Summary of study ST001057

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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Study IDST001057
Study TitleMetabolite Extractions from Cyanobacteria
Study SummaryMetabolite Extractions data from the Strains Synechococcus sp. PCC 7002, Synechococcus elongatus PCC 11801 (New strain, Manuscript submitted) and Synechococcus elongatus PCC 7942
Indian Institute of Technology Bombay
DepartmentDepartment of Chemical Engineering
LaboratoryWangikar Laboratory
Last NameWangikar
First NamePramod
AddressRoom No. 136, Biosystems Lab
Submit Date2018-09-08
Publications An improved method for extraction of polar and charged metabolites from cyanobacteria.
Raw Data AvailableYes
Raw Data File Type(s).wiff
Analysis Type DetailLC-MS
Release Date2018-09-27
Release Version1
Pramod Wangikar Pramod Wangikar application/zip

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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


Subject ID:SU001099
Subject Type:Bacteria
Subject Species:Synechococcus
Taxonomy ID:1117


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

mb_sample_id local_sample_id Extraction Method Used
SA071656PCC 7002_Method 1_Rep1Method 1
SA071657PCC 11801_Method 1_Rep4Method 1
SA071658PCC 11801_Method 1_Rep6Method 1
SA071659PCC 7942_Method 1_Rep1Method 1
SA071660PCC 7942_Method 1_Rep3Method 1
SA071661PCC 7942_Method 1_Rep2Method 1
SA071662PCC 11801_Method 1_Rep3Method 1
SA071663PCC 7002_Method 1_Rep3Method 1
SA071664PCC 7002_Method 1_Rep2Method 1
SA071665PCC 7002_Method 1_Rep4Method 1
SA071666PCC 11801_Method 1_Rep1Method 1
SA071667PCC 11801_Method 1_Rep2Method 1
SA071668PCC 11801_Method 1_Rep5Method 1
SA071669PCC 11801_Method 2A_Rep1Method 2A
SA071670PCC 11801_Method 2A_Rep5Method 2A
SA071671PCC 11801_Method 2A_Rep4Method 2A
SA071672PCC 11801_Method 2A_Rep3Method 2A
SA071673PCC 11801_Method 2A_Rep2Method 2A
SA071674PCC 7942_Method 2A_Rep3Method 2A
SA071675PCC 7002_Method 2A_Rep3Method 2A
SA071676PCC 7002_Method 2A_Rep2Method 2A
SA071677PCC 7002_Method 2A_Rep1Method 2A
SA071678PCC 7942_Method 2A_Rep2Method 2A
SA071679PCC 7942_Method 2A_Rep1Method 2A
SA071680PCC 7942_Method 2A_Rep4Method 2A
SA071681PCC 11801_Method 2A_Rep6Method 2A
SA071682PCC 11801_Method 2B-0.2M NH4OH_Rep1Method 2B-0.2M NH4OH
SA071683PCC 11801_Method 2B-0.2M NH4OH_Rep3Method 2B-0.2M NH4OH
SA071684PCC 11801_Method 2B-0.2M NH4OH_Rep5Method 2B-0.2M NH4OH
SA071685PCC 11801_Method 2B-0.2M NH4OH_Rep2Method 2B-0.2M NH4OH
SA071686PCC 11801_Method 2B-0.2M NH4OH_Rep4Method 2B-0.2M NH4OH
SA071687PCC 11801_Method 2B-0.2M NH4OH_Rep6Method 2B-0.2M NH4OH
SA071688PCC 7942_Method 2B_0.4M NH4OH_Rep3Method 2B-0.4M NH4OH
SA071689PCC 7002_Method 2B_0.4M NH4OH_Rep2Method 2B-0.4M NH4OH
SA071690PCC 7002_Method 2B_0.4M NH4OH_Rep1Method 2B-0.4M NH4OH
SA071691PCC 7002_Method 2B_0.4M NH4OH_Rep3Method 2B-0.4M NH4OH
SA071692PCC 7002_Method 2B_0.4M NH4OH_Rep4Method 2B-0.4M NH4OH
SA071693PCC 7942_Method 2B_0.4M NH4OH_Rep2Method 2B-0.4M NH4OH
SA071694PCC 7942_Method 2B_0.4M NH4OH_Rep1Method 2B-0.4M NH4OH
SA071695PCC 7942_Method 2B_0.4M NH4OH_Rep4Method 2B-0.4M NH4OH
Showing results 1 to 40 of 40


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 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.

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 instrument type Triple TOF
MS instrument name ABI Sciex 5600+ TripleTOF
Units Peak Area


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:10 mMTributylamine
Solvent B:Methanol
Chromatography Type:Reversed phase


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