Arabidopsis thaliana sprayed with cWP or water
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Exploris 240
ORGANISM(S): Arabidopsis Thaliana (ncbitaxon:3702)
SUBMITTER: 
Bret Cooper
PROVIDER: MSV000096166 | MassIVE | Tue Oct 22 11:53:00 BST 2024
REPOSITORIES: MassIVE
Similar Datasets
Project description:Primary leaves of 10-day-old Phaseolus vulgaris (common bean) variety Black Valentine plants were infiltrated with 30 uM cWP or water (control) using a flat-nosed 1 mL syringe. The two primary leaves on each plant were each infiltrated 8 times (4 times on each half leaf) with a single compound. Infiltration was performed on the abaxial side without puncturing the leaf, and each infiltration produced a 1 cm2 water-soaked area. After 24 hours, the leaf tissue at the site of infiltration was sampled with a 1 cm diameter cork-borer. Ten to twelve sites were collected from each plant to reach approximately 170 mg total tissue which was extracted in 1 mL 100% methanol. Seven separate plants of each treatment were used to generate seven replicates. Tissues were pulverized with 0.5 mm glass beads with a Qiagen PowerLyzer 24 bead mill (Qiagen, Hilden, Germany) 10 times at 5,000 rpm for 20 sec (cooled on ice for 2 min between cycles). Two matrix blank samples were prepared the same way starting with 10 mL Luria broth (without tissue or compounds). The milled extracts were centrifuged for 20 min at 12,000 x g. The supernatants were transferred to fresh tubes and centrifuged again. The supernatants were transferred to glass vials and dried under vacuum. The residues were resuspended in 115 uL 50% methanol/0.1% formic acid. Fifteen uL of each sample was pooled to create a quality control (QC) sample. Five uL of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-min linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per min. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Five subsequent injections of the QC were performed to generate tandem mass spectra (MS2). After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank 1, QC 1, sample replicate set 1, sample replicate set 2, Blank 2, QC 2, sample replicate set 3, sample replicate set 4, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. The samples also were analyzed in negative ion mode at -2,500 V but with the same other settings.
2024-10-22 | MSV000096165 | MassIVE
Project description:P. savastanoi pv. phaseolicola isolates race 5 (R5) was cultured in 10 mL Luria broth with 400 uM genistein, 400 uM daidzein, or without but with 50 uL DMSO at 28 C at 200 rpm on a shaking platform until the control cultures reached late log-phase growth measured at an optical density of 0.75-0.90 at 600 nm wavelength of visible light. Five replicate cultures of each treatment were centrifuged at 5,000 x g for 10 min, washed once in 1 mL phosphate buffered saline, centrifuged at 5,000 x g for 10 min, resuspended in 1 mL of 1:1:1:1 acetone/acetonitrile/methanol/water and 1,250 pmol prednisone, and pulverized with 0.5 mm glass beads with a Qiagen PowerLyzer 24 bead mill (Qiagen, Hilden, Germany) 10 times at 5,000 rpm for 20 sec (cooled on ice for 2 min between cycles). Two matrix blank samples were prepared the same way starting with 10 mL Luria broth (without R5 and without genistein or daidzein). The milled extracts were centrifuged for 20 min at 12,000 x g. The supernatants were transferred to fresh tubes and centrifuged again. The supernatants were transferred to glass vials and dried under vacuum. The residues were resuspended in 115 uL 50% methanol/0.1% formic acid. Fifteen uL of each sample was pooled to create a quality control (QC) sample. Five uL of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-min linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per min. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Five subsequent injections of the QC were performed to generate tandem mass spectra (MS2). After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank 1, QC 1, sample replicate set 1, Blank 2, QC 2, sample replicate set 2, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. The samples also were analyzed in negative ion mode at -2,500 V but with the same other settings.
2024-10-22 | MSV000096150 | MassIVE
Project description:P. savastanoi pv. phaseolicola isolate R5 was cultured in 10 mL Luria broth with 400 uM genistein or without (but with 50 uL DMSO) at 28 C at 200 rpm on a shaking platform. Replicate R5 cultures of each treatment were centrifuged at 5,000 x g for 10 min., washed once in 1 mL phosphate buffered saline, centrifuged at 5,000 x g for 10 min., resuspended in 1 mL of 1:1:1:1 acetone/acetonitrile/methanol/water and 1,2500 pmol prednisone, and pulverized in the bead mill as before. Two matrix blank samples were prepared the same way starting with 10 mL Luria broth (without R5 and without genistein). The milled extracts were centrifuged for 20 minutes at 12,000 x g. The supernatants were transferred to fresh tubes and centrifuged again. The supernatants were transferred to glass vials and dried under vacuum. The residues were resuspended in 115 uL 50% methanol/0.1% formic acid. Fifteen uL of each sample was pooled to create a quality control (QC) sample. Five uL of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-minute linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per minute. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Three subsequent injections of the QC were performed to generate MS2 spectra. After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank 1, QC 1, sample replicate set 1, Blank 2, QC 2, sample replicate set 2, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. The samples also were analyzed in negative ion mode at -2,500 V but with the same other settings.
