PlantMASST data submission - seed extracts
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Viridiplantae (ncbitaxon:33090)
SUBMITTER: 
Roland Kersten
PROVIDER: MSV000099793 | MassIVE | Fri Nov 07 10:34:00 GMT 2025
REPOSITORIES: MassIVE
Similar Datasets
Project description:Plant metabolic extracts. Plant seeds and plant tissues as specified in file name and metadata were collected. 0.1-0.2 g fresh weight tissue were frozen, ground in a metal Tissuelyzer homogenizer tube with one 0.25 in stainless steel ball (MP Biomedicals, Cat# MP116991006) for 1 min at 6 m/s with a MP Biomedicals FastPrep-24-5G Tissuelyser. Ground tissue was added with 1 mL 80% methanol, ground another 20 s at 6 m/s with the Tissuelyzer and then incubated for 10 min at 60 celsius in a waterbath. Methanol extract was separated from insoluble material by centrifugation at 16,000 x g for 5 min, and filtered through Whatman 0.2 um syringeless LC-MS filters (Cytiva, Cat# UN503NPEORG) before LC-MS analysis. Extract samples were analyzed by LC-MS/MS on an Thermo QExactive orbitrap with a HESI-II ion source and a Vanquish LC. LC-MS settings were as follows: Injection volume 5 uL, LC - Phenomenex Kinetex 2.6 um C18 reverse phase 100 A 150 x 3 mm LC column, LC gradient: solvent A - 0.1% formic acid, solvent B - acetonitrile (0.1% formic acid), 0 min: 10% B, 0.7 min: 10% B, 9.8 min: 95% B, 10.7 min: 95% B, 10.8 min: 10% B, 14.8 min: 10% B, 0.5 mL/min, MS - positive ion mode, Full MS: Resolution 35,000, AGC target 1e6, Maximum IT 50 ms, mass range 150-500 m/z (lowmz method) or 450-1,500 m/z (highmz method), dd-MS2 (data-dependent MS/MS): resolution 17,500, AGC target 1e5, Maximum IT 50 ms, Loop count 5, Isolation width 1.0 m/z, Collision energy 25 eV (stepped 20, 25, 30 eV), dynamic exclusion 0.5 s.
2025-11-07 | MSV000099790 | MassIVE
Project description:Plant metabolic extracts. Plant seeds as specified in file name and metadata were collected. 0.1-0.2 g fresh weight tissue were frozen, ground in a metal Tissuelyzer homogenizer tube with one 0.25 in stainless steel ball (MP Biomedicals, Cat# MP116991006) for 1 min at 6 m/s with a MP Biomedicals FastPrep-24-5G Tissuelyser. Ground tissue was added with 1 mL acetonitrile-water-formic acid (50%/48%/2%, v/v/v), ground another 20 s at 6 m/s with the Tissuelyzer and then incubated for 10 min at 60 celsius in a waterbath. The extract was separated from insoluble material by centrifugation at 16,000 x g for 5 min, transferred to a glass vial (12x75 mm) and dried in a speedvac (3 h at 45 celsius at 500 mtorr). Dried supernatant was resuspended in 80% methanol, transferred to 2mL tubes, centrifuged for 5 min at 16,000 x g and filtered through Whatman 0.2 um syringeless LC-MS filters (Cytiva, Cat# UN503NPEORG) before LC-MS analysis. Extract samples were analyzed by LC-MS/MS on an Thermo QExactive orbitrap with a HESI-II ion source and a Vanquish LC. LC-MS settings were as follows: Injection volume 5 uL, LC - Phenomenex Kinetex 2.6 um C18 reverse phase 100 A 150 x 3 mm LC column, LC gradient: solvent A - 0.1% formic acid, solvent B - acetonitrile (0.1% formic acid), 0 min: 10% B, 0.7 min: 10% B, 9.8 min: 95% B, 10.7 min: 95% B, 10.8 min: 10% B, 14.8 min: 10% B, 0.5 mL/min, MS - positive ion mode, Full MS: Resolution 35,000, AGC target 1e6, Maximum IT 50 ms, mass range 500-1,500 m/z, dd-MS2 (data-dependent MS/MS): resolution 17,500, AGC target 1e5, Maximum IT 50 ms, Loop count 5, Isolation width 2.0 m/z, Collision energy 25 eV (stepped 20, 25, 30 eV), dynamic exclusion 0.5 s.
