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ProteomicsCombining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition
In data independent acquisition, consistent, comprehensive MS1 and MS2 can be recorded. This enables statistical comparison based on the two quantitative levels.
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) Homo sapiens (Human) Mus musculus (Mouse) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) Caenorhabditis elegans 
2020-01-07 | PXD016647 | Pride
Controlled data sets Ms1 ms2 quantification Dia 
ProteomicsHigh precision iRT retention time prediction in the targeted analysis of data-independent acquisition and its impact on identification and quantitation
Targeted analysis of DIA data is a powerful mass spectrometric approach for comprehensive, reproducible and precise proteome quantitation. It requires a spectral library, which contains for all considered peptide precursor ions empirically determined fragment ion intensities and their predicted rete...
ORGANISM(S): Homo sapiens (Human) 
2016-07-14 | PXD004188 | Pride
Dia Retention time prediction 
ProteomicsAnalysis of 1,508 plasma samples of the DiOGenes study - Robust, single shot capillary flow data-independent acquisition to decipher proteomic profiles of weight loss and maintenance
Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies (1, 2), we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (D...
ORGANISM(S): Homo sapiens (Human) 
2019-04-05 | PXD013231 | Pride
Plasma proteomics Swath Library Single shot Clinical proteomics Stable isotope-based quantification High throughput Label-free quantification Data-independent acquisition 
ProteomicsOptimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the limitation of serial MS2 acquisition of data-d...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2017-10-27 | PXD005573 | Pride
Human dia proteomics 
ProteomicsEffect of LPS and the glucocorticoid dexamethasone on the mouse Bone Marrow Derived Macrophage Proteome
The concentrations and copy number of proteins in the mouse Bone Marrow Derived proteome was determined for control, 10 ng/mL LPS stimulation, and LPS stimulation plus the addition of 100 nM dexamethasone, after an incubation for 24 hours and with four biological replicates for each condition. Over ...
ORGANISM(S): Mus musculus (Mouse) 
2024-01-26 | PXD041375 | Pride
Innate immunity Glucocorticoid Macrophage Dexamethasone Mouse Type i interferon 
ProteomicsAPEX2 mediated proximity labeling to investigate the proximal proteome of mitochondria tethered ULK1 in wild type and fip200 knock down cells
The object of this project is to investigate the proximal proteome of ULK1 during mitophagy and the effects of a FIP200 knock down using the APEX2-mediated proximity labeling system. APEX2-ULK1 or APEX2 was fused to 2xFKBP-myc and stably expressed in a cell line stably expressing a truncated FIS1-FR...
ORGANISM(S): Homo sapiens (Human) 
2024-10-12 | PXD047277 | Pride
Fip200 Mitophagy Autophagy Frb-rapalog-fkbp interaction Ulk1 Apex2 Er 
ProteomicsCombining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition
In data independent acquisition, consistent, comprehensive MS1 and MS2 can be recorded. This enables statistical comparison based on the two quantitative levels.
ORGANISM(S): Arabidopsis Thaliana (ncbitaxon:3702) Escherichia Coli (ncbitaxon:562) Saccharomyces Cerevisiae (ncbitaxon:4932) Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) Caenorhabditis Elegans (ncbitaxon:6239) 
2020-01-30 | MSV000084864 | MassIVE
ProteomicsSurpassing 10,000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategy
Comprehensive proteome quantification is crucial for a better understanding of underlying mechanisms of diseases. Liquid chromatography mass spectrometry (LC-MS) has become the method of choice for comprehensive proteome quantification due to its power and versatility. Even though great advances hav...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-01-31 | MSV000084878 | MassIVE
ProteomicsComparison of DIA and TMT based protein quantification in complex background
Label free quantification (LFQ) and isobaric labelling quantification (ILQ) are among the most popular protein quantification workflows in discovery proteomics. Here, we compared the TMT 10-plex workflow to label free single shot data-independent acquisition (DIA) method on a controlled sample set. ...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2020-01-29 | MSV000084859 | MassIVE
ProteomicsOptimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results
Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the limitation of serial MS2 acquisition of data-d...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2020-01-30 | MSV000084874 | MassIVE
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