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ProteomicsIndividualized proteogenomics reveals mutational landscape of melanoma patients in response to immunotherapy
Immune checkpoint inhibitors are used to restore or augment antitumor immune response and show great promise in treatment of melanoma and other types of cancers. However, only a relatively small percentage of patients are fully responsive to immune checkpoint inhibition, mostly due to tumor heteroge...
ORGANISM(S): Homo sapiens (Human) 
2022-02-16 | PXD028700 | Pride
Melanoma Mass spectrometry Proteogenomics Whole exome sequencing Immunotherapy 
ProteomicsAnalysis of Amino Acid Variants in Malignant Melanoma Cells Resistant to BRAF inhibition
Analysis of patient-specific nucleotide variants is a cornerstone of personalised medicine. Although only 2% of the genomic sequence is protein-coding, mutations occurring in these regions have the potential to influence protein structure and may have severe impact on disease aetiology. Of special i...
ORGANISM(S): Homo sapiens (Human) 
2021-11-04 | PXD018305 | Pride
Nucleotide sequencing Melanoma Mass spectrometry Proteogenomics Cancer Brafi resistance Phosphorylation 
ProteomicsParallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics Measurements
Increasing number of studies report the relevance of protein Ser/Thr/Tyr phosphorylation in bacterial physiology, yet the analysis of this type of modification in bacteria still presents a considerable challenge. Unlike in eukaryotes, where tens of thousands of phosphorylation events likely occupy m...
ORGANISM(S): Escherichia coli 
2018-06-05 | PXD008211 | Pride
Lc-msms Phosphoproteomics Tio2 Prm E.coli Qexactive Dda 
ProteomicsQuantitative proteomics links the intermediate filament nestin to vemurafenib resistance in melanoma cell lines
Targeted inhibition of mutated kinases using selective MAP kinase inhibitors in malignant melanoma often results in temporary improvement of the metastatic disease followed by rapid development of resistance. To gain insights in molecular processes that govern resistance, we performed SILAC-based qu...
ORGANISM(S): Homo sapiens (Human) 
2019-05-14 | PXD010683 | Pride
Cytoskeletal proteins Mass spectrometry Drug resistance Melanoma 
ProteomicsDeep proteogenomics of Bacillus subtilis provides insights into function and evolution of bacterial organism
"Bacillus subtilis is an aerobic, endospore forming, rod-shaped Gram-positive bacterium. It has a relatively small genome of 4,215,606 bp with 4,197 protein coding genes. It is considered a model organism to study natural phenomena, such as chromosome replication, sporulation or swarming motility. F...
ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168 
2018-11-28 | PXD008860 | Pride
Phylostratigraphy" "bacillus subtilis Proteogenomics Acetylation Shotgun proteomics Phosphorylation 
ProteomicsArginine phosphorylation during spore germination in bacteria
Arginine phosphorylation, an emerging protein modification, has been lately described to occur in B. subtilis and Staphylococcus aureus. The kinase responsible for arginine phosphorylation in B. subtilis was shown to be McsB, which counteracts the protein arginine phosphatase YwlE. Here we demonstra...
ORGANISM(S): Bacillus subtilis 
2022-03-02 | PXD011082 | Pride
Arginine phosphorylation Spore germination 
ProteomicsStoichiometry of the bacterial type III secretion export apparatus
Bacterial type III secretion systems are cell envelope-spanning effector protein-delivery machines essential for colonization and survival of many Gram-negative pathogens and symbionts. The membrane-embedded core unit of these secretion systems is termed needle complex. The needle complex is compose...
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 
2016-02-25 | PXD003113 | Pride
Mass spectrometry Stoichiometry Salmonella Type iii secretion 
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