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ProteomicsC. elegans proteome identified by shotgun analysis
Not available
ORGANISM(S): Caenorhabditis elegans 
2009-06-01 | PRD000097 | Pride
ProteomicsPASS00589 - Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen treated 3D liver microtissues
The data set repersents a fair comparison of shotgun proteomics with HRM (swath type DIA). Additionally, a human liver microtissue was profiled with HRM.
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-12-19 | MSV000081828 | 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
ProteomicsLiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes
Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in developing optimized leads. We have developed a drug target deconvolution approach with an automated data analysis pipeline, based on limi...
ORGANISM(S): Homo sapiens (Human) Botryotinia fuckeliana (Noble rot fungus) (Botrytis cinerea) Saccharomyces cerevisiae (Baker's yeast) 
2020-09-09 | PXD015446 | Pride
Limited proteolysis Dia-ms Lip-ms Drug identification 
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
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
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 
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 (Human) 
2019-08-12 | PXD013658 | Pride
Liquid chromatography Dia Testis cancer Hybrid library 
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 
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