Brittonodoxa subpinnata polar extracts
Ontology highlight
ABSTRACT:
INSTRUMENT(S): GC-MS (Agilent 6850 Network GC System /Agilent 5975C VL MSD)
ORGANISM(S): Brittonodoxa Subpinnata
SUBMITTER: 
Wilton Ricardo Sala-Carvalho
PROVIDER: MSV000093495 | MassIVE | Sat Nov 25 12:27:00 GMT 2023
REPOSITORIES: MassIVE
Similar Datasets
Project description:For GC-MS analysis, plant material was extracted as following: 50 mg of frozen material was crushed and extracted with 700 uL of pre-cooled methanol (-20oC). Were added 60 uL of adonitol (0.2 mg mL-1, internal standard), with the mixture being centrifuged (10 min at 11000 g) and the supernatant transferred to glasses tubes to add chloroform (375 uL at -20oC) and ultrapure water (750 uL at 4oC), with the polar and non-polar phases being collected separately. The non-polar phase was derivatized with 50 uL of pyridine and 50 uL of BSTFA (N,O-bis-(trimethylsilyl)-trifluoroacetamide) for 1 h at 70oC; 5 uL of tridecanoic acid (2 mg mL-1) was used as internal standard.
The non-polar phase was analyzed by GC-MS equipped with an HP5-MS capillary column (30 m, 0.25 mm, 0.25 um). An initial column temperature was adjusted to 100oC for 5 min, and increasing at a rate of 5oC min-1 to a final temperature of 320oC, with a total run time of 49 min. 1 uL of injection volume with helium as a carrier gas. In both analyses a blank was injected in each 15 samples.
2023-11-25 | MSV000093496 | MassIVE
Project description:Samples from methanolic extracts from skins of poison frogs. Split injection mode using a desorption temperature of 250C. Separation was performed initiating to 100C for 3 min, and then increasing the temperature to 190C using a rate of 10C/min and maintaining it by 1 min, afterwards incresing to 200C changing the rate to 2C/min and maintaining it by 1 min, and finally increasing to 280C, using a rate of 10C/min, and maintaing to this temperature for 3 min. Analysis were performed in a GC HP 6890 Series equipped with an Agilent Mass Selective Detector 5973 (Agilent technologies, Palo Alto, CA, USA). Separation was performed on a BP-5 capillary GC column (30 m 0.25 mm 0.25 um, SGE, Austin, TX, USA) using helium as a carrier gas at a flow rate of 1.1 mL/mi
2019-08-16 | MSV000084212 | MassIVE
Project description:Samples from extraction of volatile organic compounds from frogs using two sampling methods: in vivo and sampling from the skin and a DVB/CAR/PDMS-SPME fiber. Splitless injection mode using a desorption temperature of 250C. Separation was performed initiating to 40C for 3 min, and then increasing the temperature to 100C using a rate of 6C/min, afterwards incresing to 200C changing the rate to 4C/min, and finally increasing to 300C, using a rate of 20C/min, and maintaing to this temperature for 3 min. Analysis were performed in a GC HP 6890 Series equipped with an Agilent Mass Selective Detector 5973 (Agilent technologies, Palo Alto, CA, USA). Separation was performed on a BP-5 capillary GC column (30 m 0.25 mm 0.25 um, SGE, Austin, TX, USA) using helium as a carrier gas at a flow rate of 1.0 mL/min.
2019-08-15 | MSV000084211 | MassIVE
Project description:All samples were collected on cotton then placed into 2 mL borosilicate vials. The GC MS analysis was carried out using the Agilent 7200 GC QTOF Agilent Technologies Santa Clara CA. equipped with a robotic sampler system. The separation was conducted on an HP 5MS column (30 m x 0.25 mm x 0.25 micro m). The patch within the vial was heated for 25 min. at 200 C to desorb volatiles from the patch and 0.5 mL of headspace injected (injector temperature set at 250 C) into the instrument with a headspace syringe heated to 145 C. The GC protocol analysis included starting temperature 45 C min oven ramp (hold of 2 min), 15 C per min oven ramp to 300 C (hold of 3 min), and 50 C per min oven ramp to 320 C purge the column. The helium carrier gas was set to constant 1.2 mL per min flow and a spitless injection mode was applied. The purge flow to split vent rate was 50 ml per min at 1 min. The scanned m z range was 35-400 with the acquisition rate of 10 spectra per s. The empty vial blanks were interspersed with the samples to assess the background signal.
