Summary of Study ST004422

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 PR002793. The data can be accessed directly via it's Project DOI: 10.21228/M8N26R This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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.

Study ID	ST004422
Study Title	Metabolomics in biotic stress: an example from potato powdery scab
Study Type	MS-Based metabolomics
Study Summary	The experimental design for this study included potato cultivars that were selected on the basis of their contrasting resistance to infection by the soilborne pathogen Spongospora subterranea. Potato plants were grown in tissue culture under standard conditions (n=8 per cultivar) and then half were selected for inoculation with Hoagland’s solution containing zoospores released from S. subterranea sporosori (aggregates of resting spores). An additional inoculum of 20 mg dried sporosori was added to each pot 14 days after planting to maintain consistent pathogen pressure. At 42 days post-inoculation, when root galls were visible, roots were harvested, washed, frozen in liquid nitrogen, and stored at -80 °C until further analysis.
Institute	University of Tasmania
Department	Science and Engineering
Laboratory	Central Science Laboratory
Last Name	Wilson
First Name	Richard
Address	University of Tasmania Chemistry Building, Room 334, Dobson Rd, Sandy Bay, Hobart 7001, TAS, Australia
Email	richard.wilson@utas.edu.au
Phone	0413535934
Submit Date	2025-12-02
Num Groups	4
Total Subjects	16
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-12-15
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR002793
Project DOI:	doi: 10.21228/M8N26R
Project Title:	Metabolomics in biotic stress: an example from potato powdery scab
Project Type:	MS-based non-targeted metabolomics
Project Summary:	Powdery scab, caused by the soilborne pathogen Spongospora subterranea, is a widespread and persistent disease affecting potato roots and tubers worldwide. The pathogen produces highly durable resting spores that can survive in soil for decades, complicating crop rotation and soil management strategies. Previous studies from our laboratory employed transcriptomics and proteomics to investigate cultivar-specific responses to infection. We observed that a set of glutathione S-transferase (GST) genes and proteins were consistently upregulated in the resistant cultivar Gladiator, whereas the susceptible cultivar Iwa showed minimal induction. The present study aimed to use untargeted metabolomics to examine root biochemical changes in resistant and susceptible potato cultivars following S. subterranea infection. The results identify clear differences in the metabolite profile of resistant and susceptible potato cultivars and demonstrate that cysteinyl-glycine accumulates only in the resistant potato cultivar during infection, providing further biochemical evidence that glutathione S-transferase-linked detoxification mediates resistance to Spongospora subterranea.
Institute:	University of Tasmania
Department:	Science and Engineering
Laboratory:	Central Science Laboratory
Last Name:	Wilson
First Name:	Richard
Address:	University of Tasmania Chemistry Building, Room 334, Dobson Rd, Sandy Bay, Hobart 7001, TAS, Australia
Email:	richard.wilson@utas.edu.au
Phone:	0413535934

Subject:

Subject ID:	SU004582
Subject Type:	Plant
Subject Species:	Solanum tuberosum
Taxonomy ID:	4113

Factors:

Subject type: Plant; Subject species: Solanum tuberosum (Factor headings shown in green)

mb_sample_id	local_sample_id	Sample source	Factor
SA522594	GC3	Potato Root	Gladiator Control
SA522595	GC4	Potato Root	Gladiator Control
SA522596	GC5	Potato Root	Gladiator Control
SA522597	GC2	Potato Root	Gladiator Control
SA522598	GT5	Potato Root	Gladiator Treated
SA522599	IC1	Potato Root	Gladiator Treated
SA522600	GT4	Potato Root	Gladiator Treated
SA522601	GT3	Potato Root	Gladiator Treated
SA522602	GT1	Potato Root	Gladiator Treated
SA522603	IC2	Potato Root	Iwa Control
SA522604	IC3	Potato Root	Iwa Control
SA522605	IC5	Potato Root	Iwa Control
SA522606	IT1	Potato Root	Iwa Treated
SA522607	IT2	Potato Root	Iwa Treated
SA522608	IT4	Potato Root	Iwa Treated
SA522609	IT5	Potato Root	Iwa Treated
SA522610	n/a	Potato Root	n/a

Showing results 1 to 17 of 17

Showing results 1 to 17 of 17

Collection:

Collection ID:	CO004575
Collection Summary:	At 42 days post-inoculation of the potato plants with Spongospora subterranea, when root galls were visible, roots were harvested, washed in PBS then frozen in liquid nitrogen and stored at -80 °C until sample preparation.
Sample Type:	Roots

Treatment:

Treatment ID:	TR004591
Treatment Summary:	Potato plants were grown in tissue culture under standard conditions using Murashige and Skoog (MS) medium supplemented with 500 mg/L casein hydrolysate, 30 g/L sucrose, and 40 mg/L ascorbic acid. After three weeks, plants were removed from the MS medium and roots were inoculated by suspending them in Hoagland’s solution containing zoospores released from S. subterranea sporosori. The inoculated plants were then transplanted into pots with sterilized potting mix and grown in a glasshouse at 25 ± 3°C and 80 ± 5% relative humidity for 6 weeks. An additional inoculum of 20 mg dried sporosori was added to each pot 14 days after planting to maintain consistent pathogen pressure. At 42 days post-inoculation, when root galls were visible, roots were harvested, washed, frozen in liquid nitrogen, and stored at -80 °C until further analysis.

