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ProteomicsShort Gradient Multi-CV FAIMSpro BoxCar DIA Facilitates Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana – Technical Dataset
A major limitation in quantitative time-course proteomics is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity, high dynamic samples such as plant extracts, this is tradeoff is especially apparent. To address this, we evaluate multiple composition voltage (CV) High Fie...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2024-01-26 | PXD038989 | Pride
Boxcardia Faimspro Arabidopsis thaliana Directdia 
ProteomicsShort Gradient Multi-CV FAIMSpro BoxCar DIA Facilitates Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana - Abiotic Stress Dataset
A major limitation in quantitative time-course proteomics is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity, high dynamic samples such as plant extracts, this is tradeoff is especially apparent. To address this, we evaluate multiple composition voltage (CV) High Fie...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2024-01-26 | PXD039004 | Pride
Boxcardia Faimspro Arabidopsis thaliana Directdia 
ProteomicsA mouse model of Fragile X Syndrome analyzed by quantitative proteomics: a comparison of methods
We have compared the performance of seven different strategies in the analysis of a mouse model of Fragile X Syndrome, involving the knockout of the fmr1 gene that is the leading cause of autism spectrum disorder. Focusing on the cerebellum, we show that Data-Independent Acquisition (DIA) and the TM...
ORGANISM(S): Mus musculus (Mouse) 
2023-08-21 | PXD039885 | Pride
Quantitative proteomics Boxcar Complementary ion quantification Dia Method comparison Label-free Tmt labeling Mouse brain proteomics Fragile x syndrome 
ProteomicsMaxDIA enables highly sensitive and accurate library-based and library-free data-independent acquisition proteomics (DIA data)
MaxDIA is a universal platform for analyzing data-independent acquisition proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves cutting-edge proteome coverage with significantly better coefficients of variation in protein quantification than other softwa...
ORGANISM(S): Candida albicans (Yeast) Homo sapiens (Human) Escherichia coli 
2021-07-09 | PXD022589 | Pride
Maxquant Benchmark 
UnknownQuantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana Using Short Gradient Multi-CV FAIMSpro BoxCar DIA.
Not available
S-EPMC10663867 | biostudies-literature
ProteomicsLibrary-free BoxCarDIA solves the missing value problem in label-free quantitative proteomics
The last decade has seen significant advances in the application of quantitative mass spectrometry-based proteomics technologies to tackle important questions in plant biology. The current standard for quantitative proteomics in plants is the use of data-dependent acquisition (DDA) analysis with or ...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2021-05-11 | PXD022448 | Pride
Arabidopsis Label-free Boxcar Dia Directdia Data acquisition 
UnknownMaxDIA enables library-based and library-free data-independent acquisition proteomics.
Not available
S-EPMC8668435 | biostudies-literature
ProteomicsComparative Analysis of Soybean Seed Proteome Based on Different Mass Spectrometry Acquisition Strategies
This study established a soybean seed proteome database and analyzed the raw mass spectrometry data of BoxCar and DIA on MaxQuant based on this database. Subsequently, the three mass spectrometry acquisition strategies, DDA, DIA and BoxCar, were compared for their depth of protein identification, da...
ORGANISM(S): Glycine Max 
PXD052278 |
ProteomicsMaxDIA enables highly sensitive and accurate library-based and library-free data-independent acquisition proteomics (DDA data)
MaxDIA is a universal platform for analyzing data-independent acquisition proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves cutting-edge proteome coverage with significantly better coefficients of variation in protein quantification than other softwa...
ORGANISM(S): Homo sapiens (Human) Escherichia coli Saccharomyces cerevisiae (Baker's yeast) 
2021-07-09 | PXD022582 | Pride
Maxquant Benchmark 
ProteomicsIntegrated systems-level proteomics and metabolomics reveals the diel molecular landscape of diverse Kale cultivars
Brassica oleracea and Brassica napus are comprised of diverse cultivars that collectively constitute an important global food source. Of those, the Brassica oleracea convar. acephala cultivar group containing var. sabellica and var. palmifolia and Brassica napus var. pabularia, collectively known as...
ORGANISM(S): Brassica napus (Rape) Brassica oleracea (Wild cabbage) 
2023-07-26 | PXD031780 | Pride
Light emitting diodes Boxcar dia proteomics Kale 
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