GC/MS_Cotton_skin_Corona_UGent
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Agilent 7200 GC QTOF
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Alexander Aksenov
PROVIDER: MSV000089708 | MassIVE | Wed Jun 22 08:51:00 BST 2022
REPOSITORIES: MassIVE
Similar Datasets
Project description:Preliminary data of volatiles from T. septentrionalis fungus gardens. Samples were obtained directly from their chambers maintained under laboratory. The samples correspond to an entire and healthy fungus garden and subcolonies of fungus garden inoculated with Trichoderma sp. A polydimethylsiloxane (PDMS) piece of approximately 1x2 cm was placed inside a fungus garden. Exposure of the SE was allowed for 3 h. Each sample was individually transferred to a clean 2 mL borosilicate vial using clean tweezers and capped with a crimp camp with silicone septum. The GC-MS analysis was carried out using the Agilent 7200 GC/QTOF equipped with robotic sampler system. The PDMS within each vial was heated for 20 minutes at 200 oC to desorb volatiles from the PDMS and 0.5 mL of headspace injected (injector temperature set at 250 oC) into the instrument with a headspace syringe heated to 145 oC. The GC parameters were set as it follows: starting temperature 45 oC; 50 oC/min oven ramp to 100 oC (hold of 0.1 min), 15 oC/min oven ramp to 300 oC (hold of 0.1 min), and 50 oC/min oven ramp to 320 oC to purge the column. The separation was conducted on HP-5MS column (30 m x 0.25mm x 0.25 um). The helium carrier gas was set to constant 1.2 mL/min flow and a splitless injection mode was applied. The scanned m/z range was 35-400 Th with the acquisition rate of 10 spectra/s.
2019-10-01 | MSV000084401 | GNPS
Project description:The exhaled breath and blank TD tubes samples were analysed using TD-GC-MS. The TD tubes were desorbed using a Markes TD-100 thermal desorption unit (Markes International Ltd, Llantrisant, UK) using a two stage desorption programme, applying a constant flow of helium at 50 ml/min. In the primary desorption stage, TD tubes were dry-purged for 3 min and heated at 280C for 10 min. In the secondary desorption stage, the cold trap (U-T12ME-2S, Markes International Ltd, Llantrisant, UK) was rapidly (99 C/min) heated to from 10C to 290C. VOCs were transferred from the TD unit to the GC by means of a capillary line heated at 140C. GC-MS analysis was performed using an Agilent 7890B GC with 5977A MSD (Agilent Technologies Ltd, Santa Clara, USA) equipped with a ZB-642 capillary column (60m x 0.25mm ID x 1.40 um df; Phenomenex Inc, Torrance, USA) with helium used as the carrier gas (1.0 ml/min flow rate). The GC column temperature programme was set as follows: 4 min at 40C, ramp to 100C at 5C/min with a 1 min hold, ramp to 110C at 5C/min with a 1 min hold, ramp to 200C at 5C/min with a 1 min hold and finally ramp to 240C at 10C/min with a 4 min hold. The MS transfer line temperature was 240C and EI source conditions were 70 eV at 230C. Mass acquisition was carried out in the range 20-250 m/z with a rate of approximately 6 scans/s-1.
| MSV000084379 | GNPS
Project description:The exhaled breath and blank TD tubes samples were analysed using TD-GC-MS. The TD tubes were desorbed using a Markes TD-100 thermal desorption unit (Markes International Ltd, Llantrisant, UK) using a two stage desorption programme, applying a constant flow of helium at 50 ml/min. In the primary desorption stage, TD tubes were dry-purged for 3 min and heated at 280C for 10 min. In the secondary desorption stage, the cold trap (U-T12ME-2S, Markes International Ltd, Llantrisant, UK) was rapidly (99 C/min) heated to from 10C to 290C. VOCs were transferred from the TD unit to the GC by means of a capillary line heated at 140C. GC-MS analysis was performed using an Agilent 7890B GC with 5977A MSD (Agilent Technologies Ltd, Santa Clara, USA) equipped with a ZB-642 capillary column (60m x 0.25mm ID x 1.40 um df; Phenomenex Inc, Torrance, USA) with helium used as the carrier gas (1.0 ml/min flow rate). The GC column temperature programme was set as follows: 4 min at 40C, ramp to 100C at 5C/min with a 1 min hold, ramp to 110C at 5C/min with a 1 min hold, ramp to 200C at 5C/min with a 1 min hold and finally ramp to 240C at 10C/min with a 4 min hold. The MS transfer line temperature was 240C and EI source conditions were 70 eV at 230C. Mass acquisition was carried out in the range 20-250 m/z with a rate of approximately 6 scans/s-1.
| MSV000084380 | GNPS
Project description:Skin samples collected from underarm w/ PDMS for 30 seconds. Samples used for optimization of GC headspace methodology wrt desorption time, cryofocusing, and size of PDMS patch (10mL vials were used).
