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ProteomicsD-score - D-score: a search engine independent MD-score
Processing of the dataset of synthetic phosphopeptides by Savitzki et al. (MCP, 2011) using multiple search engines. Establishment of the D-score: a search engine independent MD-score.
ORGANISM(S): Homo sapiens (Human) 
2013-01-23 | PXD000021 | Pride
Localization score Phosphorylation Synthetic peptides 
ProteomicsC4PR_LIV Evaluation of Parameters for Confident Phosphorylation Site Localization using an Orbitrap Fusion Tribrid Mass Spectrometer
Confident identification of sites of protein phosphorylation by mass spectrometry (MS) is essential to advance understanding of phosphorylation-mediated signaling events. However, development of novel instrumentation requires that methods for MS data acquisition and its interrogation be evaluated an...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-03-31 | MSV000085203 | MassIVE
GenomicsMBD3 localization by ChIP-seq
Maintenance of chromatin structure is essential to eukaryotic life; dysregulation is known to be causal for aberrant development and disease. The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodel...
ORGANISM(S): Homo sapiens 
2013-10-31 | E-GEOD-44737 | biostudies-arrayexpress
TranscriptomicsLooking for mitochondrial associated RNA
We investigated the peripheral mitochondrial localization of nuclear-encoded mRNAs (MLR) in various conditions in which translation was inhibited or the mRNA binding protein context altered (Delta puf3). We used cell fractionation protocols together with microarray to assess the distribution of mRNA...
ORGANISM(S): Saccharomyces cerevisiae 
2008-06-01 | E-GEOD-9393 | biostudies-arrayexpress
ProteomicsMULocDeep: An Interpretable Deep Learning Model for Protein Localization Prediction with Sub-organelle Resolution
Prediction of protein localization plays an important role in understanding protein function and mechanism. A deep learning-based localization prediction tool (“MULocDeep”) assessing each amino acid’s contribution to the localization process provides insights into the mechanism of protein sorting an...
ORGANISM(S): Solanum tuberosum (Potato) Arabidopsis thaliana (Mouse-ear cress) Vicia faba var. faba 
2022-02-15 | PXD019987 | Pride
Protein localization prediction Shotgun proteomics Protein targeting Plant mitochondria isolation Deep learning 
ProteomicsC4PR_LIV Evaluation of Parameters for Confident Phosphorylation Site Localization using an Orbitrap Fusion Tribrid Mass Spectrometer
Confident identification of sites of protein phosphorylation by mass spectrometry (MS) is essential to advance understanding of phosphorylation-mediated signaling events. However, development of novel instrumentation requires that methods for MS data acquisition and its interrogation be evaluated an...
ORGANISM(S): Homo sapiens (Human) 
2019-09-27 | PXD007058 | Pride
Mascot/ptmrs Andromeda/ptmscore Orbitrap fusion Mass spectrometry Phosphoproteomics 
TranscriptomicsAn integrated genetic-epigenetic analysis of schizophrenia: Evidence for co-localization of genetic associations and differential DNA methylation
Background: Schizophrenia is a severe, highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite success in identifying genetic variants associated with schizophrenia, there remains uncertainty about the causal genes involved in disease p...
ORGANISM(S): Homo sapiens 
2016-08-01 | E-GEOD-80417 | biostudies-arrayexpress
ProteomicsCompartmental Localization and Clinical Relevance of MICA Antibodies after Renal Transplantation
Background: Studies recently support that non-HLA antigens could be additional targets of injury in organ transplant recipients, and MICA was associated with an increased risk of graft loss. Methods: A ProtoArray platform was used to study 37 serum samples from 22 unique patients (15 renal recipien...
ORGANISM(S): Homo sapiens 
2010-05-06 | E-GEOD-14329 | biostudies-arrayexpress
TranscriptomicsAn integrated genetic-epigenetic analysis of schizophrenia: Evidence for co-localization of genetic associations and differential DNA methylation.
Abstract Background: Schizophrenia is a severe, highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite success in identifying genetic variants associated with schizophrenia, there remains uncertainty about the causal genes involved in...
ORGANISM(S): Homo sapiens 
2016-08-01 | E-GEOD-84727 | biostudies-arrayexpress
UnknownComparative study on preoperative localization techniques using microcoil and hookwire by propensity score matching.
Not available
S-EPMC7262885 | biostudies-literature
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