GNPS 20200908_maize seed_Negative ion mode
Ontology highlight
ABSTRACT:
INSTRUMENT(S): TripleTOF 5600
ORGANISM(S): Zea Mays (ncbitaxon:4577)
SUBMITTER: 
Zaifang Li
PROVIDER: MSV000086101 | GNPS |
REPOSITORIES: GNPS
Similar Datasets
Project description:Advancing Negative Ion Mode Proteomics. The main objective of the project is the exploration of the unconvetional negative ion mode for proteomics studies. In this work, we thoroughly studied the best chromatographic conditions for negative ion mode proteomics before testing different enzymatic digestion. The final goal is to establish the best working conditions in the negative polarity for negative ion mode. The method also refrains from any fragmentation events, which are unpredictable in negative ion mode.
2023-07-20 | PXD040583 | Pride
Project description:<p>Large-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (MetDNA) that expands metabolite annotations without the need for a comprehensive standard spectral library. MetDNA is based on the rationale that seed metabolites and their reaction-paired neighbors tend to share structural similarities resulting in similar MS2 spectra. MetDNA characterizes initial seed metabolites using a small library of MS2 spectra, and utilizes their experimental MS2 spectra as surrogate spectra to annotate their reaction-paired neighbor metabolites, which subsequently serve as the basis for recursive analysis. Using different LC-MS platforms, data acquisition methods, and biological samples, we showcase the utility and versatility of MetDNA and demonstrate that about 2000 metabolites can cumulatively be annotated from one experiment. Our results demonstrate that MetDNA substantially expands metabolite annotation, enabling quantitative assessment of metabolic pathways and facilitating integrative multi-omics analysis.</p><p><br></p><p><strong>Aging mouse liver positive mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS601' rel='noopener noreferrer' target='_blank'><strong>MTBLS601</strong></a>.</p><p><strong>Aging mouse liver negative mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS606' rel='noopener noreferrer' target='_blank'><strong>MTBLS606</strong></a>.</p><p><strong>Aging fruit fly positive mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS612' rel='noopener noreferrer' target='_blank'><strong>MTBLS612</strong></a>.</p><p><strong>Aging fruit fly negative mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS615' rel='noopener noreferrer' target='_blank'><strong>MTBLS615</strong></a>.</p>
2019-03-26 | MTBLS615 | MetaboLights
Project description:<p>Large-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (MetDNA) that expands metabolite annotations without the need for a comprehensive standard spectral library. MetDNA is based on the rationale that seed metabolites and their reaction-paired neighbors tend to share structural similarities resulting in similar MS2 spectra. MetDNA characterizes initial seed metabolites using a small library of MS2 spectra, and utilizes their experimental MS2 spectra as surrogate spectra to annotate their reaction-paired neighbor metabolites, which subsequently serve as the basis for recursive analysis. Using different LC-MS platforms, data acquisition methods, and biological samples, we showcase the utility and versatility of MetDNA and demonstrate that about 2000 metabolites can cumulatively be annotated from one experiment. Our results demonstrate that MetDNA substantially expands metabolite annotation, enabling quantitative assessment of metabolic pathways and facilitating integrative multi-omics analysis.</p><p><br></p><p><strong>Aging mouse liver positive mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS601' rel='noopener noreferrer' target='_blank'><strong>MTBLS601</strong></a>.</p><p><strong>Aging mouse liver negative mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS606' rel='noopener noreferrer' target='_blank'><strong>MTBLS606</strong></a>.</p><p><strong>Aging fruit fly positive mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS612' rel='noopener noreferrer' target='_blank'><strong>MTBLS612</strong></a>.</p><p><strong>Aging fruit fly negative mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS615' rel='noopener noreferrer' target='_blank'><strong>MTBLS615</strong></a>.</p>
2019-03-26 | MTBLS601 | MetaboLights
