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ProteomicsPreferential phosphorylation on old histones during early mitosis in human cells
How histone posttranslational modifications (PTMs) are inherited through cell cycle remains poorly understood. Canonical histones are made in the S phase of cell cycle. Combining mass spectrometry-based technologies and stable isotope labeling by amino acids in cell culture (SILAC), we interrogate t...
ORGANISM(S): Homo sapiens (Human) 
2016-06-01 | PXD003709 | Pride
Mass spectrometry Mitosis Histone modifications Cell cycle Histone phosphorylation 
ProteomicsHistione HCD and CID datasets for evaluation of search engines
To identify confident spectra from histone peptides containing PTMs, we present a method in which one kind of modification is searched each time. We then combine the identifications of multiple search engines to obtain confident results. We find that two search engines, pFind and Mascot, identify mo...
ORGANISM(S): Homo sapiens (Human) 
2014-09-01 | PXD001118 | Pride
Proteomics Search engine Post-translational modification Data analysis Histone 
ProteomicsEpiProfile 2.0: a proteomics tool to quantify histone modifications by mass spectrometry
The histone LC-MS/MS data analysis is challenging due to the large number and variety of isobaric histone peptides, and the high dynamic range of histone peptide abundances. We introduce EpiProfile 2.0 to quantify histone post-translational modifications from mass spectrometry data, in which fragmen...
ORGANISM(S): Homo sapiens (Human) 
2018-05-29 | PXD004166 | Pride
Proteomics Post-translational modification Mass spectrometry Histone Quantification 
ProteomicsQuantifying histone PTMs by bottom-up MS
Histone post-translational modifications (PTMs) contribute to chromatin function through their chemical properties which influence chromatin structure, and their ability to recruit chromatin interacting proteins. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry (n...
ORGANISM(S): Homo sapiens (Human) 
2015-03-27 | PXD001541 | Pride
Proteomics Post-translational modification Isobaric peptide Retention time Histone Quantification 
ProteomicsIntegrated genomic and proteomic analyses identify stimulus-dependent molecular changes associated with distinct modes of skeletal muscle atrophy
Skeletal muscle atrophy is a debilitating condition that occurs with aging and disease but the underlying mechanisms are incompletely understood. Previous work determined that common transcriptional changes occur in muscle during atrophy induced by different stimuli. However, whether this holds true...
ORGANISM(S): Mus musculus (Mouse) 
2022-02-22 | PXD027464 | Pride
Proteomics Sarcopenia Cachexia Skeletal muscle Aging Atrophy 
ProteomicsInduction of muscle atrophy by tumor and dexamethasone regulates a distinct set of proteins from atrophy caused by aging
To assess changes in the muscle proteome that due to tumor burden and dexamethasone treatments and compare proteomic changes that occur in atrophy due to tumor burden and dexamethasone treatment with atrophy caused by aging. Regulators of muscle atrophy induced by diseases such as cancer or drugs su...
ORGANISM(S): Mus musculus (Mouse) 
2022-02-22 | PXD027490 | Pride
Proteomics Sarcopenia Cachexia Skeletal muscle Aging Atrophy 
ProteomicsPROTAC repurposing uncovers a noncanonical binding surface that mediates chemical degradation of nuclear receptors
MD-224 is a PROTAC that induces degradation of the human protein MDM2. However, we have found that it also induces degradation of a subset of nuclear receptors. DIA was performed to assess the overall specificity of MD-224 in 293T cells and the colorectal cancer cell line SNU-C4.
ORGANISM(S): Homo sapiens (Human) 
2025-09-18 | PXD066110 | Pride
Dia proteomics Pxr Protac Mdm2 Nuclear receptor Md-224 
ProteomicsProteomics profiling of human CD34+ cells from MDS bone marrow and healthy control cells
Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic disorders characterized by ineffective blood cell production and a high risk of progression to acute myeloid leukemia (AML). CD34+ hematopoietic stem and progenitor cells (HSPCs) play a critical role in the pathophysiology of...
ORGANISM(S): Homo sapiens (Human) 
2025-11-14 | PXD059857 | Pride
Dia proteomics Npm1 Myelodysplastic syndromes Leukemia Mds fbxo11 
ProteomicsProteomic profiling of FBXO11 protein complexes
FBXO11, a member of the F-box protein family, plays a critical role in cellular processes such as protein degradation, cell cycle regulation, and signaling pathways by serving as a substrate recognition component of the SKP1-Cullin-F-box (SCF) ubiquitin ligase complex. Dysregulation of FBXO11 has be...
ORGANISM(S): Homo sapiens (Human) 
2025-11-14 | PXD059844 | Pride
Proteomics Mass spectrometry Fbxo11 
ProteomicsA novel quantitative mass spectrometry platform for determining site-specific protein O-GlcNAcylation dynamics
Over the past decades, protein O-GlcNAcylation has been found to play a fundamental role in cell cycle control, metabolism, transcriptional regulation, and cellular signaling. Nevertheless, quantitative approaches to determine in vivo GlcNAc dynamics at a large-scale are still not readily available....
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-28 | MSV000080705 | MassIVE
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