GNPS - Piper plants timsTOF fleX - MZmine 3 benchmark
Ontology highlight
ABSTRACT:
INSTRUMENT(S): timsTOF fleX
ORGANISM(S): Piper (ncbitaxon:13215)
SUBMITTER: 
Tomas Pluskal
PROVIDER: MSV000090327 | GNPS |
REPOSITORIES: GNPS
Similar Datasets
Project description:Ethanolic extracts of piper plants (leafs, fruits) were dissolved in H2O/ACN (75/25) and analysed on a timsTOF fleX mass spectrometer.
| MSV000090327 | MassIVE
Project description:LC-MS/MS metabolomics data of Komagataella phaffii recorded on a timsTOF fleX with AutoMSMS acquisition in negative ion mode. SeQuant ZIC-pHILIC column (150 x 2.1 mm, 5 um, polymer, Merck-Millipore) A: 90% NH4HCO3 pH 9.2 10% ACN B: 100% ACN
2022-08-01 | MSV000090052 | GNPS
Project description:Many Trichoderma spp. are successful plant beneficial microbial inoculants due to their ability to act as biocontrol agents with direct antagonistic activities to phytopathogens, and as biostimulants capable of promoting plant growth. This work investigates the effects of treatments with three selected Trichoderma (strains T22, TH1 and GV41) to strawberry plants on the productivity and proteome of the formed fruit. Proteomic analysis of fruits,harvested from the plants previously treated with Trichoderma and control plants was performed by using a TMT-based protein quantification strategy. Bioinformatic analysis of the differential proteins accumulation in fruits, harvested from the treated plants, revealed a central network of interacting molecular species, that demonstrated the modulation of different plant physiological processes following the microbial inoculation.
2020-06-09 | PXD016951 | Pride
Project description:The experiments were performed to elucidate the enigmatic enzymatic formation of the pungent principle, piperine, from black pepper (Piper nigrum L.), the world´s most popular spice. Based a differential RNA-Seq approach including immature fruits, flowers, and leaves, the gene encoding piperine synthase, encoding a BAHD-type acyltransferase and several other candidate genes encoding various enzymatic functions in the biosynthetic pathway were identified. Recombinant piperine synthase and additional promiscuous piperamide synthases were used to facilitate the microbial production of a broad range of medicinally relevant piperamides. Subsequent investigations will also include the identification of enzymatic steps in the phenylpropanoid pathway and the amino acid derived biosynthesis of piperidine Based on the assumption that piperine encoding genes are highly expressed shortly before the slope of piperine accumulation reaches its maximum, RNA from greenhouse grown black pepper plants was extracted from young fruits at two different stages of development, flowers, and leaves were harvested for a differential RNA-Seq approach. Candidate transcripts associated with piperine biosynthesis were identified by comparative transcript abundance and sequence annotation tools.
2021-04-28 | E-MTAB-9029 | biostudies-arrayexpress
Project description:Serine hydrolases from E. Coli cells were labelled with fluorophosphonate probe (ABP-probe): Intact cells labelling by adding probe to media: GPM77700012901 and GPM00300015270 Cell lysate labelling: GPM77700012904 and GPM77700012905 Blank sample (no probe addition): GPM77700012906 and GPM77700012909 2D-LC-MS experiment was done with C18-chromatography at pH10 for first dimension (0.66% AcN/min gradient). Fractions (1 min each) from the first dimension were collected and concatenated: 1,2,3 and 4: 00-EColi2DFASP 45,46 and 47: 99-EColi2DFASP 5 and 25: 01-EColi2DFASP 6 and 26: 02-EColi2DFASP 7 and 27: 03-EColi2DFASP 24 and 44: 20-EColi2DFASP Concatenated fractions were dryed, redissolved in H2O-FA-AcN 97.9:0.1:2% and analysed with LC-MS using C18-chromatography at pH=2 as a second-dimension separation method. Combined datasearch results for 2D-LC-MS of E. Coli Dh5a could be seen on local laboratory server: http://140.193.59.4/tandem/thegpm_tandem.html with lookup model ID: GPM22200000195
2014-05-20 | PXD000241 | Pride
Project description:Tissue samples were cut into 8-µm frozen sections and then microdissected to obtain ~4,000 breast cancer epithelial cells using a P.A.L.M. MicroBeam system (Carl Zeiss MicroImaging, GmbH, Munich, Germany). Proteins were extracted from microdissected cells, followed by denaturation, reduction and alkylation. Protein samples were digested at 37oC for 4 h using MS-grade trypsin (Promega, Madison, WI, USA) at a 1:4 (enzyme:protein) ratio, and then acidified for further analysis. Global proteomic profiles of 126 TNBC samples were recorded on a nanoscale LC hyphenated LTQ-Orbitrap-XL MS system (ThermoElectron, Bremen, Germany). Peptide mixtures were separated on the nLC system (Ultimate 3000, Dionex, Amsterdam, The Netherlands) with a 3-h binary gradient (mobile phase A: H2O, mobile phase B: ACN) in a 3-μm C18 silica packed 50-cm capillary column with 75-μm inner-diameter. Mass spectra were acquired over a mass-to-charge ratio (m/z) range of 400–1,800 at a resolving power of 30,000 at 400 m/z. The top five most intensive parent ions from the full scan were isolated and fragmented by collisional activated dissociation in the linear ion trap. Dynamic exclusion was used to increase number of parent ions selected for fragmentation. MaxQuant search used Carbamidomethylation as a fixed modification for cysteine-containing peptides, and oxidation of methionine and N-terminal acetylation as variable modification.
2014-01-13 | PXD000260 | Pride
Project description:SCOPE2 analysis of single human cells treated with a KRAS G12C inhibitor and analyzed on a TIMSTOF Flex instrument
2021-07-08 | MSV000087780 | MassIVE
Project description: Not available
| S-EPMC10496610 | biostudies-literature
Project description:An Ac/Ds transposon tagged mutant population was screened for changes in visible fruit phenotypes. One line showed orange, yellow sectors in the fruit and was named Orange ripening (Orr), its transposase free offspring showed Mendelian segregation yielding red, yellow and orange fruit bearing plants in a ratio of 1:2:1. Crossing the an orange fruit plant line to the wild-type yielded only plants bearing yellow fruit. A cross between the yellow fruit bearing progeny yielded 26 plants having red and 17 plants having yellow fruit, suggesting an over-dominant allele. Using inverse PCR analysis showed an insertion in the putative subunit M of the tomato Ndh complex. Subsequently, an Orr Ds transposon excision line was recovered which only showed red pigmented fruit. Here, we describe microarray profiling of tomato fruits from wild-type, heterozygous and homozygous Orr insertion plants and from fruits harvested from the Orr excision line. Keywords: mutant wild type Tomato fruits were harvested at breaker stage using wild-type, ORR homozygouse and heterozygous lines as well as Orr excision lines. To investigate the expression changes in the ORR mutants, wildtype and ORR mutant line fruits were harvested at the breaker stage and subjected to Affymetrix microarray profiling
2010-06-16 | E-GEOD-22110 | biostudies-arrayexpress