Summary of Study ST001141

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 PR000762. The data can be accessed directly via it's Project DOI: 10.21228/M86103 This work is supported by NIH grant, U2C- DK119886.

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Study ID	ST001141
Study Title	Evaluation of metabolome sample preparation and extraction methodologies for oleaginous filamentous fungi Mortierella alpina
Study Type	method optimization
Study Summary	In this study, based on the method of fast filtration, we evaluated the three metabolomics analysis protocols commonly used for microbial metabolomics analysis in M. alpina and systematically optimised the metabolite extraction solvent.
Institute	Jiangnan University
Department	School of Food Science and Technology
Laboratory	State Key Laboratory of Food Science and Technology
Last Name	Hengqian
First Name	Lu
Address	1800 Lihu Ave, Wuxi, Jiangsu 214122, P.R. China.
Email	hengqianlu@163.com
Phone	+86 15006176136
Submit Date	2019-02-24
Analysis Type Detail	GC-MS
Release Date	2019-09-23
Release Version	1

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Project:

Project ID:	PR000762
Project DOI:	doi: 10.21228/M86103
Project Title:	Evaluation of metabolome sample preparation and extraction methodologies for oleaginous filamentous fungi Mortierella alpina
Project Type:	Method Optimization
Project Summary:	In this study, based on the method of fast filtration, we evaluated the three metabolomics analysis protocols commonly used for microbial metabolomics analysis in M. alpina and systematically optimised the metabolite extraction solvent.
Institute:	Jiangnan University
Department:	School of Food Science and Technology
Laboratory:	State Key Laboratory of Food Science and Technology
Last Name:	Hengqian
First Name:	Lu
Address:	1800 Lihu Ave, Wuxi, Jiangsu 214122, P.R. China.
Email:	hengqianlu@163.com
Phone:	+86 15006176136
Funding Source:	National Natural Science Foundation of China

Subject:

Subject ID:	SU001205
Subject Type:	Fungi
Subject Species:	Mortierella alpina
Taxonomy ID:	64518

Factors:

Subject type: Fungi; Subject species: Mortierella alpina (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA078327	SM1-1	SM1
SA078328	SM1-5	SM1
SA078329	SM1-4	SM1
SA078330	SM1-2	SM1
SA078331	SM1-3	SM1
SA078332	SM2-5	SM2
SA078333	SM2-4	SM2
SA078334	SM2-2	SM2
SA078335	SM2-3	SM2
SA078336	SM2-1	SM2
SA078337	SM3-4	SM3
SA078338	SM3-5	SM3
SA078339	SM3-3	SM3
SA078340	SM3-2	SM3
SA078341	SM3-1	SM3
SA078342	SM4-4	SM4
SA078343	SM4-5	SM4
SA078344	SM4-3	SM4
SA078345	SM4-1	SM4
SA078346	SM4-2	SM4
SA078347	SM5-5	SM5
SA078348	SM5-4	SM5
SA078349	SM5-2	SM5
SA078350	SM5-1	SM5
SA078351	SM5-3	SM5

Showing results 1 to 25 of 25

Showing results 1 to 25 of 25

Collection:

Collection ID:	CO001199
Collection Summary:	Mycelia were collected by vacuum filtration at 120 h using a paper filter (Whatman no. 1) and washed with 4°C 0.9% NaCl at room temperature, the sampling time was less than 45s. After quick-freezing in liquid nitrogen, the frozen cell pellets were further ground into powder (fresh biomass) and stored at -80°C for further use.
Sample Type:	fungi

Treatment:

Treatment ID:	TR001220
Treatment Summary:	1.Sample preparation: Two forms of biomass, including fresh weight and freeze-dried, have been used for the extraction of metabolites. Three forms of quantified biomass, including fresh weight, freeze-dried and cell debris, have been used for data normalisation. 2. We create a pooled culture and split to produce identical samples for the different methods tested. Before extraction, three ways(fresh sample,freeze-dried sample, freeze-dried sample(water added)) were adopted to prepare the metabolomics analytical sample.To test the effect of the water contained in the fresh biomass on the extraction of metabolites from M. alpina, we repeated the freeze-dried biomass with additional water added to the account for the water content in fresh biomass. 2. Five solvent mixtures (SM) were used for the extraction of the intracellular metabolites of M. alpina. The five SM were: SM1, MTBE:methanol:water (20:6:5, vol:vol:vol) at -20°C; SM2, methanol:acetonitrile:water (2:2:1, vol:vol:vol) at -20°C; SM3, methanol:water (8:2, vol:vol) at -20°C; SM4, methanol:water (1:1, vol:vol); and SM5, Ethanol:water (3:1, vol:vol) at -20°C. 3. The mycelia were harvested at 24h and 120h for metabolomics analysis.