2022-06-22 | MSV000089708 | MassIVE
Project description:We reported that the microRNA profiling of exosome isolated from 58 cerebrospinal fluid (CSF) of 38 medulloblastoma (MBL) patient with or without letomeningeal metastases (LM). CSF exosome was precipitated using Exo2DTM for RNA assay (EXOSOME plus, Suwon, South Korea) according to the manufacture’s protocol (Kim, et al. 2017). 2 ml of CSF were added to Exo2DTM reagent B following mixing by inverting, and incubated at room temperature for 30 min. The supernatant was discarded and the exosome containing pellet was resuspended in 100 ul of PBS to further RNA isolation. Total RNA was extracted from the CSF exosome fraction using a microRNA purification kit (Norgen Biotek corp., Thorold, Canada) according to the manufacture’s protocol. Briefly, samples were mixed with lysis buffer, and the lysate was added to absolute ethanol. The lysate was applied up to the column and centrifuged at 8,000 rpm for 1 min. The column was washed with wash solution and centrifuged at 14,000 rpm for 1 min. Finally, the column was applied to 20 ul of elution solution and centrifuged at 14,000 rpm for 2 min, and the flow-through was stored at –80 ℃ for storage. RNA precipitates were quantified and qualified with Bioanalyzer Pico 6000 Chip (Agilent Technologies, Santa Clara, CA). The 10 ng of total RNA was provided to the cDNA library generation using SMARTer smRNA-Seq kit (Illumina Inc., San Diego, CA), according to the user manual. The cDNA library was subjected to sequencing using Truseq SBS Kit and HiSeq 2500 System (Illumina Inc., San Diego, CA), according to user guide.
2020-09-15 | GSE157916 | GEO
Project description:Female Sprague-Dawley rats were randomly separated into two groups: i) trained (Ex group) and ii) sedentary (Cont group). Animals from the Ex group were adapted to treadmill exercise for two consecutive weeks, involving a gradual increase in the running time till 60 min/day at 20 m/min, 0% grade, 5 days/week. This exercise program remained constant until the end of the 54 weeks. Mitochondria isolation from 10 animals (5 Ex group and 5 Cont group) was performed using the conventional methods of differential centrifugation. Mitochondrial protein extracts were reduced with dithiothreitol, alkylated with iodoacetamide and digested with trypsin using the FASP procedure (18). Briefly, each sample was solubilized in 4 % SDS, 0.1 M DTT, 0.1 M HEPES and incubated for 30 min at 60 C. Then, samples were mixed with 0.2 mL of a solution of 8 M Urea, 0.1 M HEPES, pH 8.5 (UH solution), loaded into the filtration devices (3k Microcon, Millipore), centrifuged at 14,000 g for 20 min, and washed twice with UH solution. After centrifugation, the concentrates were alkylated with 50 mM iodoacetamide in UH solution (dark, 25 C, 20 min), and washed twice with UH solution. The concentrate was diluted with 0.1 mL of 50 mM ammonium bicarbonate (ABC) and digested overnight (37 C) with the addition of 2 ug of trypsin diluted in 30 uL of 50 mM ABC. The resulting tryptic peptides were collected by centrifugation and the filter were washed twice with 50 uL of 50 mM ABC. Eluted peptides were acidified with 10 uL of formic acid and cleaned up on a homemade Empore C18 column (3M, St. Paul, MN, USA) (ref) for subsequent phospho-enrichment and/or analysis by LC-MS/MS. The dried protein digest was dissolved with 10 uL (3 % ACN, 0.1 % TFA), diluted 1:5 with loading buffer (1 M glycolic acid, 5 % TFA, 80 % ACN) and phosphopeptides were enriched on TiO2-beads as previously described (19). Briefly 5 mg of "Titansphere TiO2 5 um" were suspended in 100 uL of 100 % ACN, immobilized in a pipette-column and washed using 5 uL of loading buffer. Each sample was loaded in each pipette-column and then washed with 30 uL of washing buffer (1 % TFA, 80 % ACN). Phosphopeptides were eluted