2018-06-26 | MSV000082511 | MassIVE
Project description:Flag-YBX1 overexpressed T24 cells pellets were resuspended with 2 volume of lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 400 U/ml RNase inhibitor), and incubated at 4 °C for 30 min with rotation. Then the lysate was centrifuged at 15 000 g for 20 min. Before incubating the lysate with Flag beads, 100ul were taken as input. The anti-Flag M2 magnetic beads (Sigma, 10 μl per mg lysate) were washed with NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 200 U/ml RNase inhibitor) four times. Cell lysate was mixed with M2 beads and incubated at 4 °C for 4 h with rotation. The beads were washed two times with 1 ml ice-cold NT2 buffer. Then the beads were subject to Micrococal nuclease (NEB) digestion (1:1 000 000 dilution) for 8 min at 37 °C. The beads were cooled on ice immediately for 5 min and washed two times with 1 ml ice-cold 1× PNK+EGTA buffer (50 mM Tris-HCl pH 7.5, 20 mM EDTA, 0.05% NP-40, 200 U/ml RNase inhibitor) and two times with 1 ml ice-cold 1× PK buffer (50 mM NaCl, 100 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.2% SDS, 200 U/ml RNase inhibitor). Then the beads were digested with 200 μl pre-heated (20 min at 50 °C) Proteinase K and RNAs were extracted with an equal volume of Acid-Phenol: Chloroform, pH 4.5 (Ambion). The RNAs were subjected to rRNA removal and Bisseq. The libraries were sequenced on the Illumina HiSeq X-Ten platform at Novogene (Tianjin, CA) with paired-end 150 bp read length.The m5C sites were called using meRanCall from meRanTK (FDR < 0.01).
2019-07-02 | GSE133625 | GEO
Project description:Skin sampling has been conducted as described in the [Molecular cartography of the human skin surface in 3D Amina Bouslimani, Carla Porto, Christopher M. Rath, Mingxun Wang, Yurong Guo, Antonio Gonzalez, Donna Berg-Lyon, Gail Ackermann, Gitte Julie Moeller Christensen, Teruaki Nakatsuji, Lingjuan Zhang, Andrew W. Borkowski, Michael J. Meehan, Kathleen Dorrestein, Richard L. Gallo, Nuno Bandeira, Rob Knight, Theodore Alexandrov, and Pieter C. Dorrestein PNAS April 28, 2015 112 (17) E2120-E2129] by swabbing areas of skin with a cotton swab and extracting the swabs using ethanol. The samples were stored in -80 C freezer until analysis. The GC-MS analysis was carried out on a Thermo Scientific TRACE 1310 GC-MS [TG-5ms 5; length, 30 m; ID (inner diameter), 0.25 mm; film thickness column, 0.25 um] and a TSQ 8000 EVO mass spectrometer (Thermo Fisher Scientific), equipped with electron ionization (EI) source, equipped with robotic sampler system. 1uL aliquot of sample was injected into the GC inlet maintained at 250C. The GC protocol was as follows: starting temperature 40 C (hold of 0.1 min), 15 C/min oven ramp to 280 C (hold of 0.1 min), and a 3 min hold period to purge the column. The helium carrier gas was set to constant 2 mL/min flow, splitless injection mode was used throughout. The scanned m/z range in a single quadrupole was 35-350 Th with solvent delay of 4 minutes.
| MSV000084378 | GNPS
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
Project description:Skin samples collected from underarm w/ PDMS for 30 seconds. Samples used for optimization of GC headspace methodology wrt desorption time, cryofocusing, and size of PDMS patch (10mL vials were used).
2018-06-26 | MSV000082511 | GNPS
Project description:Odor-active volatile sulfur compounds are formed in heated food protein systems. In the present study, hydrogen sulfide (H2S) was found to be the most abundant sulfur volatile in whey protein systems (whey protein isolate (WPI), a whey model system and single whey proteins) by Gas Chromatography-Flame Photometric Detector (GC-FPD) analysis after different heat treatments (60-90 C for 10 min, 90 C for 120 min and a UHT-like condition). Site-specific LC-MS/MS-based proteomic analysis was conducted to monitor desulfurization reactions in these protein systems to investigate the mechanism of H2S formation in heated WPI. H2S was detected in WPI after heating at 90 C for 10 min, and significantly increased at higher heat load (90 C for 120 min and the UHT treatment), which revealed the temperature- and time-dependence of heat-induced H2S generation in WPI. Cysteine (Cys) residues from beta-lactoglobulin were found to be responsible for the formation of H2S in heated WPI, presumably via beta-elimination.
2022-02-10 | MSV000088811 | MassIVE
Project description:High and moderate intensity endurance exercise alters gene expression in human white blood cells (WBCs), but the understanding of how this effect occurs is limited. To increase our knowledge of the nature of this process, we investigated the effects of passing the anaerobic threshold (AnT) on the gene expression profile in WBCs of athletes. Nineteen highly trained skiers participated in a treadmill test with an incremental step protocol until exhaustion (ramp test to exhaustion; RTE). The average total time to exhaustion was 14:40 min and time after AnT was 4:50 min. Two weeks later, seven of these skiers participated in a moderate treadmill test (MT) at 80% peak O2 uptake for 30 min, which was slightly below their AnTs. Blood samples were obtained before and immediately after both tests. RTE was associated with substantially greater leukocytosis and acidosis than MT. Gene expression in WBCs was measured using whole genome microarray expression analysis before and immediately after each test. A total of 310 upregulated genes were found after RTE, and 69 genes after MT, of which 64 were identical to RTE. Both tests influenced a variety of known gene pathways related to inflammation, stress response, signal transduction and apoptosis. A large group of differentially expressed, and previously unknown, small nucleolar RNA and small Cajal body RNA was found. In conclusion, a 15 min test to exhaustion was associated with substantially greater changes of gene expression than a 30 min test just below the AnT. After a general medical checkup, the subjects performed a ramp-type progressive exercise test on a treadmill. Blood samples were taken from the antecubital vein using indwelling catheter before (T0) and immediately after ramp test to exaustion (T1), and before (T2) and immediately after moderate treadmill test (T3).
2011-04-09 | E-GEOD-28498 | biostudies-arrayexpress