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UnknownCalibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics.
Not available
S-EPMC8821666 | biostudies-literature
ProteomicsData-independent immunopeptidomics discovery of low-abundant bacterial epitopes
Mass spectrometry-based immunopeptidomics is a powerful approach to uncover peptides presented by human leukocyte antigen (HLA) molecules and serves as an important discovery tool guiding vaccine design and immunotherapies. While data-dependent acquisition (DDA) has been the standard for navigating ...
ORGANISM(S): Listeria monocytogenes Homo sapiens (Human) 
2025-08-21 | PXD063560 | Pride
Listeria Spectrum-centric Dia Immunopeptidomics Peptide-centric 
UnknowndiaTracer enables spectrum-centric analysis of diaPASEF proteomics data.
Not available
S-EPMC11696033 | biostudies-literature
ProteomicsdiaTracer enables spectrum-centric analysis of diaPASEF proteomics data
Data-independent acquisition (DIA) has become a widely used strategy for peptide and protein quantification in mass spectrometry-based proteomics studies. The integration of ion mobility separation into DIA analysis, such as the diaPASEF technology available on Bruker's timsTOF platform, further imp...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2024-05-19 | MSV000094803 | MassIVE
UnknownEdge-centric analysis of time-varying functional brain networks with applications in autism spectrum disorder.
Not available
S-EPMC12403185 | biostudies-literature
TranscriptomicsTMPRSS2-ERG, HDACs and EZH2 are involved in an AR-centric transcriptional circuitry that calibrates androgenic response for prostate cancer progression (gene expression data)
Deregulation of the Androgen Receptor (AR) transcriptional network is a common hallmark in prostate cancers. To achieve its precise transcriptional role, AR needs to co-operate specifically with a plethora of cofactors. In prostate cancers, AR transcription collaborators are frequently aberrantly ov...
ORGANISM(S): Homo sapiens 
2012-04-26 | E-GEOD-28948 | biostudies-arrayexpress
TranscriptomicsTMPRSS2-ERG, HDACs and EZH2 are involved in an AR centric transcriptional circuitry that calibrates androgenic response for prostate cancer progression (gene expression after ERG KD)
Deregulation of the Androgen Receptor (AR) transcriptional network is a common hallmark in prostate cancers. To achieve its precise transcriptional role, AR needs to co-operate specifically with a plethora of cofactors. In prostate cancers, AR transcription collaborators are frequently aberrantly ov...
ORGANISM(S): Homo sapiens 
2012-04-26 | E-GEOD-35540 | biostudies-arrayexpress
GenomicsTMPRSS2-ERG, HDACs and EZH2 are involved in an AR-centric transcriptional circuitry that calibrates androgenic response for prostate cancer progression (ChIP-Seq data)
Deregulation of the Androgen Receptor (AR) transcriptional network is a common hallmark in prostate cancers. To achieve its precise transcriptional role, AR needs to co-operate specifically with a plethora of cofactors. In prostate cancers, AR transcription collaborators are frequently aberrantly ov...
ORGANISM(S): Homo sapiens 
2012-04-26 | E-GEOD-28950 | biostudies-arrayexpress
TranscriptomicsTranscriptional Atlas of Cardiogenesis Maps Congenital Heart Disease Interactome
Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, the transcriptional landscape of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candida...
ORGANISM(S): Mus musculus 
2014-05-19 | E-GEOD-51483 | biostudies-arrayexpress
ProteomicsConsiderations for peptide and protein error rate control in large-scale targeted DIA analyses
Liquid chromatography coupled to tandem mass spectrometry has become the main method for high-throughput identification and quantification of peptides and the inferred proteins. Discovery proteomics commonly employs data-dependent acquisition in combination with spectrum-centric analysis. The accumu...
ORGANISM(S): Homo sapiens (Human) 
2017-08-03 | PXD004884 | Pride
Proteomics Error rate control Swath-ms Dia 
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