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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
ProteomicsComparison of fractionation proteomics for local SWATH library building
For data-independent acquisition by means of sequential window acquisition of all theoretical fragment ion spectra (SWATH), a reference library of data-dependent acquisition (DDA) runs is typically used to correlate the quantitative data from the fragment ion spectra with peptide identifications. Th...
ORGANISM(S): Homo sapiens (Human) 
2017-07-04 | PXD006190 | Pride
Library building Comparative study Swath-ms Fractionation proteomics Hesc 
ProteomicsA comprehensive CHO SWATH-MS spectral library for accurate quantitative profiling of 10k proteins
A comprehensive Chinese hamster ovary (CHO)-cell specific spectral library, containing extensive information of high-quality spectral ions covering more than 10k CHO cell proteins, was constructed to provide confident and reproducible protein identification and quantification in data-independent SWA...
ORGANISM(S): Cricetulus griseus (Chinese hamster) (Cricetulus barabensis griseus) 
2020-07-20 | PXD016047 | Pride
Tripletof 6600 Swath-ms Chinese hamster ovary cells Lc-ms/ms 
ProteomicsRecombinant SWATH library for identification of low abundant human plasma proteins
Recombinant SWATH library for identification of low abundant human plasma proteins
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-11-04 | MSV000086411 | MassIVE
MetabolomicsDIAMetAlyzer allows automated false-discovery rate-controlled analysis for data-independent acquisition in metabolomics
The extraction of meaningful biological knowledge from high-throughput mass spectrometry data relies on limiting false discoveries to a manageable amount. For targeted approaches in metabolomics a main challenge is the detection of false positive metabolic features in the low signal-to-noise ranges ...
2022-09-05 | MTBLS1108 | MetaboLights
ProteomicsSpectral library of Drosophila melanogaster for SWATH-MS
A spectral library was built for Drosophila melanogaster. The spectral library allows reproducible quantification for thousands of peptides per SWATH-MS analysis. Proteins from Drosophila melanogaster embryo, adult flies were digested with trypsin using in-gel digestion and the peptides were fracti...
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) 
2017-05-11 | MSV000081075 | MassIVE
ProteomicsSpectral library of Solanum lycopersicum for SWATH-MS
A spectral library was built for Solanum lycopersicum. The spectral library allows reproducible quantification for thousands of peptides per SWATH-MS analysis. Proteins from Solanum lycopersicum pericarp were digested with trypsin using in-gel digestion and the peptides were fractionated by high-pH...
ORGANISM(S): Solanum Lycopersicum (ncbitaxon:4081) 
2017-05-11 | MSV000081074 | MassIVE
ProteomicsZebrafish SWATH-MS spectral library to quantify 10,000 proteins
Sequential window acquisition of all theoretical mass spectra (SWATH-MS) requires a spectral library to extract quantitative measurements from the mass spectrometry data acquired in data-independent acquisition mode (DIA). Large combined spectral libraries containing SWATH assays have been generated...
ORGANISM(S): Danio rerio (Zebrafish) (Brachydanio rerio) 
2018-12-18 | PXD010876 | Pride
Eye Intestine Heart Brain Liver Zebrafish Ovaries Spleen Testes Muscle 
ProteomicsA mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts
SWATH-MS enables accurate and reproducible label-free quantification of proteomes including in extensively studied model organisms such as the mouse. Here we present a comprehensive mouse reference spectral library (MouseRefSWATH) that allows quantification of up to 10,597 proteins (62.2% of mouse p...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2020-06-23 | PXD017209 | Pride
Swath-ms  breast cancer  dcis  mouse  human  xenograft model 
ProteomicsBuilding high-quality assay libraries for targeted analysis of SWATH MS data
Targeted proteomics by selected/multiple reaction monitoring or, on a larger scale, by SWATH MS relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of critical importance. Here we present a detailed protocol that has been successfu...
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2018-06-26 | MSV000082506 | MassIVE
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