Summary of Study ST001934

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001223. The data can be accessed directly via it's Project DOI: 10.21228/M8MQ47 This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001934
Study TitleDifferential Accumulation of Metabolites and Transcripts Related to Flavonoid, Styrylpyrone, and Galactolipid Biosynthesis in Equisetum Species and Tissue Types
Study SummaryMembers of the genus Equisetum are often referred to as “living fossils”, partly because they are the only extant representatives of the Equisetidae, a subclass that was once prominent in late Paleozoic forests. Several classes of specialized metabolites have been reported to occur in the genus Equisetum. However, while steady progress is being made with identifying individual novel metabolites of Equisetum, few if any analyses have focused on assessing the chemical diversity across the genus. The present study focused on three species: E. hyemale subsp. affine (rough horsetail or scouring rush), which is native to the temperate to artic portions of North America; E. arvense (common horsetail), which is endemic to the arctic and temperate regions of the northern hemisphere; and Equisetum telmateia subsp. braunii (Milde) Hauke (giant horsetail), which is native to western North America. Both below-ground rhizome and above-ground shoot material was harvested from each species, extracted with aqueous methanol, and subjected to non-targeted HPLC-QTOF-MS analysis. This research project was designed to lay the foundation for continued research to capture the metabolic capabilities in the ferns and fern allies.
Institute
Washington State University
DepartmentInstitute of Biological Chemistry
LaboratoryLange
Last NameLange
First NameMark
AddressPlant Sciences Building, Pullman, Washington 99164
Emaillange-m@wsu.edu
Phone+1-509-335-3794
Submit Date2021-09-24
Num Groups6
Total Subjects30
Publicationshttps://doi.org/10.3390/metabo12050403
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2022-05-09
Release Version1
Mark Lange Mark Lange
https://dx.doi.org/10.21228/M8MQ47
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001223
Project DOI:doi: 10.21228/M8MQ47
Project Title:Differential Accumulation of Metabolites and Transcripts Related to Flavonoid, Styrylpyrone, and Galactolipid Biosynthesis in Equisetum Species and Tissue Types
Project Summary:Members of the genus Equisetum are often referred to as “living fossils”, partly because they are the only extant representatives of the Equisetidae, a subclass that was once prominent in late Paleozoic forests. Several classes of specialized metabolites have been reported to occur in the genus Equisetum. However, while steady progress is being made with identifying individual novel metabolites of Equisetum, few if any analyses have focused on assessing the chemical diversity across the genus. The present study focused on three species: E. hyemale subsp. affine (rough horsetail or scouring rush), which is native to the temperate to artic portions of North America; E. arvense (common horsetail), which is endemic to the arctic and temperate regions of the northern hemisphere; and Equisetum telmateia subsp. braunii (Milde) Hauke (giant horsetail), which is native to western North America. Both below-ground rhizome and above-ground shoot material was harvested from each species, extracted with aqueous methanol, and subjected to non-targeted HPLC-QTOF-MS analysis. This research project was designed to lay the foundation for continued research to capture the metabolic capabilities in the ferns and fern allies.
Institute:Washington State University
Department:Institute of Biological Chemistry
Laboratory:Lange
Last Name:Lange
First Name:Mark
Address:Plant Sciences Building, Pullman, Washington 99164
Email:lange-m@wsu.edu
Phone:+1-509-335-3794

Subject:

Subject ID:SU002012
Subject Type:Plant
Subject Species:Equisetum arvense;Equisetum hyemale;Equisetum telmateia

Factors:

Subject type: Plant; Subject species: Equisetum arvense;Equisetum hyemale;Equisetum telmateia (Factor headings shown in green)

mb_sample_id local_sample_id Species Organ
SA181847Ea_rhiz_1E. arvense rhizome
SA181848Ea_rhiz_5E. arvense rhizome
SA181849Ea_rhiz_4E. arvense rhizome
SA181850Ea_rhiz_2E. arvense rhizome
SA181851Ea_rhiz_3E. arvense rhizome
SA181852Ea_stem_5E. arvense stem
SA181853Ea_stem_4E. arvense stem
SA181854Ea_stem_2E. arvense stem
SA181855Ea_stem_1E. arvense stem
SA181856Ea_stem_3E. arvense stem
SA181857Eh_rhiz_5E. hyemale rhizome
SA181858Eh_rhiz_4E. hyemale rhizome
SA181859Eh_rhiz_3E. hyemale rhizome
SA181860Eh_rhiz_1E. hyemale rhizome
SA181861Eh_rhiz_2E. hyemale rhizome
SA181862Eh_stem_5E. hyemale stem
SA181863Eh_stem_4E. hyemale stem
SA181864Eh_stem_1E. hyemale stem
SA181865Eh_stem_3E. hyemale stem
SA181866Eh_stem_2E. hyemale stem
SA181867Et_rhiz_4E. telmateia rhizome
SA181868Et_rhiz_5E. telmateia rhizome
SA181869Et_rhiz_3E. telmateia rhizome
SA181870Et_rhiz_1E. telmateia rhizome
SA181871Et_rhiz_2E. telmateia rhizome
SA181872Et_stem_5E. telmateia stem
SA181873Et_stem_4E. telmateia stem
SA181874Et_stem_2E. telmateia stem
SA181875Et_stem_1E. telmateia stem
SA181876Et_stem_3E. telmateia stem
Showing results 1 to 30 of 30

