Dataset Information

MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments

ABSTRACT: This dataset reports the UPLC-QTof MS untargeted analysis of Vitis vinifera L. leaves, collected from Italy (Trentino) and Germany (Mecklenburg West-Pomerania), from two fungus-resistant grape varieties (PIWI), Regent and Phoenix. For each variety, 40 leaves were sampled from 10 plants (4 leaves/plant) in Italy, and other 40 with the same process in Germany. The leaves from each plant were homogenized and extracted separately, in the same day, under a randomized order. A quality control (QC) sample was prepared by pooling a small aliquot from each sample.

The aim of the project, was to use this sample/data set as an illustrative example for the use the pipeline MetaDB (https://github.com/rmylonas/MetaDB). MetaDB has been developed in order to combine, with a user-friendly web based, different bioinformatic tools used in metabolomics, which takes care a) metadata organization, b) creation of randomized sequences including QC sample, c) data quality evaluation, d) data storage organization, e) data analysis and f) submission to public repositories.

INSTRUMENT(S): SYNAPT HDMS (Waters)

PROVIDER: MTBLS137 | MetaboLights | 2014-11-09

REPOSITORIES: MetaboLights

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 105

Publications

MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments.

Franceschi Pietro P Mylonas Roman R Shahaf Nir N Scholz Matthias M Arapitsas Panagiotis P Masuero Domenico D Weingart Georg G Carlin Silvia S Vrhovsek Urska U Mattivi Fulvio F Wehrens Ron R

Frontiers in bioengineering and biotechnology 20141216

Due to their sensitivity and speed, mass-spectrometry based analytical technologies are widely used to in metabolomics to characterize biological phenomena. To address issues like metadata organization, quality assessment, data processing, data storage, and, finally, submission to public repositories, bioinformatic pipelines of a non-interactive nature are often employed, complementing the interactive software used for initial inspection and visualization of the data. These pipelines often are c ...[more]

PMID: 25566535

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.

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.

			Action	DRS
	L001_BLANK_RP_POS01.CDF	Other
	L001_Blank_RP_pos.mzML	Mzml
	L002_QC_RP_POS01.CDF	Other
	L002_QC_RP_pos.mzML	Mzml
	L003_QC_RP_pos.mzML	Mzml