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ProteomicsOpen database searching enables the identification and comparison of glycoproteomes without defining glycan compositions prior to searching
Mass spectrometry has become an indispensable tool for the characterisation of glycosylation across biological systems. Our ability to generate rich fragmentation data of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag be hide. This is especially ...
ORGANISM(S): Campylobacter fetus subsp. fetus Burkholderia cenocepacia J2315 Burkholderia pseudomallei (strain K96243) Acinetobacter baumannii 
2020-06-24 | PXD018587 | Pride
Wide tolerant database searching Bacterial glycosylation Open searching Glycosylation Glycopeptides Post-translational modifications Proteomics Atypical glycosylation 
ProteomicsA mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides
Less than half of all MS/MS spectra acquired in shotgun proteomics typically result in a confident peptide match. Here we present an ultra-tolerant Sequest database search that allowed peptide matching even with modifications of unknown masses up to ±500 Da. From an HEK293 cell proteome-wide datase...
ORGANISM(S): Homo sapiens (Human) 
2015-06-03 | PXD001468 | Pride
Sequest Large scale Modifications Proteomics 
ProteomicsTowards an upgraded honey bee (Apis mellifera L.) genome annotation using proteogenomics.
The honey bee is a key pollinator in many agricultural operations as well as a model organism for studying the genetics and evolution of social behaviour. The Apis mellifera genome has been sequenced and annotated twice over, enabling proteomics and functional genomics methods for probing relevant a...
ORGANISM(S): Mus musculus (Mouse) Homo sapiens (Human) Apis mellifera (Honeybee) Drosophila melanogaster (Fruit fly) Saccharomyces cerevisiae (Baker's yeast) Caenorhabditis elegans 
2016-01-18 | PXD002275 | Pride
Honey bees Proteogenomics Mass spectrometry Gene annotation Apis mellifera 
ProteomicsOryza sativa cv. Nipponbare and Oryza barthii as unexpected tolerance and susceptibility sources against Schizotetranychus oryzae (Acari: Tetranychidae) mite infestation
Cultivated rice (Oryza sativa L.) is frequently exposed to multiple stresses, including Schizotetranychus oryzae mite infestation. Rice domestication has narrowed the genetic diversity of the species, leading to a wide susceptibility. This work aimed to observe the response of two wild rice species ...
ORGANISM(S): Oryza barthii Oryza sativa (Rice) 
2021-09-09 | PXD020940 | Pride
Wild species Protease inhibitors Resistance Proline Osmotin 
ProteomicsE. coli source tracking - A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation
We report a novel, peptide identification-free shotgun proteomics workflow as a bacterial fingerprinting method. This method uses a similarity-clustering algorithm to segregate the mass spectra that are presumably derived from individual peptide speciess and merge them into discrete units of consens...
ORGANISM(S): Escherichia coli 
2015-10-05 | PXD001646 | Pride
73 e. coli strains from different animal hosts(cow  pig  dog and human)  environmental samples  ltq 
ProteomicsTLR9-activated B cells imprint adoptively transferred CD8+ T cells with potent tumor immunity and persistence
Here we report a new way to reverse the tolerant state of adoptively transferred CD8+ T cells against melanoma through ex vivo expansion with the TLR9 agonist CpG. CpG-generated T cells elicited potent immunity without co-administration of high dose IL-2 or vaccination, which are adjuvants classical...
ORGANISM(S): Mus musculus (Mouse) 
2022-02-22 | PXD022909 | Pride
T cells adoptive cell transfer therapy toll-like receptors melanoma b cells 
ProteomicsNeutrophil depletion experiment in ischemia reperfusion mouse model
To elucidate the role of neutrophils in the molecular alterations observed after I/R, we performed an experiment of I/R in neutrophil-depleted mice. Neutrophil depletion was performed by anti-Ly6G injection and IgG was used as vehicle. We have performed an unbiased, open-search analysis of the oxida...
ORGANISM(S): Mus musculus (Mouse) 
2024-05-24 | PXD045756 | Pride
Ischemia reperfusion Mouse Heart tissue Quantitative proteomics 
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