| MSV000092831 | MassIVE
Project description:Primary leaves of 10-day-old Phaseolus vulgaris (common bean) variety Black Valentine plants were infiltrated with 30 uM cFP, cGP, cLP, cWP, or auxin (indole-3-acetic acid, Sigma Aldrich), or water (control) using a flat-nosed 1 mL syringe. The two primary leaves on each plant were each infiltrated 8 times (4 times on each half leaf) with a single compound. Infiltration was performed on the abaxial side without puncturing the leaf, and each infiltration produced a 1 cm2 water-soaked area. After 24 hours, the leaf tissue at the site of infiltration was sampled with a 1 cm diameter cork-borer. Ten to twelve sites were collected from each plant to reach approximately 170 mg total tissue which was extracted in 1 mL 100% methanol. Four separate plants of each treatment were used to generate four replicates. Tissues were pulverized with 0.5 mm glass beads with a Qiagen PowerLyzer 24 bead mill (Qiagen, Hilden, Germany) 10 times at 5,000 rpm for 20 sec (cooled on ice for 2 min between cycles). Two matrix blank samples were prepared the same way but without tissue or compounds. The milled extracts were centrifuged for 20 min at 12,000 x g. The supernatants were transferred to fresh tubes and centrifuged again. The supernatants were transferred to glass vials and dried under vacuum. The residues were resuspended in 115 uL 50% methanol/0.1% formic acid. Fifteen uL of each sample was pooled to create a quality control (QC) sample. Five uL of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-min linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per min. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Five subsequent injections of the QC were performed to generate tandem mass spectra (MS2). After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank 1, QC 1, sample replicate set 1, Blank 2, QC 2, sample replicate set 2, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. The samples also were analyzed in negative ion mode at -2,500 V but with the same other settings.
2024-10-22 | MSV000096164 | MassIVE
Project description:R5 was cultured in 10 mL Luria broth with 1.0 mM resveratrol or without (but with 50 uL DMSO) at 28 C at 200 rpm on a shaking platform until the cultures reached an average O.D. of 1.0 at 600 nm. Five replicate cultures were used for metabolomics experimentation. The samples were centrifuged at 5,000 x g for 10 min., washed once in 1 mL phosphate buffered saline, centrifuged at 5,000 x g for 10 min., resuspended in 1 mL of 1:1:1:1 acetone/acetonitrile/methanol/water and 1,2500 pmol prednisone, and pulverized in the bead mill. Two matrix blank samples were prepared the same way starting with 10 mL Luria broth (without R5 and without resveratrol). The milled extracts were centrifuged for 20 minutes at 12,000 x g. The supernatants were transferred to fresh tubes and centrifuged again. The supernatants were transferred to glass vials and dried under vacuum. The residues were resuspended in 115 ul 50% methanol/0.1% formic acid. Fifteen ul of each sample was pooled to create a QC sample. Five ul of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-minute linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per minute. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Four subsequent injections of the QC were performed to generate MS2 spectra. After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank1, QC1, sample replicates 1, Blank2, QC2, sample replicates 2, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%.
2022-08-22 | MSV000090172 | MassIVE
Project description:P. savastanoi pv. phaseolicola isolate R5 was cultured in 10 mL Luria broth with 400 uM genistein or without (but with 50 uL DMSO) at 28 C at 200 rpm on a shaking platform. Replicate R5 cultures of each treatment were centrifuged at 5,000 x g for 10 min., washed once in 1 mL phosphate buffered saline, centrifuged at 5,000 x g for 10 min., resuspended in 1 mL of 1:1:1:1 acetone/acetonitrile/methanol/water and 1,2500 pmol prednisone, and pulverized in the bead mill as before. Two matrix blank samples were prepared the same way starting with 10 mL Luria broth (without R5 and without genistein). The milled extracts were centrifuged for 20 minutes at 12,000 x g. The supernatants were transferred to fresh tubes and centrifuged again. The supernatants were transferred to glass vials and dried under vacuum. The residues were resuspended in 115 uL 50% methanol/0.1% formic acid. Fifteen uL of each sample was pooled to create a quality control (QC) sample. Five uL of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-minute linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per minute. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Three subsequent injections of the QC were performed to generate MS2 spectra. After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank 1, QC 1, sample replicate set 1, Blank 2, QC 2, sample replicate set 2, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. The samples also were analyzed in negative ion mode at -2,500 V but with the same other settings.
