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ProteomicsproteiNorm – A user-friendly tool for normalization and analysis of TMT and label-free protein quantification
The technological advances in mass spectrometry allow us to collect more comprehensive data with higher quality and increasing speed. With the rapidly increasing amount of data generated, the need for streamlining analyses becomes more apparent. Proteomic data is known to be often affected by system...
ORGANISM(S): Homo sapiens (Human) 
2021-09-09 | PXD018152 | Pride
Differential analysis Proteomics Normalization 
ProteomicsMulti-omics data integration reveals correlated regulatory features of triple negative breast cancer
Triple negative breast cancer is an aggressive type of breast cancer with very little treatment options. TNBC is very heterogeneous with large alterations in the genomic, transcriptomic, and proteomic landscapes leading to various subtypes with differing responses to therapeutic treatments. We appli...
ORGANISM(S): Homo sapiens (Human) 
2021-06-24 | PXD025238 | Pride
Multi-omics data integration Phosphoproteomics Triple negative breast cancer Histone posttranslational modification Rna-seq 
ProteomicsProteoViz: A toolset for interactive analysis of phosphoproteomics data
Quantitative proteomics generates large datasets with increasing depth and quantitative information. Even after data processing and statistical analysis, interpreting the results and relating their significance back to the system of study remains challenging. Often, this process is performed by sc...
ORGANISM(S): Homo sapiens (Human) 
2020-05-07 | PXD015606 | Pride
Phosphoproteomics Shiny Tmt 
ProteomicsQuantitative histone mass spectrometry identifies elevated histone H3 lysine 27 trimethylation in melanoma
Normal cell growth is characterized by a regulated epigenetic program that drives cellular activities such as gene transcription, DNA replication and DNA damage repair. Perturbation of this epigenetic program can lead to events such as mis-regulation of gene transcription and diseases such as cancer...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-07-22 | MSV000079979 | MassIVE
ProteomicsQuantitative analysis of the exoproteome from a Staphylococcus aureus LAC sarA mutant
The staphylococcal accessory regulator A (sarA) impacts the extracellular accumulation of Staphylococcus aureus virulence factors at the level of intracellular production and extracellular protease-mediated degradation. To assess the relative impact of these two functions, we previously used a prote...
ORGANISM(S): Staphylococcus aureus 
2018-11-21 | PXD009614 | Pride
Protease Sara Staphylococcus aureus Proteolysis Gelcms 
ProteomicsA phase separation mechanism underlies development of cancer and aberrant organization of three-dimensional chromatin structure
Development of cancer is intimately associated with genetic abnormalities that target proteins with intrinsically disordered regions (IDRs). In human hematological malignancies, recurrent chromosomal translocation of nucleoporin (NUP98 or NUP214) generates an aberrant chimera that invariably retains...
ORGANISM(S): Homo sapiens (Human) 
2021-04-22 | PXD023548 | Pride
Oncogenesis Homeodomain-containing transcription factor Intrinsically disordered regions (idrs) Bioid 
ProteomicsProteomic Analysis of an Arsenic Response Locus
Arsenic exposure is a global health problem. Millions of people encounter arsenic through contaminated drinking water, consumption, and inhalation. The arsenic response locus in budding yeast is responsible for the detoxification of arsenic and its removal from the cell. This locus constitutes a con...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-05-07 | PXD009902 | Pride
Arsenic Yeast Chap-ms Crispr 
ProteomicsTargeting mitochondria in the aged vasculature with SS-31, a proteomic study of brain microvessels.
Functional decline and structural alterations of the brain microvasculature are associated with cognitive impairment and development of dementias such as Alzheimer’s disease during aging. Although mechanisms of leading to microvascular changes during aging are not clear, the loss of mitochondria and...
ORGANISM(S): Mus musculus (Mouse) 
2024-01-26 | PXD038483 | Pride
Brain Tmt Mitochondria Microvessels 
ProteomicsProteomics Indicates Lactate Dehydrogenase is Prognostic in Acetaminophen-induced Acute Liver Failure Patients and Reveals a Role for LKB1-AMPK Signaling
Better biomarkers to predict death early in acute liver failure (ALF) are needed. To that end, we obtained early (study day 1) and later (day 3) serum samples from transplant-free survivors (n=28) and non-survivors (n=30) of acetaminophen (APAP)-induced ALF from the NIH-sponsored Acute Liver Failure...
ORGANISM(S): Homo sapiens (Human) 
2022-08-12 | PXD029576 | Pride
Liver regeneration Acute liver injury Drug-induced liver injury Biomarkers 
ProteomicsComprehensive Proteogenomic Analysis of the Anti-tumor Immunoactivity of a Novel Oncolytic Vesiculovirus in Hepatocellular Carcinoma
Oncolytic viruses can effectively unwrap a multimodal anti-tumor activity, encompassing a selective tumor cell killing and promoting a systemic anti-tumor immunity, making them a formidable foe against cancer. Among these, several members of the Rhabdoviridae family are particularly attractive as on...
ORGANISM(S): Mus musculus (Mouse) 
2025-05-06 | PXD035806 | Pride
Rhabdoviruses  hepatocellular carcinoma  jurona virus  oncolytic virotherapy 
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