Collection:

Collection ID:CO002005
Collection Summary:E. arvense, E. hyemale and E. telmateia (voucher specimens deposited with the John G. Searle Herbarium of the Field Museum, Chicago, IL, USA) were maintained in a greenhouse under ambient lighting, with supplemental lighting from sodium- vapor lamps. The photosynthetically active radiation varied from 15 to 25 mol m-2 d-1. Temperatures ranged between 22 and 27 °C and the humidity was set to 70 ± 10 %. Five biological replicates (separate plants) were harvested at the same time of day for below-ground rhizomes and above-ground stems of vegetative shoots. Samples were snap-frozen in liquid nitrogen and freeze-dried (aerial parts for 5 days, rhizomes for 7 days). Lyophilized material was submerged in liquid nitrogen, homogenized using mortar and pestle.
Sample Type:Tissue homogenate
Storage Conditions:-80 °C

Treatment:

Treatment ID:TR002024
Treatment Summary:No Treatment

Sample Preparation:

Sampleprep ID:SP002018
Sampleprep Summary:Five biological replicates (separate plants) were harvested at the same time of day for below-ground rhizomes and above-ground stems of vegetative shoots. Samples were snap-frozen in liquid nitrogen and freeze-dried (aerial parts for 5 days, rhizomes for 7 days). Lyophilized material was submerged in liquid nitrogen, homogenized using mortar and pestle.
Extraction Method:Frozen tissue homogenate (30 mg per sample) was transferred to a 2 ml reaction tube and extracted with 1 ml of 80 % aqueous methanol (containing 10 mg/l anthracene-9-carboxylic acid as internal standard) by vigorous shaking (VX-2500 multi-tube vortexer, VWR Scientific, South Plainfield, NY, USA) for 10 min and subsequent sonication for 20 min (FS30 ultrasonic cleaner, Fisher Scientific, Hampton, NY, USA). Following centrifugation for 10 min at 13,000 × g (5415 microfuge, Eppendorf, Enfield, CT, USA), the supernatant was filtered through 0.22 μm polypropylene syringe filter tips, and the flow-through collected in plastic inserts for 2 ml reaction vials.

Combined analysis:

Analysis ID AN003144
Analysis type MS
Chromatography type HPLC
Chromatography system Agilent 1290 HPLC
Column HD Zorbax SB-Aq (100 × 2.1 × mm, 1.8 µm)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6530 QTOF
Ion Mode POSITIVE
Units Peak area

Chromatography:

Chromatography ID:CH002326
Instrument Name:Agilent 1290 HPLC
Column Name:HD Zorbax SB-Aq (100 × 2.1 × mm, 1.8 µm)
Column Temperature:60 °C
Flow Gradient:5 % B to 10 % B at 5 min, 20 % B at 10 min, 80 % B at 35 min, 95 % B at 45 min
Flow Rate:0.6 ml/min
Internal Standard:10 mg/l Anthracene-9-carboxylic acid
Sample Injection:10 ul
Solvent A:0.1 % formic acid in water
Solvent B:0.1 % formic acid in acetonitrile
Target Sample Temperature:Autosampler set to 4 °C
Chromatography Type:HPLC

MS:

MS ID:MS002924
Analysis ID:AN003144
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:HPLC–QTOF–MS with electrospray ion source (positive ion mode) Raw data sets were opened in the Profinder B.06.00 build 6.0.0625.0 software package (Agilent Technologies, Santa Clara, CA, USA) and molecular feature elements (MFEs) obtained using the Batch Recursive Feature Extraction algorithm. Binning and alignment tolerances were set to 10 % + 20 s for the retention time and 10 ppm + 2 mDa for the mass accuracy, and 0.0025 m/z + 5.0 ppm for the isotope grouping space tolerance. Additional parameters that were considered for feature extraction were quasi-molecular ions and adducts ([M+H]+, [M+Na]+, [M+K]+, [M+NH4]+), dimers, neutral losses (H2O, H3PO4, C6H10O5 (glucose), C12H20O9 (rutinose), C12H20O10 (sophorose), C6H10O4 (rhamnose), and C5H8O4 (xylose)), absolute peak height ≥ 2000 counts, and occurrence required in a minimum of four of the five replicates of each sample type. These pre-processing steps generated 848 MFEs (849 including ISTD), and exported into an Excel spreadsheet. Additional exclusion criteria for MFEs were: relative standard deviation of mass accuracy > 5.0 ppm; percent relative standard deviation returned as ”NaN” (Not a Number) or an empty cell; an unacceptably close accurate mass and retention time (± 0.010 m/z and ± 0.02 min.; screened as duplicates); or if it was a fragment. This additional filtering returned 544 remaining MFEs. Peak areas of MFEs for each sample were normalized based on sample weight and the peak area of the internal standard (MFEs without a peak area were filled in with a nominal value of two).
Ion Mode:POSITIVE
Source Temperature:325 °C
Dataformat:.d
Nebulizer:2.4 bar
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