| MSV000092831 | GNPS
Project description:R5 was cultured in 10 mL Luria broth with 1.0 mM resveratrol or without (but with 50 uL DMSO) at 28 C at 200 rpm on a shaking platform until the cultures reached an average O.D. of 1.0 at 600 nm. Five replicate cultures were used for metabolomics experimentation. The samples were centrifuged at 5,000 x g for 10 min., washed once in 1 mL phosphate buffered saline, centrifuged at 5,000 x g for 10 min., resuspended in 1 mL of 1:1:1:1 acetone/acetonitrile/methanol/water and 1,2500 pmol prednisone, and pulverized in the bead mill. Two matrix blank samples were prepared the same way starting with 10 mL Luria broth (without R5 and without resveratrol). The milled extracts were centrifuged for 20 minutes at 12,000 x g. The supernatants were transferred to fresh tubes and centrifuged again. The supernatants were transferred to glass vials and dried under vacuum. The residues were resuspended in 115 ul 50% methanol/0.1% formic acid. Fifteen ul of each sample was pooled to create a QC sample. Five ul of the samples were separated on a 150 x 2.1 mm Hypersil GOLD VANQUISH HPLC column with 1.9 um particles (Thermo Fisher Scientific) coupled to a Vanquish HPLC pump (Thermo Fisher Scientific) controlling a 10-minute linear gradient from 0% to 95% acetonitrile and 0.1% formic acid at a flow rate of 0.2 mL per minute. Eluent was electrosprayed at 3.5 kV positive polarity into an Exploris 240 mass spectrometer (Thermo Fisher Scientific) using an internal mass calibrant. Sheath gas was 35, auxiliary gas was 7, and sweep gas was 1 (arbitrary units). The ion transfer tube temperature was 325 C and the vaporizer temperature was 275 C. Advanced peak determination, mild trapping, and internal mass calibration was enabled. Default charge state was 1 and the expected peak width was 6 sec. AcquireX software was used to create a background ion exclusion list from the matrix blank sample and an inclusion ion list from the QC sample. Four subsequent injections of the QC were performed to generate MS2 spectra. After each QC injection, the resolved ions were appended to the exclusion list. Survey scans were recorded in the Orbitrap at 60,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%. Monoisotopic precursor selection was enabled, the minimum intensity was 5,000, and charge states were filtered to 1. Precursors selected within a 1.0 Da isolation window were fragmented by high energy collision-induced dissociation (30%, 50%, 70% normalized stepped collision energy), and fragment ions were resolved in the Orbitrap at 30,000 resolution. Subsequently, all test samples were analyzed alongside QC and matrix blank samples in the following order: Matrix blank1, QC1, sample replicates 1, Blank2, QC2, sample replicates 2, etc. Survey scans were recorded in the Orbitrap at 120,000 resolution over a mass range of 70-800 m/z. The RF lens was 70%.
2022-08-22 | MSV000090172 | GNPS
Project description:A Thermo Vanquish UPLC system (ThermoFisher, Waltham, MA, USA) coupled with a Hybrid Quadrupole Orbitrap Q Exactive mass spectrometer (ThermoFisher) was used for small molecule analysis of study samples. Bourbon molecules were separated using an Xbridge BEH Amide (2.5 um, 2.1 x 150 mm, Waters, Milford, MA, USA) column. The mobile phases consisted of solvents A and B, where A contained 5 mM ammonium acetate, 0.1% acetic acid in 90% H2O/10% acetonitrile (ACN) and B contained 5 mM ammonium acetate, 0.1% acetic acid in 10% H2O/90% ACN. A gradient of mobile phase injection was used for 20 minutes at a flow rate of 0.3 mL/min, starting with 30% of mobile phase A and increasing to 70% at 5 min. The proportion of mobile phase A was maintained at 70% until 9 min, and then started to decrease to 30% until 11 min. The percentage of solvent A was then kept at 70% until 20 min, after which it gradually returned to 30% to prepare for the next injection. To observe and prove the consistency of the instrument during testing and to enable data normalization, a pooled quality control (QC) was added to the sample tray after every ten sample injections in both sequences. A blank sample was added after each QC sample.
2023-08-18 | MSV000092689 | MassIVE
Project description:We observed the expression profile of the total mRNA in Thermus thermophilus HB8 csrR deficient strain at 0 and 30 min after the addition of CuSO4. Three csoR deficient strain of T. thermophilus HB8 were pre-cultured at 70 degC for 16 hours in 3 mL of TT medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (1 mL) were inoculated into 250 mL of the synthetic medium and then cultivated at 70°C for 8 hours (A600 value being ~0.4). Then the 1.25 mM of CuSO4 was added into the medium, and continued cultivation. Cells were collected at 0 and 30 min time point after the addition of copper ion, and then crude RNA was extracted. The expression of each mRNA at each time point was analyzed on a GeneChip as described under Sample Description Sheet of each sample.
2010-04-13 | E-GEOD-19509 | biostudies-arrayexpress