Treatment ID:

TR001220

Treatment Summary:

1.Sample preparation: Two forms of biomass, including fresh weight and freeze-dried, have been used for the extraction of metabolites. Three forms of quantified biomass, including fresh weight, freeze-dried and cell debris, have been used for data normalisation. 2. We create a pooled culture and split to produce identical samples for the different methods tested. Before extraction, three ways(fresh sample,freeze-dried sample, freeze-dried sample(water added)) were adopted to prepare the metabolomics analytical sample.To test the effect of the water contained in the fresh biomass on the extraction of metabolites from M. alpina, we repeated the freeze-dried biomass with additional water added to the account for the water content in fresh biomass. 2. Five solvent mixtures (SM) were used for the extraction of the intracellular metabolites of M. alpina. The five SM were: SM1, MTBE:methanol:water (20:6:5, vol:vol:vol) at -20°C; SM2, methanol:acetonitrile:water (2:2:1, vol:vol:vol) at -20°C; SM3, methanol:water (8:2, vol:vol) at -20°C; SM4, methanol:water (1:1, vol:vol); and SM5, Ethanol:water (3:1, vol:vol) at -20°C. 3. The mycelia were harvested at 24h and 120h for metabolomics analysis.

Sample Preparation:

Sampleprep ID:	SP001213
Sampleprep Summary:	The obtained supernatants were vacuum dried at 30°C prior to derivatisation. The extraction solution served as a negative control to subtract from the background spectrum. The dried extract was derivatised. Briefly, the vacuum dried samples were resuspended in 100 μL of MeOX (10 mg/mL) in pyridine and incubated at 37°C for 90 min in a block heater. Then, 40 μL of MSTFA+1%TMCS was pipetted into each sample and incubated at 37°C for another 30 min. The resulting solution from each sample was collected and transferred into gas chromatography (GC) vials for analysis.

Sampleprep ID:

SP001213

Sampleprep Summary:

The obtained supernatants were vacuum dried at 30°C prior to derivatisation. The extraction solution served as a negative control to subtract from the background spectrum. The dried extract was derivatised. Briefly, the vacuum dried samples were resuspended in 100 μL of MeOX (10 mg/mL) in pyridine and incubated at 37°C for 90 min in a block heater. Then, 40 μL of MSTFA+1%TMCS was pipetted into each sample and incubated at 37°C for another 30 min. The resulting solution from each sample was collected and transferred into gas chromatography (GC) vials for analysis.

Combined analysis:

Analysis ID	AN001874
Analysis type	MS
Chromatography type	GC
Chromatography system	Thermo Trace 1310
Column	RTX-5MS
MS Type	EI
MS instrument type	Triple quadrupole
MS instrument name	Thermo TSQ8000_evo
Ion Mode	POSITIVE
Units	Peak Area

Chromatography:

Chromatography ID:	CH001355
Instrument Name:	Thermo Trace 1310
Column Name:	RTX-5MS
Chromatography Type:	GC

MS:

MS ID:	MS001730
Analysis ID:	AN001874
Instrument Name:	Thermo TSQ8000_evo
Instrument Type:	Triple quadrupole
MS Type:	EI
MS Comments:	The “raw” format files were converted to “abf ” format with the ABF converter. The MSDIAL3.40 equipped with DB_FiehnBinbase-FiehnRI database was used for peaks exaction, retention time adjustment, peak alignment, deconvolution analysis and identification.All metabolite annotations were checked again by using the the TraceFinder 3.3 software (Thermo Fisher Scientific, Waltham, MA, USA), Xcalibur 3.1 and NIST MS search.
Ion Mode:	POSITIVE