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MetabolomicsMetabolic Footprinting of a Clear Cell Renal Cell Carcinoma in vitro Model for Human Kidney Cancer Detection
A protocol for harvesting and extracting extracellular metabolites from an in vitro model of human renal cell lines was developed to profile the exometabolome by means of a discovery-based metabolomics approach using ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass sp...
2018-11-14 | MTBLS737 | MetaboLights
TranscriptomicsGenome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting
So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells to generate a transcriptome-wide map of TISs in a human monocytic cell line. A neural network was tr...
ORGANISM(S): Homo sapiens 
2012-08-08 | E-GEOD-39561 | biostudies-arrayexpress
ProteomicsNanoparticles and photochemistry for Native-like transmembrane protein footprinting
Mass spectrometry based footprinting can probe higher order structure of proteins. We bond photocatalytic nanoparticles to a lipid bilayer that, upon laser irradiation, produce high local concentrations of radicals that penetrate the lipid layer made permeable by a simultaneous laser-initiated PB re...
ORGANISM(S): Homo sapiens (Human) 
2021-09-26 | PXD027819 | Pride
Footprinting Membrane protein 
TranscriptomicsThe ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome pr...
ORGANISM(S): Homo sapiens 
2012-07-26 | E-GEOD-37744 | biostudies-arrayexpress
TranscriptomicsIdentification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged t...
ORGANISM(S): Danio rerio 
2014-04-04 | E-GEOD-53693 | biostudies-arrayexpress
ProteomicsCarbene Footprinting Accurately Maps Binding Sites in Protein-Ligand and Protein-Protein Interactions
Specific interactions between proteins and their binding partners are fundamental to life processes. Differential protein footprinting using a new and efficient, photo-activated aryltrifluromethylcarbene probe together with mass spectrometry has been employed to identify protein-ligand and protein-p...
ORGANISM(S): Homo sapiens (Human) Gallus gallus (Chicken) 
2016-12-19 | PXD004971 | Pride
Lysozyme Carbene footprinting Usp5 Covalent labelling 
ProteomicsCarbene footprinting reveals binding interfaces of a multimeric membrane spanning protein
Mapping the interaction sites between membrane spanning proteins is a key challenge in structural biology. Here we develop and apply carbene footprinting technology to identify the interfacial sites of a trimeric membrane protein. We show how the footprinting probe is effectively incorporated into d...
ORGANISM(S): Escherichia coli 
2017-09-29 | PXD007207 | Pride
Footprinting Protein Carbene Lc-ms Membrane 
ProteomicsCampylobacter jejuni MOMP carbene footprinting
Using carbene footprinting, we map the MOMP-QPLEX interaction and show by complementary in silico docking that QPLEX enters the porin channel through interactions at the extracellular face, translocates down the channel through a dipole transverse electric field towards the opposite end and is relea...
ORGANISM(S): Campylobacter jejuni subsp. jejuni NCTC 11168-PO 
2022-09-26 | PXD035978 | Pride
Carbene footprinting Campylobacter jejuni Lc-ms/ms 
ProteomicsMapping the Interaction between Eukaryotic Initiation Factor 4A (eIF4A) and the Inhibitor Hippuristanol Using Carbene Footprinting and Mass Spectrometry
Protein-ligand interactions are central to protein activity and cell functionality. Improved knowledge of these relationships greatly benefits our understanding of key biological processes and aids in rational drug design towards the treatment of clinically relevant diseases. Carbene footprinting is...
ORGANISM(S): Homo sapiens (Human) 
2021-08-25 | PXD025105 | Pride
Protein footprinting Mapping ligand binding Carbene labelling 
ProteomicsDimethylthiourea as a Quencher in Hydroxyl Radical Protein Footprinting Experiments
Hydroxyl radical protein footprinting (HRPF) is a mass spectrometry (MS)-based method for studying protein structures, interactions, conformations, and folding. We evaluated dimethylthiourea (DMTU) as a replacement for catalase in quenching HRPF reactions. We observed that the DMTU is highly effecti...
ORGANISM(S): Escherichia coli 
2025-09-12 | PXD046435 | Pride
Hrpf Dimethylthiourea Quencher 
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