Treatment ID:

TR004591

Treatment Summary:

Potato plants were grown in tissue culture under standard conditions using Murashige and Skoog (MS) medium supplemented with 500 mg/L casein hydrolysate, 30 g/L sucrose, and 40 mg/L ascorbic acid. After three weeks, plants were removed from the MS medium and roots were inoculated by suspending them in Hoagland’s solution containing zoospores released from S. subterranea sporosori. The inoculated plants were then transplanted into pots with sterilized potting mix and grown in a glasshouse at 25 ± 3°C and 80 ± 5% relative humidity for 6 weeks. An additional inoculum of 20 mg dried sporosori was added to each pot 14 days after planting to maintain consistent pathogen pressure. At 42 days post-inoculation, when root galls were visible, roots were harvested, washed, frozen in liquid nitrogen, and stored at -80 °C until further analysis.

Sample Preparation:

Sampleprep ID:	SP004588
Sampleprep Summary:	Briefly, 50 mg of frozen potato root tissue was homogenized in a protein extraction buffer using a bead beater. Following homogenization, the extracts were centrifuged at 16,000 g for 10 minutes in a cold room (4°C). The supernatant was then mixed with six volumes of absolute acetone, precooled to -20°C, and stored at -20°C overnight. The samples were centrifuged at 10,000 g for 8 minutes to separate the proteins from the soluble components. The supernatant was used for metabolite analysis, providing a distinct phase for the evaluation of metabolites without the interference of proteins.

Sampleprep ID:

SP004588

Sampleprep Summary:

Briefly, 50 mg of frozen potato root tissue was homogenized in a protein extraction buffer using a bead beater. Following homogenization, the extracts were centrifuged at 16,000 g for 10 minutes in a cold room (4°C). The supernatant was then mixed with six volumes of absolute acetone, precooled to -20°C, and stored at -20°C overnight. The samples were centrifuged at 10,000 g for 8 minutes to separate the proteins from the soluble components. The supernatant was used for metabolite analysis, providing a distinct phase for the evaluation of metabolites without the interference of proteins.

Combined analysis:

Analysis ID	AN007399
Chromatography ID	CH005606
MS ID	MS007092
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Thermo Dionex Ultimate 3000 RS
Column	Thermo Acclaim Polar Advantage II (150 x 3 mm, 3 µm)
MS Type	ESI
MS instrument type	Orbitrap
MS instrument name	Thermo Q Exactive HF hybrid Orbitrap
Ion Mode	POSITIVE
Units	Intensity

Chromatography:

Chromatography ID:	CH005606
Chromatography Summary:	Stepped gradient separation over 20 minutes, using HPLC column held at 35 degrees and 0.3 mL/min flow rate.
Instrument Name:	Thermo Dionex Ultimate 3000 RS
Column Name:	Thermo Acclaim Polar Advantage II (150 x 3 mm, 3 µm)
Column Temperature:	35°C
Flow Gradient:	0-1 min 2%B; 1-2.5 min 2-20%B; 2.5-13 min 20-65%B; 13-14 min 65-95%B; 14-15 min 95%B held; 15-20 min 2%B held
Flow Rate:	0.3 mL/min
Solvent A:	Water + 0.1% formic acid
Solvent B:	Acetonitrile + 0.1% formic acid
Chromatography Type:	Reversed phase

MS:

MS ID:	MS007092
Analysis ID:	AN007399
Instrument Name:	Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	Full scan MS1 spectra were acquired at 120,000 resolution over the m/z range 70-1000 (AGC target of 3e6 ions) while MS2 spectra were acquired at 15,000 resolution (AGC target of 1e5 ions) using a Top10 data-dependent acquisition method and a stepped normalized collision energy of 15, 35 and 60. Both MS1 and MS2 spectra were acquired in profile mode. Raw MS files were processed using Compound Discoverer (version 3.1) using the default workflow for untargeted metabolomics and statistical analysis to identify compounds that showed significant differences. The dataset acquired in PI mode was filtered to include only named compounds with delta ppm values between -5 and +5 and MS2 spectra for the preferred precursor ion only.
Ion Mode:	POSITIVE