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MetabolomicsCustomized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow
Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions t...
2018-03-26 | MTBLS417 | MetaboLights
MetabolomicsMetaboKit: a comprehensive data extraction tool for untargeted metabolomics (Mouse liver assays)

We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identit...

2021-11-02 | MTBLS1266 | MetaboLights
MetabolomicsMetaboKit: a comprehensive data extraction tool for untargeted metabolomics (Standard mixture assay)

We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identit...

2021-11-05 | MTBLS1311 | MetaboLights
ProteomicsPhosphoprotein network analysis of white adipose tissues unveils deregulated pathways in response to high-fat diet
Despite wide efforts in the last decade, signaling aberrations associated with obesity remain enigmatic. Here, we carried out phosphoproteomic analysis of mouse white adipose tissues (WAT) upon low-fat diet (LFD) and high-fat diet (HFD) to dissect underlying molecular mechanisms of obesity. Of the 7...
ORGANISM(S): Mus musculus (Mouse) 
2016-05-20 | PXD002927 | Pride
Diet Mouse phosphoproteome 
ProteomicsEBprot: Bayesian Analysis of Labelling-based Quantitative Proteomics Data
Labelling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs) between biological samples. The current data analysis platform relies on protein-level ratios, where peptide-level ratios are averaged to yield a single summary ratio for each protein. In shotgu...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080742 | MassIVE
TranscriptomicsTranscription profiling of Saccharomyces cerevisiae pGAL1-MKS1, pGAL1-NNK1, and pGAL1-FMP48 overexpression
Analysis of the transcriptional effects of pGAL1-MKS1, pGAL1-NNK1, and pGAL1-FMP48 overexpression. BY4700 gal1::NAT ura3delta0 S. cerevisiae cells carrying a [pGAL1-MKS1-HA, URA3, CEN], [pGAL1-NNK1-HA, URA3, CEN], or [pGAL1-FMP48-HA, URA3, CEN] plasmid, or empty vector BG1805, were grown to early lo...
ORGANISM(S): Saccharomyces cerevisiae 
2010-05-25 | E-MEXP-2171 | biostudies-arrayexpress
ProteomicsAdjuvant Secretomes
Adjuvant-induced human monocyte secretome profiles reveal adjuvant- and age-specific protein signatures.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-07-20 | MSV000079960 | MassIVE
ProteomicsKOPI - Kinase inhibitor proteome impact analysis
Kinase inhibitors often exhibit on/off-target effects, and efficient data analysis is essential for assessing these effects on the proteome. We developed a workflow for rapidly performing such a proteomic assessment, termed as kinase inhibitor proteome impact analysis (KOPI). We demonstrate KOPI’s ...
ORGANISM(S): Homo Sapiens (human) 
2022-06-16 | PXD029924 | JPOST Repository
ProteomicsTaipale_HSP90_cochaperone_P77_VS1
This submission is part of the mass spectrometry datasets for the manuscript by Taipale et al. (HSP90 cochaperone interaction network). This submission contains files for the first batch (2011) of the files included in the manuscript, all acquired on a 5600 TripleTOF mass spectrometer. See the RE...
2013-08-02 | MSV000078466 | MassIVE
ProteomicsTaipale_HSP90_cochaperone_P77_VS3
This submission is part of the mass spectrometry datasets for the manuscript by Taipale et al. (HSP90 cochaperone interaction network). This submission contains files for the second batch (2012) of the files included in the manuscript, all acquired on a 5600 TripleTOF mass spectrometer. See the RE...
2013-08-02 | MSV000078465 | MassIVE
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