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ProteomicsIsotopomer analysis of quiescent primary human fibroblasts
To ensure that the pool of precursor amino acids utilized for protein synthesis is completely labeled prior to the first labeling time-point, we conducted an isotopomer analysis. After adaption to media, cells were plated at a density of 500,000 cells per 10 cm plate. 8 days after plating, the confl...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080738 | MassIVE
ProteomicsIsotopomer analysis of quiescent primary human fibroblasts
To ensure that the pool of precursor amino acids utilized for protein synthesis is completely labeled prior to the first labeling time-point, we conducted an isotopomer analysis. After adaption to media, cells were plated at a density of 500,000 cells per 10 cm plate. 8 days after plating, the confl...
ORGANISM(S): Homo sapiens (Human) 
2016-06-14 | PXD003559 | Pride
Isotopomer analysis 15n labeling 
ProteomicsGlobal analysis of protein degradation rates in wildtype, Atg5-/- and Atg7-/- primary human fibroblasts
In this project, we employed a dynamic mass spectrometry-based proteomic approach to obtain global maps of basal autophagic flux in human primary fibroblasts (HCA2-hTert). The data provide a comparison of protein degradation rates between wildtype and autophagy deficient (Atg5-/- and Atg7-/-) cells....
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-28 | MSV000080694 | MassIVE
ProteomicsGlobal analysis of impact of Atg5 mutation on steady-state protein levels
This experiment analyzes the global impact of Atg5-/- mutation on steady-state protein levels by a standard SILAC experiment. WT+vector cells were grown in isotopically labeled media for multiple passages in order to fully label the proteome. Unlabeled Atg5-/- cells and labeled WT+vector cells were ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080752 | MassIVE
TranscriptomicsGenome-Wide Analysis In Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Techniques for systematically monitoring protein translation have lagged far behind methods for measuring mRNA levels. Here we present a ribosome profiling strategy, based on deep sequencing of ribosome protected mRNA fragments, that enables genome-wide investigation of translation with sub-codon re...
ORGANISM(S): Saccharomyces cerevisiae 
2009-02-12 | E-GEOD-13750 | biostudies-arrayexpress
ProteomicsStructural proteomics reveals that misfolded nascent proteins expose buried lysines for ubiquitination and rapid proteasomal degradation
In this study, we combine structural proteomics and time-resolved isotopic labeling to profile the modification sites, dynamics, and conformational properties of the human ubiquitinome.
ORGANISM(S): Homo sapiens (Human) 
2026-04-26 | PXD069668 | Pride
ProteomicsQuantitative analysis of in vivo methionine oxidation of the human proteome
A novel stable isotope labelling strategy was developed to quantify methionine oxidation in an unstressed human proteome. Cell extracts were oxidized with 18O labelled hydrogen peroxide following cell lysis in order to convert all unoxidized methionine residues to an oxidized version with a heavy l...
ORGANISM(S): Homo sapiens (Human) 
2019-12-09 | PXD014629 | Pride
Methionine oxidation Unstressed proteome Human cell line 
ProteomicsTime-resolved analysis of proteome dynamics by TMT-SILAC hyperplexing
In this project, a more efficient methodology for obtaining multi-timepoint kinetic data for proteome-wide analyses of protein turnover is developed and used to globally measure the kinetics of protein turnover in primary human fibroblasts (HCA2-hTert). This approach takes advantage of the multiplex...
ORGANISM(S): Homo sapiens (Human) 
2016-12-14 | PXD004725 | Pride
Tmt-silac Protein degrdation Tmt Proteome dynamics Silac Human primary fibroblasts Protein synthesis Hyperplexing 
ProteomicsGlobal analysis of protein degradation rates during prion infection
Prion diseases are rare, neurological disorders caused by the misfolding of the cellular prion protein (PrPC). The misfolded conformers aggregate into cytotoxic fibrils (PrPSc) that facilitate the conversion of additional prion proteins into their misfolded form. Intracellular PrPSc aggregates prima...
ORGANISM(S): Mus musculus (Mouse) 
2021-09-08 | PXD014577 | Pride
N2a Lysosome Cell culture Prion Rml 
ProteomicsAccurate proteome-wide measurement of methionine oxidation in aging mouse brains
The oxidation of methionine side chains has emerged as an important posttranslational modification of proteins. A diverse array of low-throughput and targeted studies have suggested that the oxidation of methionine residues in select proteins can have diverse impacts on cell physiology, ranging from...
ORGANISM(S): Mus musculus (Mouse) 
2022-05-23 | PXD031238 | Pride
Methionine oxidation Brain Mouse Aging 
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