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ProteomicsUniversal antimicrobial resistance detection from clinical bacterial isolates using proteomics
Antimicrobial resistance (AMR) is an increasing challenge for therapy and management of bacterial infections. Currently, antimicrobial resistance detection relies on phenotypic assays, which are performed independently of species identification. On the contrary, phenotypic prediction from molecular ...
ORGANISM(S): Klebsiella pneumoniae subsp. pneumoniae Salmonella enterica subsp. enterica serovar Typhimurium Salmonella enterica subsp. enterica serovar Infantis Enterococcus faecium Citrobacter freundii Escherichia coli Enterobacter cloacae subsp. cloacae 
2021-11-25 | PXD022425 | Pride
Carbapenemases Proteomics Lc-ms Mass spectrometry Antibiotic resistance mechanism Amr Bacteria Esbl Data-independent acquisition Mcr 
ProteomicsIncreasing proteome depth while maintaining quantitative precision in short gradient data-independent acquisition proteomics
The combination of short liquid chromatography (LC) gradients and data independent acquisition (DIA) by mass spectrometry (MS) has proven its huge potential for high-throughput proteomics. However, the optimization of isolation window schemes resulting in a certain number of data points per peak (DP...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2023-05-10 | PXD036451 | Pride
Isolation windows Dia Multi-species Short-gradient 
ProteomicsSample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics based on Acid Extraction
We report a universal detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even ...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) Bacillus cereus ATCC 10987 Escherichia coli Staphylococcus aureus 
2019-11-25 | PXD011189 | Pride
Speed Sample preparation Quantitative proteomics 
ProteomicsSurviving Martian Brines: Proteomic Analysis of Escherichia coli’s Adaptation to Perchlorate Stress
Brines, potentially formed by the deliquescence and freezing point depression of highly hygroscopic salts, such as perchlorates (ClO4-), may allow for the spatial and temporal stability of liquid water on present-day Mars. It is therefore of great interest to explore the microbial habitability of Ma...
ORGANISM(S): Escherichia coli 
2025-01-21 | PXD055273 | Pride
Mars Adaptation Astrobiology Brines Perchlorate Habitability 
ProteomicsPerchlorate-Specific Proteomic Stress Responses of Debaryomyces hansenii Could Enable Microbial Survival in Martian Brines
If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganism on the cellular level. Here we present a proteomic investigation o...
ORGANISM(S): Debaryomyces hansenii 
2023-06-06 | PXD033237 | Pride
Debaryomyces hansenii Astrobiology Mars Martian brines Perchlorate Stress response 
ProteomicsvPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics
Viral infections are commonly diagnosed by the detection of viral genome fragments or proteins using targeted methods such as PCR and immunoassays. In contrast, metagenomics enables the untargeted identification of viral genomes, expanding its applicability across a broader spectrum. In this study, ...
ORGANISM(S): Homo sapiens (Human) 
2025-08-04 | PXD055135 | Pride
Pathogen detection Virus identification Virome Virus 
ProteomicsSilence as a way of niche adaptation: mecC-MRSA with variations in the accessory gene regulator (agr) functionality express kaleidoscopic phenotypes
Functionality of the accessory gene regulator (agr) quorum sensing system is an important switch promoting either acute or chronic infections, mediated by the notorious opportunistic human and veterinary pathogen Staphylococcus aureus. Spontaneous alterations of the agr system are known to frequentl...
ORGANISM(S): Staphylococcus aureus 
2021-09-09 | PXD016486 | Pride
Bacteria Mecc-mrsa S. aureus 
ProteomicsIsolation window optimization using predicted libraries for deep and accurate proteome profiling by data-independent acquisition
In silico spectral library prediction of all possible peptides from whole organisms has a great potential for improving proteome profiling by data-independent acquisition and extending its scope of application. In combination with other recent improvements in the field, including sample preparation,...
ORGANISM(S): Candida albicans (Yeast) Homo sapiens (Human) Escherichia coli Staphylococcus aureus 
2020-08-25 | PXD017639 | Pride
Isolation window Predicted spectral library Speed Quantitative proteomics Data-independent acquisition 
ProteomicsProteomic identification of a Toxoplasma gondii sporozoite-specific antigen using HDAC3 inhibitor-treated tachyzoites as surrogate
The apicomplexan parasite Toxoplasma gondii has a complex life cycle involving multiple host species. Access to sexual stages and sporozoite-containing oocysts, essential for the parasite’s environmental transmission, is limited and requires animal experiments with cats. In vitro alternatives and re...
ORGANISM(S): Toxoplasma gondii Homo sapiens (Human) 
2025-05-07 | PXD055279 | Pride
Toxoplasma gondii Protein-protein interaction Ip-ms 
UnknownTree mortality submodels drive simulated long-term forest dynamics: assessing 15 models from the stand to global scale.
Not available
S-EPMC8609442 | biostudies-literature
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