Summary of Study ST001057

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 PR000710. The data can be accessed directly via it's Project DOI: 10.21228/M8WT20 This work is supported by NIH grant, U2C- DK119886.

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

Study ID	ST001057
Study Title	Metabolite Extractions from Cyanobacteria
Study Summary	Metabolite Extractions data from the Strains Synechococcus sp. PCC 7002, Synechococcus elongatus PCC 11801 (New strain, Manuscript submitted) and Synechococcus elongatus PCC 7942
Institute	Indian Institute of Technology Bombay
Department	Department of Chemical Engineering
Laboratory	Wangikar Laboratory
Last Name	Wangikar
First Name	Pramod
Address	Room No. 136, Biosystems Lab
Email	wangikar@iitb.ac.in
Phone	2225764215
Submit Date	2018-09-08
Publications	https://doi.org/10.1371/journal.pone.0204273 An improved method for extraction of polar and charged metabolites from cyanobacteria.
Raw Data Available	Yes
Raw Data File Type(s)	wiff
Analysis Type Detail	LC-MS
Release Date	2018-09-27
Release Version	1

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Project:

Project ID:	PR000710
Project DOI:	doi: 10.21228/M8WT20
Project Title:	Improved Extraction method of Polar and Charged Metabolites from Cyanobacteria.
Project Summary:	We report excellent extraction method for cyanobacteria of the genus Synechococcus, viz., Synechococcus sp. PCC 7002, Synechococcus elongatus PCC 7942, and a newly isolated Synechococcus elongatus PCC 11801 (manuscript under review). High resolution-LC/MS was used to assess the relative abundance of the extracted metabolites. The different solvent systems used for extraction led to statistically significant changes in the extraction efficiency for a large number of metabolites. While a few hundred m/z features or potential metabolites were detected with different solvent systems, the abundance of over a quarter of all metabolites varied significantly from one solvent system to another. Further, the extraction methods were evaluated for a targeted set of metabolites that are important in 13C-MFA studies of photosynthetic organisms. While for the strain PCC 7002, the reported method using methanol-chloroform-water system gave satisfactory results, a mild base in the form of NH4OH had to be used in place of water to achieve adequate levels of extraction for PCC 7942 and PCC 11801.
Institute:	Indian Institute of Technology Bombay
Department:	Department of Chemical Engineering
Laboratory:	Wangikar Laboratory
Last Name:	Wangikar
First Name:	Pramod
Address:	Room No. 136, Biosystems Lab
Email:	wangikar@iitb.ac.in
Phone:	02225764215

Subject:

Subject ID:	SU001099
Subject Type:	Bacteria
Subject Species:	Synechococcus
Taxonomy ID:	1129

Factors:

Subject type: Bacteria; Subject species: Synechococcus (Factor headings shown in green)

mb_sample_id	local_sample_id	Extraction Method Used
SA071656	PCC 7002_Method 1_Rep1	Method 1
SA071657	PCC 11801_Method 1_Rep4	Method 1
SA071658	PCC 11801_Method 1_Rep6	Method 1
SA071659	PCC 7942_Method 1_Rep1	Method 1
SA071660	PCC 7942_Method 1_Rep3	Method 1
SA071661	PCC 7942_Method 1_Rep2	Method 1
SA071662	PCC 11801_Method 1_Rep3	Method 1
SA071663	PCC 7002_Method 1_Rep3	Method 1
SA071664	PCC 7002_Method 1_Rep2	Method 1
SA071665	PCC 7002_Method 1_Rep4	Method 1
SA071666	PCC 11801_Method 1_Rep1	Method 1
SA071667	PCC 11801_Method 1_Rep2	Method 1
SA071668	PCC 11801_Method 1_Rep5	Method 1
SA071669	PCC 11801_Method 2A_Rep1	Method 2A
SA071670	PCC 11801_Method 2A_Rep5	Method 2A
SA071671	PCC 11801_Method 2A_Rep4	Method 2A
SA071672	PCC 11801_Method 2A_Rep3	Method 2A
SA071673	PCC 11801_Method 2A_Rep2	Method 2A
SA071674	PCC 7942_Method 2A_Rep3	Method 2A
SA071675	PCC 7002_Method 2A_Rep3	Method 2A
SA071676	PCC 7002_Method 2A_Rep2	Method 2A
SA071677	PCC 7002_Method 2A_Rep1	Method 2A
SA071678	PCC 7942_Method 2A_Rep2	Method 2A
SA071679	PCC 7942_Method 2A_Rep1	Method 2A
SA071680	PCC 7942_Method 2A_Rep4	Method 2A
SA071681	PCC 11801_Method 2A_Rep6	Method 2A
SA071682	PCC 11801_Method 2B-0.2M NH4OH_Rep1	Method 2B-0.2M NH4OH
SA071683	PCC 11801_Method 2B-0.2M NH4OH_Rep3	Method 2B-0.2M NH4OH
SA071684	PCC 11801_Method 2B-0.2M NH4OH_Rep5	Method 2B-0.2M NH4OH
SA071685	PCC 11801_Method 2B-0.2M NH4OH_Rep2	Method 2B-0.2M NH4OH
SA071686	PCC 11801_Method 2B-0.2M NH4OH_Rep4	Method 2B-0.2M NH4OH
SA071687	PCC 11801_Method 2B-0.2M NH4OH_Rep6	Method 2B-0.2M NH4OH
SA071688	PCC 7942_Method 2B_0.4M NH4OH_Rep3	Method 2B-0.4M NH4OH
SA071689	PCC 7002_Method 2B_0.4M NH4OH_Rep2	Method 2B-0.4M NH4OH
SA071690	PCC 7002_Method 2B_0.4M NH4OH_Rep1	Method 2B-0.4M NH4OH
SA071691	PCC 7002_Method 2B_0.4M NH4OH_Rep3	Method 2B-0.4M NH4OH
SA071692	PCC 7002_Method 2B_0.4M NH4OH_Rep4	Method 2B-0.4M NH4OH
SA071693	PCC 7942_Method 2B_0.4M NH4OH_Rep2	Method 2B-0.4M NH4OH
SA071694	PCC 7942_Method 2B_0.4M NH4OH_Rep1	Method 2B-0.4M NH4OH
SA071695	PCC 7942_Method 2B_0.4M NH4OH_Rep4	Method 2B-0.4M NH4OH