2025-11-07 | MSV000099794 | MassIVE
Project description:Plant metabolic extracts. Plant seeds as specified in file name and metadata were collected. 0.1-0.2 g fresh weight tissue were frozen, ground in a metal Tissuelyzer homogenizer tube with one 0.25 in stainless steel ball (MP Biomedicals, Cat# MP116991006) for 1 min at 6 m/s with a MP Biomedicals FastPrep-24-5G Tissuelyser. Ground tissue was added with 1 mL acetonitrile-water-formic acid (50%/48%/2%, v/v/v), ground another 20 s at 6 m/s with the Tissuelyzer and then incubated for 10 min at 60 celsius in a waterbath. The extract was separated from insoluble material by centrifugation at 16,000 x g for 5 min, transferred to a glass vial (12x75 mm) and dried in a speedvac (3 h at 45 celsius at 500 (m)torr). Dried supernatant was resuspended in 80% methanol, transferred to 2mL tubes, centrifuged for 5 min at 16,000 x g filtered through Whatman 0.2 um syringeless LC-MS filters (Cytiva, Cat# UN503NPEORG) before LC-MS analysis. Extract samples were analyzed by LC-MS/MS on an Thermo QExactive
orbitrap with a HESI-II ion source and a Vanquish LC. LC-MS settings were as follows: Injection volume 5 uL, LC - Phenomenex Kinetex 2.6 um C18 reverse phase 100 A 150 x 3 mm LC column, LC gradient: solvent A - 0.1% formic acid, solvent B - acetonitrile (0.1% formic acid), 0 min: 10% B, 0.7 min: 10% B, 9.8 min: 95% B, 10.7 min: 95% B, 10.8 min: 10% B, 14.8 min: 10% B, 0.5 mL/min, MS - positive ion mode, Full MS: Resolution 35,000, AGC target 1e6, Maximum IT 50 ms, mass range 150-500 m/z (lowmz method) or 450-1,500 m/z (highmz method), dd-MS2 (data-dependent MS/MS): resolution 17,500, AGC target 1e5, Maximum IT 50 ms, Loop count 5, Isolation width 1.0 m/z, Collision energy 25 eV (stepped 20, 25, 30 eV), dynamic exclusion 0.5 s.
2025-11-07 | MSV000099788 | MassIVE
Project description:Plant metabolic extracts. Plant seedlings were grown in Premier Horticulture Pro Mix HP High Porosity with Mycorrhizae for plant growth under plant growth lights with a 16 h light/8 h dark cycle for 6-8 weeks at room temperature. Plant tissue samples were collected as specified in file name and metadata. 0.1-0.2 g fresh weight tissue were frozen, ground in a metal Tissuelyzer homogenizer tube with one 0.25 in stainless steel ball (MP Biomedicals, Cat# MP116991006) for 1 min at 6 m/s with a MP Biomedicals FastPrep-24-5G Tissuelyser. Ground tissue was added with 1 mL 80% methanol, ground another 20 s at 6 m/s with the Tissuelyzer and then incubated for 10 min at 60 celsius in a waterbath. Methanol extract was separated from insoluble material by centrifugation at 16,000 x g for 5 min, and filtered through Whatman 0.2 um syringeless LC-MS filters (Cytiva, Cat# UN503NPEORG) before LC-MS analysis. Extract samples were analyzed by LC-MS/MS on an Thermo QExactive orbitrap with a HESI-II ion source and a Vanquish LC. LC-MS settings were as follows: Injection volume 5 uL, LC - Phenomenex Kinetex
2.6 um C18 reverse phase 100 A 150 x 3 mm LC column, LC gradient: solvent A - 0.1% formic acid, solvent B - acetonitrile (0.1% formic acid), 0 min: 10% B, 0.7 min: 10% B, 9.8 min: 95% B, 10.7 min: 95% B, 10.8 min: 10% B, 14.8 min: 10% B, 0.5 mL/min, MS - positive ion mode, Full MS: Resolution 35,000, AGC target 1e6, Maximum IT 50
ms, mass range 150-500 m/z (lowmz method) or 450-1,500 m/z (highmz method), dd-MS2 (data-dependent MS/MS): resolution 17,500, AGC target 1e5, Maximum IT 50 ms, Loop count 5, Isolation width 1.0 m/z, Collision energy 25 eV (stepped 20, 25, 30 eV), dynamic exclusion 0.5 s.
