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ProteomicsComBat HarmonizR enables the integrated analysis of independently generated proteomic datasets through data harmonization with appropriate handling of missing values
The integration of proteomic datasets, generated by non-cooperating laboratories using different LC-MS/MS setups can overcome limitations in statistically underpowered sample cohorts but has not been demonstrated to this day. In proteomics, differences in sample preservation and preparation strateg...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2022-05-23 | PXD027467 | Pride
Swath Metastudy Missing values Dda Dia Tmt Data integration Ffpe Silac Tissue Harmonisazion Fresh-frozen Combat 
UnknownHarmonizR: blocking and singular feature data adjustment improve runtime efficiency and data preservation.
Not available
S-EPMC11817103 | biostudies-literature
UnknownHarmonizR enables data harmonization across independent proteomic datasets with appropriate handling of missing values.
Not available
S-EPMC9209422 | biostudies-literature
UnknownHigh performance data integration for large-scale analyses of incomplete Omic profiles using Batch-Effect Reduction Trees (BERT).
Not available
S-EPMC12318123 | biostudies-literature
UnknownMass spectrometry-based proteomics of cerebrospinal fluid in pediatric central nervous system malignancies: a systematic review with meta-analysis of individual patient data.
Not available
S-EPMC10863112 | biostudies-literature
ProteomicsCDKL1 risk variants predispose to a connective tissue disorder with thoracic aortic aneurysm and dissection
Genetic factors are fundamental in the etiology of thoracic aortic aneurysm and dissection (TAAD), but the genetic cause is detected in only about 30% of cases. To define unreported TAAD-associated sequence variants, exome and gene panel sequencing was performed in 323 patients. We identified hetero...
ORGANISM(S): Homo sapiens (Human) 
2025-09-09 | PXD048044 | Pride
Cdkl1 Cgmp signaling Thoracic aortic aneurysm and dissection Arterial aneurysm and dissection Hereditary aortopathy Connective tissue disorder 
ProteomicsComparative wheat phosphoproteome profiling pinpoints high temperature-associated breeding markers
Elevated temperatures resulting from climate change are adversely impacting natural and crop ecosystems, necessitating the development of heat-tolerant crops. We established a framework to precisely identify wheat protein-phosphorylated sites associated with varying temperature sensitivities. Our fi...
ORGANISM(S): Triticum aestivum (Wheat) 
2024-12-02 | PXD047670 | Pride
Abiotic stress Temperature Wheat 
ProteomicsMultiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level
Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically very heterogenous. To unravel phenotypically relevant MB subtypes, we compiled a harmonized proteome dataset of 167 MBs and integrated findings with DNA methylation and N-glycome data. Six proteome MB sub...
ORGANISM(S): Homo sapiens (Human) 
2024-06-05 | PXD039319 | Pride
Medulloblastoma subtypes Mass spectrometry 850k Tnc Multiomics Wnt Palmd N-glycan Tric/cct N-glycome Myc Harmonizr Dna methylation Shh Proteome 
ProteomicsDirect 3D sampling of the embryonic mouse head: Layer-wise nanosecond infrared laser (NIRL) ablation from scalp to cortex for spatially resolved proteomics
Common workflows in bottom-up proteomics require homogenization of tissue samples giving to get access to the biomole-cules within the cells. The homogenized tissue samples often contain many different cell types, thereby representing an average of the natural proteome composition and rare cell type...
ORGANISM(S): Mus musculus (Mouse) 
2024-01-26 | PXD043011 | Pride
Nirl ablation Spatial proteomics Tissue sampling Bottom-up proteomics 
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