VOCs (isoprenoids and acetates) fro database search
Ontology highlight
ABSTRACT:
INSTRUMENT(S): GC/MS
ORGANISM(S): N/a
SUBMITTER: 
Roman Borisov
PROVIDER: MSV000088980 | MassIVE | Thu Mar 03 11:37:00 GMT 2022
REPOSITORIES: MassIVE
Similar Datasets
Project description:Set of isoprenoids and acetetes analyzed by EI-GC/MS for molecular networking and databse search
2022-03-03 | MSV000088980 | GNPS
Project description:GC/MS analysis of isoprenoids and alkyl acetates mixtures for molecular networking
2022-02-22 | MSV000088885 | MassIVE
Project description:GC/MS analysis of isoprenoids and alkyl acetates mixtures for molecular networking
2022-02-22 | MSV000088885 | GNPS
Project description:Grapes (Vitis species) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening in berries as well as how aroma is developed are aspects not fully understood. In an attempt to identify the common mechanisms associated with the onset of ripening independently of the cultivar, grapes of Portuguese elite cultivars, Trincadeira, Aragonês, and Touriga Nacional, were studied. The mRNA expression profiles corresponding to veraison (EL35) and to mature berries (EL36) were compared. Across the three varieties, 9,8% (2255) probesets corresponding to 1915 unigenes were robustly differentially expressed at EL 36 compared to EL 35. Eleven functional categories were represented in this differential gene set: primary metabolism, “secondary metabolism”, cellular metabolism”, development”, “cellular process”, “diverse functions”, “regulation overview”, response to stimulus, stress”, “signaling”, “transport overview”, and “xenoprotein, transposable element” besides 32.24% genes of “unknown” function. Information on gene expression related to primary and secondary metabolism was verified by RT-qPCR analysis of selected candidate genes at four developmental stages (EL32, EL35, EL36 and EL 38). Gene expression data were integrated with metabolic profiling data from GC-EI-TOF/ MS and headspace GC-EI-MS platforms. Molecular and metabolic markers of grape ripening related to primary and secondary metabolism were established and revealed a substantial developmental reprogramming of cellular metabolism. Altogether the results provide valuable new information on the main metabolic events leading to grape ripening. Furthermore, we provide first hints about how the development of a cultivar specific aroma is controlled at the transcriptional level.
2012-10-30 | GSE35172 | GEO
Project description:Bottom-up proteomics database search algorithms used for peptide identification cannot comprehensively identify posttranslational modifications (PTMs) in a single-pass because of high false discovery rates (FDRs). A new approach to database searching enables Global PTM (G-PTM) identification by exclusively looking for curated PTMs, thereby avoiding the FDR penalty experienced during conventional variable modification searches. We identified nearly 2500 unique, high-confidence modified peptides comprising 31 different PTM types in single-pass database searches.
2015-07-31 | GSE59956 | GEO
Project description:Open (mass tolerant) search of tandem mass spectra shows great potential in the comprehensive detection of post-translational modifications in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms for automated and reliable post-processing of the coarse and error-prone search results. Here we present PTMiner, a software tool for confident filtering and localization of modifications (mass shifts) identified by open search. After mass-shift-grouped FDR control of peptide-spectrum matches (PSMs), PTMiner uses an empirical Bayesian method to localize modifications through iterative learning of the prior probabilities of each type of modification occurring on different amino acids. In the validation experiments on a large data set of simulated spectra, PTMiner effectively controlled the FDRs of individual modification groups, and achieved a total spectral identification rate four times higher than the classic FDR estimation method. At 1% real false localization rate (FLR), PTMiner localized 93.06% of the modifications, far higher than two used open search engines and the extended Ascore localization algorithm. We then used PTMiner to analyze the draft map of human proteome containing 25 million spectra from 30 tissues, and confidently identified over 1.7 million modified PSMs at 1% FDR and 1% FLR, which provided a system-wide view of both known and unknown modifications in the human proteome.