Project description:<p>Large-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (MetDNA) that expands metabolite annotations without the need for a comprehensive standard spectral library. MetDNA is based on the rationale that seed metabolites and their reaction-paired neighbors tend to share structural similarities resulting in similar MS2 spectra. MetDNA characterizes initial seed metabolites using a small library of MS2 spectra, and utilizes their experimental MS2 spectra as surrogate spectra to annotate their reaction-paired neighbor metabolites, which subsequently serve as the basis for recursive analysis. Using different LC-MS platforms, data acquisition methods, and biological samples, we showcase the utility and versatility of MetDNA and demonstrate that about 2000 metabolites can cumulatively be annotated from one experiment. Our results demonstrate that MetDNA substantially expands metabolite annotation, enabling quantitative assessment of metabolic pathways and facilitating integrative multi-omics analysis.</p><p><br></p><p><strong>Aging mouse liver positive mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS601' rel='noopener noreferrer' target='_blank'><strong>MTBLS601</strong></a>.</p><p><strong>Aging mouse liver negative mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS606' rel='noopener noreferrer' target='_blank'><strong>MTBLS606</strong></a>.</p><p><strong>Aging fruit fly positive mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS612' rel='noopener noreferrer' target='_blank'><strong>MTBLS612</strong></a>.</p><p><strong>Aging fruit fly negative mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS615' rel='noopener noreferrer' target='_blank'><strong>MTBLS615</strong></a>.</p>
2019-03-26 | MTBLS606 | MetaboLights
Project description:<p>Large-scale metabolite annotation is a challenge in liquid chromatogram-mass spectrometry (LC-MS)-based untargeted metabolomics. Here, we develop a metabolic reaction network (MRN)-based recursive algorithm (MetDNA) that expands metabolite annotations without the need for a comprehensive standard spectral library. MetDNA is based on the rationale that seed metabolites and their reaction-paired neighbors tend to share structural similarities resulting in similar MS2 spectra. MetDNA characterizes initial seed metabolites using a small library of MS2 spectra, and utilizes their experimental MS2 spectra as surrogate spectra to annotate their reaction-paired neighbor metabolites, which subsequently serve as the basis for recursive analysis. Using different LC-MS platforms, data acquisition methods, and biological samples, we showcase the utility and versatility of MetDNA and demonstrate that about 2000 metabolites can cumulatively be annotated from one experiment. Our results demonstrate that MetDNA substantially expands metabolite annotation, enabling quantitative assessment of metabolic pathways and facilitating integrative multi-omics analysis.</p><p><br></p><p><strong>Aging mouse liver positive mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS601' rel='noopener noreferrer' target='_blank'><strong>MTBLS601</strong></a>.</p><p><strong>Aging mouse liver negative mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS606' rel='noopener noreferrer' target='_blank'><strong>MTBLS606</strong></a>.</p><p><strong>Aging fruit fly positive mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS612' rel='noopener noreferrer' target='_blank'><strong>MTBLS612</strong></a>.</p><p><strong>Aging fruit fly negative mode</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS615' rel='noopener noreferrer' target='_blank'><strong>MTBLS615</strong></a>.</p>
2019-03-22 | MTBLS612 | MetaboLights
Project description:Phenotypes of maize male sterile 8 plants are small anthers, meiotic failure, shorter epidermal cells, and non-secreting tapetal cells. Excess callose accumulates around meiotic cells, which later abort. Thousands of transcriptome changes occur including ectopic activation of genes not expressed in fertile siblings, failure to express genes, and differential expression of genes shared with fertile siblings. Sixty-three differentially expressed proteins were identified after 2-D DIGE followed by LC/MS/MS, including those involved in metabolism and cell division. The majority were not identified by differential RNA expression. Keywords: anther development, maize, male-sterile, ms8
2010-08-20 | GSE23615 | GEO
Project description:Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.
2023-11-09 | GSE234833 | GEO
Project description:Phenotypes of maize male sterile 8 plants are small anthers, meiotic failure, shorter epidermal cells, and non-secreting tapetal cells. Excess callose accumulates around meiotic cells, which later abort. Thousands of transcriptome changes occur including ectopic activation of genes not expressed in fertile siblings, failure to express genes, and differential expression of genes shared with fertile siblings. Sixty-three differentially expressed proteins were identified after 2-D DIGE followed by LC/MS/MS, including those involved in metabolism and cell division. The majority were not identified by differential RNA expression. Keywords: anther development, maize, male-sterile, ms8 4 replicates of ms8 mutant and 4 replicates of ms8 fertile siblings at 3 anther stages. Spike-in controls were included.
2010-08-20 | E-GEOD-23615 | biostudies-arrayexpress