from the beads with 25 uL of 25 % ACN (v/v) containing 25 % NH4OH (m/v), acidified with 10 uL of 10 % TFA and vacuum- concentrated to approximately 4 uL. Samples were finally diluted to 10 uL with H2O + 0.1% formic acid prior to injection. The peptides mixtures were analyzed by online nanoflow liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) on an EASY-nLC system (Proxeon Biosystems, Odense, Denmark) connected to the LTQ Orbitrap Velos instrument (Thermo Fisher Scientific, Bremen, Germany) through a nanoelectrospray ion source. Six microliters of the peptide mixture were auto-sampled directly onto the analytical HPLC column (120 mm x75 um I.D., 3 um particle size (Nikkyo Technos Co., Ltd.) with a 120-min gradient from 5 % to 50 % ACN in 0.1 % FA. The effluent from the HPLC column was directly electrosprayed into the mass spectrometer. The LTQ Orbitrap Velos instrument was operated in data-dependent acquisition mode to automatically switch between full scan MS and MS/MS acquisition. The MS survey scan was performed in the FT cell recording a window between 350 and 2000 m/z. The resolution was set to 60 000, and the automatic gain control was set to 1,000,000 ions with a maximal acquisition time of 400 ms. The 20 most intense peptide ions with charge states great than or equal to 2 were sequentially isolated to a target value of 5,000 and fragmented in the high-pressure linear ion trap by low-energy CID with normalized collision energy of 35% Q value of 0.25, and an activation time of 10 ms. Raw files were processed using Proteome Discoverer version 1.3 (Thermo Fisher Scientific, Bremen). Peak lists were searched using Mascot software version 2.3 (Matrix Science, UK) against a SwissProt database containing entries corresponding to Rattus norvegicus (version of July 2012), a list of common contaminants, and all the corresponding decoy entries. Trypsin was chosen as enzyme and a maximum of two miscleavages were allowed. Carbamidomethylation (C) was set as a fixed modification, whereas oxidation (M) and phosphorylation (STY) were used as variable modifications. Searches were performed using a peptide tolerance of 7 ppm, a product ion tolerance of 0.5 Da. Resulting data files were filtered for FDR less than 1 % at peptide level.
2014-02-14 | PXD000354 | Pride
Project description:Washed three times in NaCl (150 mM). Cells were resuspended in 1 ml TSU buffer (50 mM Tris pH 8.0, 0.1% SDS, 2.5 M urea) and lysed by two freeze-thaw cycles in liquid nitrogen. Lysate proteins (40 ug) were separated and digested. Digested peptides were separated by nano-LC using an Ultimate 3000 HPLC and autosampler system (Dionex; Amsterdam, Netherlands). Samples (1 ul) were concentrated and desalted onto a micro C18 pre-column (500 um×2 mm, Michrom Bioresources; Auburn, CA, USA) with H2O:CH3CN (98:2, 0.05% trifluoroacetic acid) at 15 ul min−1. After a 4 min wash the pre-column was switched (Valco 10 port valve; Dionex) into line with a fritless nano column (75 u×~10 cm) containing C18 media (5 u, 200 A Magic; Michrom) manufactured according to Gatlin. Peptides were eluted using a linear gradient of H2O:CH3CN (98:2, 0.1% formic acid) to H2O:CH3CN (64:36, 0.1% formic acid) at 250 nl min−1 over 30 min. High voltage (2000 V) was applied to low volume tee (Upchurch Scientific) and the column tip positioned ~0.5 cm from the heated capillary (T = 280 degrees C) of an Orbitrap Velos (Thermo Electron; Bremen, Germany) mass spectrometer. Positive ions were generated by electrospray and the Orbitrap operated in data dependent acquisition mode (DDA). A survey scan m/z 350–1750 was acquired in the Orbitrap (Resolution = 30,000 at m/z 400, with an accumulation target value of 1,000,000 ions) with lockmass enabled. Up to the 10 most abundant ions (>5,000 counts) with charge states >+2 were sequentially isolated and