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ProteomicsDeciphering the interplay of aflatoxin B1 and Epstein-Barr virus on the histone landscape in Burkitt Lymphoma cells
Aflatoxin B1 (AFB1), a potent dietary carcinogen, and Epstein-Barr virus (EBV), an oncogenic virus, are both implicated in cancer development, particularly in endemic regions. However, the combined effects of AFB1 exposure and EBV infection on the epigenetic landscape remain poorly understood. This ...
ORGANISM(S): Homo sapiens (Human) 
2025-10-23 | PXD060719 | Pride
Human Epstein-barr virus Aflatoxin b1 Hptms Burkitt lymphoma cells Lc-ms/ms 
ProteomicsComprehensive Histone Epigenetics (CHEpi): A mass spectrometry based screening assay to measure epigenetic toxicity
Epigenetics have taken center stage in the study of diseases such as cancer, diabetes, and neurodegeneration. For nearly thirty years, it has been known that cancer cells exhibit abnormal DNA methylation patterns. In contrast, the large scale analysis of histone posttranslational modifications (hPTM...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2020-10-12 | PXD019652 | Pride
Histone post-translational modifications Drug safety Toxicoepigenetics Pharmacoepigenetics Screening Proteomics Lc-ms/ms 
ProteomicsLarge scale toxicoepigenetics on histones: a mass spectrometry-based screening assay applied to developmental toxicity
Toxicoepigenetics is an emerging field that studies the toxicological impact of compounds on protein expression through heritable, non-genetic mechanisms, such as histone post-translational modifications (hPTMs). Due to substantial progress in the large-scale study of hPTMs, integration into the fie...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2022-02-17 | PXD026468 | Pride
Histone post-translational modifications Drug screening Toxicoepigenetics Developmental toxicity Lc-ms/ms 
ProteomicsHistone Sample Preparation for Bottom-Up Mass spectrometry: A Roadmap to Informed Decisions
we aimed to provide an objective roadmap for histone sample preparation wherein the most notable findings and most important metrics were highlighted. This roadmap included a Histone Coverage Tool that allows researchers to make a snapshot of public or in-house data in search of a protocol that suit...
ORGANISM(S): Bos taurus (Bovine) 
2021-04-27 | PXD024423 | Pride
Histone code  coverage  epigenetics  mass spectrometry  sample preparation  work-flow optimization  gingisrex 
ProteomicsAn experimental design to extract more information from MS-based histone studies
The combinatorial complexity of histone samples is manifold higher than what is usually encountered in proteomics. Consequently, a considerably bigger part of the acquired MSMS spectra remains unannotated to date. Adapted search parameters can dig deeper into the dark histone ion space, but the lack...
ORGANISM(S): Bos taurus (Bovine) 
2022-10-04 | PXD009910 | Pride
Histone post-translational modifications  lc-ms/ms  proteomics  identification  hdac 
ProteomicsMicro-topographies induce epigenetic reprogramming and quiescence in human mesenchymal stem cells
Biomaterials can control cell and nuclear morphology. Since the shape of the nucleus influences chromatin architecture, gene expression, and cell identity, surface topography can control cell phenotype. This study explores how surface topography influences nuclear morphology, histone modifications, ...
ORGANISM(S): Homo sapiens (Human) 
2022-12-03 | PXD037954 | Pride
Nucleus Epigenetics Biomaterials Mesenchymal stem cells Mechanobiology Dda 
ProteomicshSWATH: Unlocking SWATH’s full potential for an untargeted histone perspective
Mass spectrometry (MS) has become the technique of choice for large-scale analysis of histone post-translational modifications (hPTMs) and their combinatorial patterns, especially in untargeted settings where novel discovery-driven hypotheses are being generated. However, MS-based histone analysis r...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2019-08-27 | PXD011198 | Pride
Sequential window acquisition of all theoretical fragment ion spectra (swath)  data independent acquisition (dia)  histone  mass spectrometry (ms)  post-translational modification (ptm)  epigenetics 
ProteomicsUntargeted histone profiling of human embryonic stem cell conversion over time reveals fundamental epigenetic changes between pluripotent and naive states
Recently, various groups managed to isolate naïve human embryonic stem cell (hESC) state in vitro has come into acceptance. However, a thorough epigenetic characterization of this human ground state, defined as a state without any epigenetic restrictions, and how that compares to mouse is currently ...
ORGANISM(S): Homo sapiens (Human) 
2019-11-27 | PXD013067 | Pride
Human embryonic stem cells  pluripotency  naïve  epigenetics  histone modification  mass spectrometry 
ProteomicsIntegrated Multi-Omics Reveal Polycomb Repressive Complex 2 Restricts Human Trophoblast Induction
Human naive pluripotent stem cells have unrestricted lineage potential. Underpinning this property, naive cells are thought to lack chromatin-based lineage barriers. However, this assumption has not been tested. Here, we apply multi-omics to comprehensively define the chromatin-associated proteome, ...
ORGANISM(S): Homo sapiens (Human) 
2022-05-06 | PXD028162 | Pride
Histone post-translational modifications Hpscs Trophoblast Prc2 Lc-ms/ms 
ProteomicsCov-MS: a community-based template assay for clinical MS-based protein detection in Sars-Cov-2 patients
Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the f...
ORGANISM(S): SARS Coronavirus CDC#200301157 Homo sapiens (Human) 
2021-07-16 | PXD022550 | Pride
Sars-cov2 Covid-19 Dda Narrow-window dia 
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