq Lc-ms/ms 
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