Showing results 1 to 40 of 40

Showing results 1 to 40 of 40

Collection:

Collection ID:	CO001093
Collection Summary:	20 mL Cyanobacterial cells grown at exponential phase were filtered and extracted with the extraction buffers suggested.
Sample Type:	Bacterial cells

Treatment:

Treatment ID:	TR001113
Treatment Summary:	Various cells were extracted using the extraction solutions described as Method 1, Method 2A and Method 2B

Sample Preparation:

Sampleprep ID:	SP001106
Sampleprep Summary:	The cell suspension was filtered through a 0.8 µm nylon membrane and the filtered cells was quickly placed in 1.6 ml cold methanol (100%) or methanol-water mixture (80:20 v/v). The mixture was incubated at -80 °C for 1 hour following which the cell-solvent mixture was removed and placed in a 15 mL centrifuge tube. The cells sticking to the filter were then scraped off with chloroform (2.4 mL) and mixed with the cell-solvent mixture. The mixture was vortexed for 20 minutes under cold conditions (vortexed for 30s and kept on ice for 1 minute and the cycle repeated). Two mL of MilliQ water or NH4OH solution in water (at concentrations of 0.2 M, 0.4 M) was added into the mixture to separate the phases. The mixture was vortexed for 10 minutes, centrifuged for 15 minutes at 3200g at 4 °C to obtain two separate phases and the top aqueous-rich layer was collected (approximately 3 mL), evaporated to dryness and stored at -80 °C until further analysis. The stored pellets were reconstituted in 100 μL of 50/50 methanol-water mixture and filtered before injecting on LC/MS.

Sampleprep ID:

SP001106

Sampleprep Summary:

The cell suspension was filtered through a 0.8 µm nylon membrane and the filtered cells was quickly placed in 1.6 ml cold methanol (100%) or methanol-water mixture (80:20 v/v). The mixture was incubated at -80 °C for 1 hour following which the cell-solvent mixture was removed and placed in a 15 mL centrifuge tube. The cells sticking to the filter were then scraped off with chloroform (2.4 mL) and mixed with the cell-solvent mixture. The mixture was vortexed for 20 minutes under cold conditions (vortexed for 30s and kept on ice for 1 minute and the cycle repeated). Two mL of MilliQ water or NH4OH solution in water (at concentrations of 0.2 M, 0.4 M) was added into the mixture to separate the phases. The mixture was vortexed for 10 minutes, centrifuged for 15 minutes at 3200g at 4 °C to obtain two separate phases and the top aqueous-rich layer was collected (approximately 3 mL), evaporated to dryness and stored at -80 °C until further analysis. The stored pellets were reconstituted in 100 μL of 50/50 methanol-water mixture and filtered before injecting on LC/MS.

Combined analysis:

Analysis ID	AN001726
Analysis type	MS
Chromatography type	Reversed phase
Chromatography system	Shimadzu 20AD
Column	Phenomenex Synergi Hydro RP (100 x 2mm,2.5um)
MS Type	ESI
MS instrument type	Triple TOF
MS instrument name	ABI Sciex 5600+ TripleTOF
Ion Mode	NEGATIVE
Units	Peak Area

Chromatography:

Chromatography ID:	CH001220
Instrument Name:	Shimadzu 20AD
Column Name:	Phenomenex Synergi Hydro RP (100 x 2mm,2.5um)
Flow Rate:	300 microliter/min
Solvent A:	100% water; 10 mM tributylamine
Solvent B:	100% methanol
Chromatography Type:	Reversed phase

MS:

MS ID:	MS001596
Analysis ID:	AN001726
Instrument Name:	ABI Sciex 5600+ TripleTOF
Instrument Type:	Triple TOF
MS Type:	ESI
Ion Mode:	NEGATIVE