2025-11-07 | MSV000099792 | MassIVE
Project description:Leaf and stem plant material (0.2 g fresh weight) was collected from aerial tissues, frozen and ground with a MP Biomedicals FastPrep-24-5G Tissuelyser in 2ml MP Biomedicals tubes with 2.3mm Zirconia beads for 60 s at 6 m/s. 1 mL of 80% methanol was added to ground tissue and ground as before for 20 s at 6 m/s. The methanolic extract was incubated for 10 min in a 60C water bath, centrifuged for 5 min at 16000 x g at room temperature, and filtered through Whatman 0.2 um syringeless LCMS filters (UN503NPEORG) before LCMS analysis. Filtered extracts were transferred to LCMS vials and analyzed by LC-MS/MS with the following settings: LC - Phenomenex Kinetex 2.6 um C18 reverse phase 100A 150 x 3 mm LC column; LC gradient, solvent A, 0.1% formic acid; solvent B, acetonitrile (0.1% formic acid); 0 min, 10% B; 5 min, 60% B; 5.1 min, 95% B; 6 min, 95% B; 6.1 min, 10% B; 9.9 min, 10% B; 0.5 mL/min; MS, positive ion mode; full MS, resolution 70000; mass range 400-1200 m/z; dd-MS2 (data-dependent MS/MS), resolution 17500; AGC target 1e5, loop count 5, isolation width 1.0 m/z, collision energy 25 eV and dynamic exclusion 0.5 s.
2024-10-14 | MSV000096083 | MassIVE
Project description:Proteomic analysis of pervanadate-induced tyrosine-phosphorylated proteins in hepatocellular carcinoma WRL 68 cells Protein tyrosine phosphorylation plays critical roles in modulating biological processes such as cellular proliferation, differentiation, migration, apoptosis and metabolism. To profile tyrosine phosphorylated (pTyr) proteins as well as search novel pTyr proteins as cross-talk points among different cellular pathways, we developed a rapid and efficient approach to identify cellular pTyr proteins and their complexes by a combination of subcellular proteomics approach with signal transduction strategies. Human hepatocytic cells from WRL68 cell line were treated with pervanadate (POV), subfractionated into four fractions and then subjected to immunoaffinity purification with anti-pTyr antibody. The eluted mixtures of the anti-pTyr purification were identified by LC-MS/MS. Subcellular fractionation and affinity purification of tyrosine-phosphorylated proteins: WRL68 cells were first grown to 80% confluence in MEM complete medium and then the medium replaced with serum free media. After 15 h, the cells were either untreated or stimulated with 0.1 mM pervanadate (1 mM sodium orthovanadate, 3 mM H2O2) for 10 min. 150-mm cultures of WRL 68 cells were rinsed twice with 4? PBS and then scraped from the dish in 750?l of hypotonic buffer (10 mM Tris, 1 mM NaF, 10 mM IAA, pH 7.5) containing a cocktail of protein inhibitors. After a 20-min incubation on ice, the cells were passed about five times through a 25-g needle. The resulting lysate was subjected to a 15min centrifugation at 1000 rpm at 4?, after which the pellet was resuspended in 250?l of hypotonic buffer and re-extracted by a second round of the trituration and centrifugation. The supernatants of the first and second spins were combined, adjusted to 0.25 M NaCl, and separated into cytosolic (supernatant) and membrane (pellet) fractions bycentrifugation at 19,000 rpm (43,000 g) for 90 min at 4?. All