2019-01-17 | PXD012394 |
Project description:Grapes (Vitis species) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening in berries as well as how aroma is developed are aspects not fully understood. In an attempt to identify the common mechanisms associated with the onset of ripening independently of the cultivar, grapes of Portuguese elite cultivars, Trincadeira, AragonM-CM-*s, and Touriga Nacional, were studied. The mRNA expression profiles corresponding to veraison (EL35) and to mature berries (EL36) were compared. Across the three varieties, 9,8% (2255) probesets corresponding to 1915 unigenes were robustly differentially expressed at EL 36 compared to EL 35. Eleven functional categories were represented in this differential gene set: primary metabolism, M-bM-^@M-^\secondary metabolismM-bM-^@M-^], cellular metabolismM-bM-^@M-^], developmentM-bM-^@M-^], M-bM-^@M-^\cellular processM-bM-^@M-^], M-bM-^@M-^\diverse functionsM-bM-^@M-^], M-bM-^@M-^\regulation overviewM-bM-^@M-^], response to stimulus, stressM-bM-^@M-^], M-bM-^@M-^\signalingM-bM-^@M-^], M-bM-^@M-^\transport overviewM-bM-^@M-^], and M-bM-^@M-^\xenoprotein, transposable elementM-bM-^@M-^] besides 32.24% genes of M-bM-^@M-^\unknownM-bM-^@M-^] function. Information on gene expression related to primary and secondary metabolism was verified by RT-qPCR analysis of selected candidate genes at four developmental stages (EL32, EL35, EL36 and EL 38). Gene expression data were integrated with metabolic profiling data from GC-EI-TOF/ MS and headspace GC-EI-MS platforms. Molecular and metabolic markers of grape ripening related to primary and secondary metabolism were established and revealed a substantial developmental reprogramming of cellular metabolism. Altogether the results provide valuable new information on the main metabolic events leading to grape ripening. Furthermore, we provide first hints about how the development of a cultivar specific aroma is controlled at the transcriptional level. 2 time points in 2008 season. 3 biological replicates. 3 cultivars
2012-10-30 | E-GEOD-35172 | biostudies-arrayexpress
Project description:The small proteome has already been well explored in eukaryal and bacterial species, but so far, archaeal genomes have not yet been analysed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental information from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq) to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii. Translation was demonstrated for 67% of the annotated small coding sequences by both methods. Annotation-independent data analysis allowed for the prediction of 47 sites of ribosomal engagement outside known coding regions by Ribo-seq, seven of whom correspond to the eight un-annotated small proteins identified by a similar independent analysis of proteomic data. We also present independent evidence in vivo for the translation of a subset of small proteins (comprising both previously annotated and newly identified), underlining the validity of our identification scheme. Moreover, several of these translated sORFs are conserved in Haloferax and might have important functions. Based on our findings, we conclude that the small proteome of H. volcanii is larger than previously expected and that the combined use of mass spectrometry to detect protein presence with Ribo-seq to inform on translation is a powerful tool for the discovery of new small protein-coding genes in diverse organisms. This data-set contains the search results obtained from an MS-Fragger search against six-frame genome translation-derived database that were mapped to the genome by Stephan Fuchs “Salt & Pepper” software suite for bacterial proteogenomics.
2023-02-01 | PXD031691 | Pride
Project description:Volatile organic compounds for library search and gnps molecular networking
2021-11-23 | MSV000088433 | GNPS
Project description:Bottom-up proteomics database search algorithms used for peptide identification cannot comprehensively identify posttranslational modifications (PTMs) in a single-pass because of high false discovery rates (FDRs). A new approach to database searching enables Global PTM (G-PTM) identification by exclusively looking for curated PTMs, thereby avoiding the FDR penalty experienced during conventional variable modification searches. We identified nearly 2500 unique, high-confidence modified peptides comprising 31 different PTM types in single-pass database searches. Male C57BL/6J (B6) and CAST/EiJ (CAST) mice were purchased from The Jackson Laboratories (Bar Harbor, Maine) and housed in an environmentally controlled vivarium at the University of Wisconsin Biochemistry Department. Mice were provided standard rodent chow (Purina no. 5008) and water ad libitum, and maintained on a 12-hour light/dark cycle (6 AM – 6 PM). At 10 weeks of age, mice were sacrificed by CO2 asphyxiation. All animal procedures were preapproved by the University of Wisconsin Animal Care and Use Committee.
2015-07-31 | E-GEOD-59956 | biostudies-arrayexpress