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ProteomicsDevelopment of a method for quantitative analysis of in vivo interactions of pluripotency transcription factors Sox2, Oct4, Nanog by mass spectrometry
Protein-protein proximity of core pluripotency transcription factors plays an important role during cell reprogramming. Pluripotent embryonic stem (ES) cell identity is controlled by a trio of transcription factors: Sox2, Oct4, and Nanog. These proteins often bind to closely localized genomic sites....
ORGANISM(S): Homo sapiens (Human) 
2020-01-21 | PXD015756 | Pride
Mass spectrometry Oct4 Proximity utilizing biotinylation Transcription factors Sox2 Pluripotency 
ProteomicsEvaluating Mascot version and percolator-based rescoring on protein identification confidence, with a Mascot Distiller quantitation pipeline demonstration
We compared two versions of the Mascot search engine (2.6.2 and 3.1) and evaluated Mascot’s Percolator-based machine-learning rescoring (ML-boost) on HeLa and CHO LC-MS/MS datasets. The version change had little effect on identifications, while ML-boost substantially increased protein numbers, by ab...
ORGANISM(S): Cricetulus Griseus 
PXD085963 |
ProteomicsEffects of gradient lengths and acquisition frequency on the number of protein identifications in nanoflow LCMSMS of complex proteomic samples CHO
A liquid chromatography-tandem mass-spectrometry LC-MS/MS is now an indispensable method for shotgun proteomics. The combination of chromatographic separation and MS/MS identification provides valuable information about protein compositions from different biological samples. In this article, we exam...
ORGANISM(S): Cricetulus Griseus (ncbitaxon:10029) 
2024-06-05 | MSV000094944 | MassIVE
ProteomicsEffects of gradient lengths and acquisition frequency on the number of protein identifications in nanoflow LCMSMS of complex proteomic sample homo sapiens
A liquid chromatography-tandem mass-spectrometry LC-MS/MS is now an indispensable method for shotgun proteomics. The combination of chromatographic separation and MS/MS identification provides valuable information about protein compositions from different biological samples. In this article, we exam...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-06-05 | MSV000094936 | MassIVE
ProteomicsEffects of gradient lengths and acquisition frequency on the number of protein identifications in nanoflow LCMSMS of complex proteomic sample Escherichia coli
A liquid chromatography-tandem mass-spectrometry LC-MS/MS is now an indispensable method for shotgun proteomics. The combination of chromatographic separation and MS/MS identification provides valuable information about protein compositions from different biological samples. In this article, we exam...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) 
2024-06-05 | MSV000094935 | MassIVE
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