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ProteomicsHigher-throughput and sensitive immunopeptidomics profiling
We developed a refined sample preparation workflow that is fully optimized to process low-input and crude samples in 96-well plates, aiming to combine high-throughput with maximal sensitivity. We implemented a miniaturized and automated workflow in a 96-well format using the Tecan Resolvex® A200 liq...
ORGANISM(S): Homo sapiens (Human) 
2026-04-03 | PXD062352 | Pride
Immunopeptidomics Bacterial infection 
GenomicsSelection for improved energy efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Brassica napus 
2015-06-28 | E-GEOD-65578 | biostudies-arrayexpress
TranscriptomicsPhotorespiratory stress low CO2 conditions
Six weeks old Arabidopsis plants were transferred to a low CO2 (100 ppm) environment during 24 hours and compared to control plants kept under ambient CO2 conditions. Limited CO2 availability will cause higher rates of photorespiration and affect the plant redox homeostasis. We studied the transcrip...
ORGANISM(S): Arabidopsis thaliana 
2016-06-10 | E-GEOD-80158 | biostudies-arrayexpress
ProteomicsSalmonella Typhimurium SL1344 proteogenomics
We describe how searching chimeric spectra with post-processing including MS²PIP-derived features aids the identification of hypothetical and unannotated proteins. We apply our workflow to the well-characterized human bacterial pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) and va...
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 
2020-10-13 | PXD016377 | Pride
Proteogenomics Ribosome profiling Ribo-seq Post-processing Salmonella typhimurium sl1344 
ProteomicsCysQuant: simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry
Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function, urging the need for accurate cysteine oxidation quantification to decode protein redox regulation. Here, we present a novel approach called CysQuant that enables simultaneous quantification...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2023-07-21 | PXD043895 | Pride
Cysteine oxidation Redox Data-independent acquisition Plexdia 
ProteomicsRelease of the plant peptide hormone PEP1 from its precursor PROPEP1 in response to physical damage is due to Ca2+-dependent activation of METACASPASE4.
Physical damage to cells leads to the release of immunomodulatory peptides in order to elicit wound defense responses in the surrounding tissue. In Arabidopsis thaliana, the intracellular PROPEP1 protein precursor is processed into the mature 2.5 kDa PEP1 before release. However, the maturation mech...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2019-04-18 | PXD010816 | Pride
Arabidopsis Protease Metacaspase4 Proteolysis Propep Physical damage 
ProteomicsSynthetic peptides - Data-independent immunopeptidomics discovery of low-abundant bacterial epitopes
Synthetic peptide standards for validation of diaPASEF-only immunopeptides of Listeria monocytogenes. More info see PXD063560.
ORGANISM(S): Listeria monocytogenes EGD 
2025-09-16 | PXD068414 | Pride
Listeria monocytogenes Immunopeptidomics Synthetic peptides Diapasef 
TranscriptomicsTranscriptional responses in Arabidopsis seedlings after hydrogen peroxide treatment
Excessive levels of reactive oxygen species (ROS) cause cellular stress through damage to all classes of macromolecules and result in cell death. However, ROS can also act as signaling molecules in various biological processes. In plants, ROS signaling has been documented in environmental stress per...
ORGANISM(S): Arabidopsis thaliana 
2016-06-10 | E-GEOD-80200 | biostudies-arrayexpress
ProteomicsN-terminomics Proteogenomics - N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana
Proteogenomics is a research field where proteome data is used to improve gene annotation. To achieve this, customized protein databases are constructed to match proteomic data. We perform a proteogenomic analysis using N-terminal COFRADIC data in order to identify novel translational initiation sta...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2017-04-24 | PXD004896 | Pride
Arabidopsis thaliana Proteogenomics N-terminal cofradic Ribosome profiling Positional proteomics Ribo-seq 
TranscriptomicsSelection for improved energy efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes [RNA-Seq]
Integrated breeding strategies are used to increase both the yield potential and stability of crops. Most of these approaches have a direct genetic basis. The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear. A better understanding of th...
ORGANISM(S): Brassica napus 
2015-06-28 | E-GEOD-65572 | biostudies-arrayexpress
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