the pellets and total cell lysate were resuspended in RIPA buffer (50 mM Tris-HCl, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid sodium) containing 1mM pervanadate with a cocktail of protein inhibitors with sonication aid. Cleared cell lysates were incubated overnight at 4? with 30?l monoclonal anti-phosphotyrosine-agrose (Sigma). Precipitated immune complexes were washed three times with 1×HNTG (20 mM HEPES, 150 mM NaCl, 0.1% Triton X-100, 10% Glycerol, pH 7.5) and then eluted with 100 mM phenyl phosphate (Sigma) in lysis buffer at 4?. Enzyme digestion, mass spectrometry and protein identification: The sample was digested according to the published method. Chromatography was performed using a surveyor LC system (Thermo Finnigan,SanJose,CA) on C18 reverse phase column(RP, 180 µm x 150 mm, BioBasic® C18, 5 µm, Thermo Hypersil-Keystone). The pump flow rate is split 1:100 for a colum flow rate of 1.5 µL/min.The column effluent is directly electrosprayed using the orthogonal metal needle source without further splitting.Mobile phase A is 0.1% formic acid in water,and the B mobile phase is 0.1% formic acid in acetonitrile. The separation of peptides obtained by enzymatic digest of bile sample was achieved with a gradient of 2-80% B over 360 min.The column effluent from the reverse phase column was analyzed by LCQ Deca XP ion-trap mass spectrometer.The micro-electrospray interface uses a 30 µm metal needle that is orthogonal to the inlet of the LCQ.The mass spectrometer was set that one full MS scan was followed by three MS/MS scans on the three most intense ion from the MS spectrum with the following Dynamic Exclusion™ settings: repeat count, 1; repeat duration, 0.5 min; exclusion duration, 3.0 min. The acquired MS/MS spectra were automatically searched against protein database for human proteins (SWISS-PROT/TrEMBL) using the TurboSEQUEST program in the BioWorks™ 3.0 software suite. An accepted SEQUEST result had to have a ?Cn score of at least 0.1 (regardless of charge state) and Xcorr (one charge?1.5, two charges?2.0, three charges?2.5). Single peptides that alone identify a protein were manually validated after meeting the above criteria. Bioinformatics analysis: The pI and MW of the proteins were analyzed using ExPASy proteomics tools accessed from http://cn.expasy.org/tools/#proteome. The grand average hydropathicity (GRAVY) values were determined according to Kyte-Doolittle. The protein subcellular location annotation was from SwissProt &TrEMBL protein database (http://us.expasy.org/sprot/). The protein function family was categorized according to Gene Ontology (GO) annotation terms extracted by InterPro (http://www.ebi.ac.uk./interpro/). The annotation of protein phosphorylation was from SwissProt &TrEMBL protein database (http://us.expasy.org/sprot/) and PhosphoSite (http://www.phosphosite.org). The kinases were annotated according to human kinome. Keywords: other
2005-04-07 | GSE2408 | GEO