fragmented within the linear ion trap using collisionally induced dissociation with an activation q = 0.25 and activation time of 30 ms at a target value of 30,000 ions. M/z ratios selected for MS/MS were dynamically excluded for 30 s. Peak lists were generated using Mascot Daemon/extract_msn (Matrix Science, Thermo; London, England) using the default parameters, and submitted to the database search program Mascot (version 2.1, Matrix Science). Search parameters were: Precursor tolerance 4 ppm and product ion tolerances +/-0.4 Da Oxidation (M) and Carbamidomethyl (C) specified as variable modifications Enzyme specificity was trypsin, 1 missed cleavage was possible
2014-04-28 | PXD000505 | Pride
Project description:Bacteria were washed three times in NaCl (150 mM). Cells were resuspended in 1 ml TSU buffer (50 mM Tris pH 8.0, 0.1% SDS, 2.5 M urea) and lysed by two freeze-thaw cycles in liquid nitrogen. Lysate proteins (40 ug) were separated and digested. Digested peptides were separated by nano-LC using an Ultimate 3000 HPLC and autosampler system (Dionex; Amsterdam, Netherlands). Samples (1 ul) were concentrated and desalted onto a micro C18 pre-column (500 um×2 mm, Michrom Bioresources; Auburn, CA, USA) with H2O:CH3CN (98:2, 0.05% trifluoroacetic acid) at 15 ul min−1. After a 4 min wash the pre-column was switched (Valco 10 port valve; Dionex) into line with a fritless nano column (75 u×~10 cm) containing C18 media (5 u, 200 A Magic; Michrom) manufactured according to Gatlin. Peptides were eluted using a linear gradient of H2O:CH3CN (98:2, 0.1% formic acid) to H2O:CH3CN (64:36, 0.1% formic acid) at 250 nl min−1 over 30 min. High voltage (2000 V) was applied to low volume tee (Upchurch Scientific) and the column tip positioned ~0.5 cm from the heated capillary (T = 280 degrees C) of an Orbitrap Velos (Thermo Electron; Bremen, Germany) mass spectrometer. Positive ions were generated by electrospray and the Orbitrap operated in data dependent acquisition mode (DDA). A survey scan m/z 350–1750 was acquired in the Orbitrap (Resolution = 30,000 at m/z 400, with an accumulation target value of 1,000,000 ions) with lockmass enabled. Up to the 10 most abundant ions (>5,000 counts) with charge states >+2 were sequentially isolated and fragmented within the linear ion trap using collisionally induced dissociation with an activation q = 0.25 and activation time of 30 ms at a target value of 30,000 ions. M/z ratios selected for MS/MS were dynamically excluded for 30 s. Peak lists were generated using Mascot Daemon/extract_msn (Matrix Science, Thermo; London, England) using the default parameters, and submitted to the database search program Mascot (version 2.1, Matrix Science). Search parameters were: Precursor tolerance 4 ppm and product ion tolerances +/-0.4 Da; Oxidation (M) and Carbamidomethyl (C) specified as variable modifications, Enzyme specificity was trypsin, 1 missed cleavage was possible
2014-04-28 | PXD000504 | Pride
Project description:We describe the use of conventional flow proteomics (200 uL/min) on an optimized system for the analysis of highly fractionated TMT labeled materials. We compare 20ug injections on column using NanoFreeProteomics (NFP) to 1uL injections on a convenentional nanoLC system
2020-02-25 | PXD016704 | Pride
Project description:Samples from extraction of volatile organic compounds from Malassezia species growing in solid mDixon media using DVB/CAR/PDMS-SPME fiber. Splitless injection mode using a desorption temperature of 250C. Analysis were performed in a GC HP 6890 Series equipped with an Agilent Mass Selective Detector 5973 (Agilent technologies, Palo Alto, CA, USA). Separation was performed on a BP-5 capillary GC column (30 m 0.25 mm 0.25 um, SGE, Austin, TX, USA) using helium as a carrier gas at a flow rate of 1.1 mL/min.
2020-04-09 | MSV000085267 | GNPS