Project description:Pretreated human follicular fluid was prepared for targeted metabolomics experiments. For this purpose, 12-point standard calibration curves in the respective range with reference material were measured, and the limit of detection (LOD) and limit of quantification (LOQ) for each neurotransmitter under investigation were calculated. LC-MS/MS was conducted by an ultra-performance liquid chromatography method using a Waters ACQUITY UPLC BEH C18 column (2.1 mm×100 mm, 1.7 µm, Waters, USA). The Waters acquisition UPLC was coupled to an API 4000 triple quadrupole mass spectrometer (AB SCIEX, USA). The mobile phase A buffer was 10% methanol in water (containing 0.1% formic acid), and the mobile phase B buffer was 50% methanol in water (containing 0.1% formic acid). The LC gradient elution was at a flow rate of 0.3 mL/min at 0-8.0 min and 0.4 ml/min at 8.0-17.5 min, then 10%-30% B at 0-6.5 min; 30%-100% B at 6.5-7 min; 100% B at 7-14min; and 100%-10% B at 14-17.5min. The injection volume was 5 µl and the column temperature was set to 40 °C. Twenty-three metabolites (Ach: Acetylcholine chloride; Gln: Glutamine; Glu: Glutamate; His: L-Histidine; NE: norepinephrine; Tyr:Tyrosine; Trp:Tryptophan; Kyn: Kynurenine; GABA: 4-Aminobutyric acid;HisA:Histamine; PA:Picolinic acid;TyrA:Tyramine;DA:Hydroxytyramine hydrochloride; TrpA:Tryptamine;5-HT:Serotonin hydrochloride;E:Adrenaline hydrochloride;KynA:Kynurenic acid;5-HIAA:5-Hydroxyindole-3-acetic acid;DOPA:Levodopa;XA:Xanthurenic acid;VWA:Vanillymandelic Acid; 5-HTTP:5-Hydroxytryptophan;MT:Melatonine)were simultaneously reported in LC-MS/MS multiple reaction monitoring (MRM) mode. Data analysis was performed with Analyst 1.6 software.
2022-08-12 | PXD031560 | Pride
Project description:Carfilzomib-sensitive (AMO1) and resistant (AMO1-CFZ) MM cells were grown in RPMI-1640 medium supplemented with 10 % FBS and 0.68 mM L-glutamine, in a humidified incubator at 5% CO2 and 37 °C. The AMO1-CFZ medium was additionally added 90 nM CFZ, while the CFZ sensitive AMO1 cells were added vehicle (0.009 % DMSO) only. AMO1-CFZ was either harvested directly or grown for 1 week in CFZ free medium (vehicle only) prior to harvest. AMO1 and carfilzomib-resistant AMO1-CFZ cells were resuspended in 100 µl 1% sodium deoxycholate, 100 mM Tris-HCl pH 8.5, 10 mM tris(2-carboxyethyl)phosphine (TCEP), 40 mM chloroacetamide (CAA), heated at 90 °C for 45 min and sonicated for 10 cycles (30 s ON/30 s OFF) using a Bioruptor pico sonicator. After centrifugation at 16000 × g for 10 min, 50 µg soluble protein from each sample was added 100 µl 0.1M ammonium bicarbonate, 0.5 µg trypsin and digested overnight at 37°C. Peptides were desalted using C18 spin columns, dried in a speedvac centrifuge and resuspended in 0.1% formic acid prior to MS analysis. Label-free quantitatative (LFQ) LC-MS/MS was performed on a timsTOF Pro (Bruker Daltonics) connected to a nanoElute (Bruker Daltonics) HPLC. Peptides were separated over a Bruker PepSep C18 (75 µm × 15 cm) column with running buffers A (0.1 % formic acid) and B (0.1 % formic acid in acetonitrile) using a 100 min gradient from 2 % B to 40 % B. The timsTof instrument was operated in the DDA PASEF mode with 10 PASEF scans per acquisition cycle and accumulation and ramp times of 100 ms each. The ‘target value’ was set to 20000 and dynamic exclusion was activated and set to 0.4 min. The quadrupole isolation width was set to 2 Th for m/z < 700 and 3 Th for m/z > 800.
2024-06-07 | PXD045439 | Pride