Summary of Study ST002245

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 PR001433. The data can be accessed directly via it's Project DOI: 10.21228/M8GX29 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.

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Study IDST002245
Study TitleDeciphering the metabolomic differences between two fast-growing cyanobacteria, S.elongatus PCC 11801 and 11802 via metabolite profiling
Study SummaryThe study aims to identify the metabolic differences between two promising fast-growing, non-model cyanobacterial strains, S. elongatus PCC 11801 and PCC 11802. To this end, experiments were carried out to measure metabolite levels in the two cyanobacterial strains grown in shake flasks at a similar light intensity of approx. 300-350 µmole photons.m-2. s-1. The samples for metabolomics analysis were collected during the exponential growth phase at an optical cell density of 0.5-0.6. Isotopic ratio method was utilized to compare the metabolite levels and delineate the differences in their metabolic pathways.
Institute
Indian Institute of Technology Bombay
DepartmentChemical Engineering
Last NameWangikar
First NamePramod
AddressBiosystems and Bioengineering Lab, Department of Chemical Engineering, IIT Bombay, Powai, Mumbai, Maharashtra, India -400076
Emailwangikar@iitb.ac.in
Phone+91 22 2576 72 32
Submit Date2022-07-28
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2023-07-05
Release Version1
Pramod Wangikar Pramod Wangikar
https://dx.doi.org/10.21228/M8GX29
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001433
Project DOI:doi: 10.21228/M8GX29
Project Title:Comparative Metabolome Profiling of Synechococcus elongatus PCC 11801 and 11802
Project Summary:The project aims to identify the metabolic differences between two promising non-model cyanobacterial strains, Synechococcus elongatus PCC 11801 and PCC 11802.
Institute:Indian Institute of Technology Bombay
Department:Chemical Engineering
Laboratory:Biosystems and Bioengineering Lab
Last Name:Wangikar
First Name:Pramod
Address:Biosystems and Bioengineering Lab, Department of Chemical Engineering, IIT Bombay, Powai, Mumbai, Maharashtra, India -400076
Email:wangikar@iitb.ac.in
Phone:+91 22 2576 72 32
Funding Source:Department of Biotechnology, Ministry of Science, India

Subject:

Subject ID:SU002331
Subject Type:Bacteria
Subject Species:Synechococcus elongatus
Taxonomy ID:2219813

Factors:

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

mb_sample_id local_sample_id Strain
SA21461211801 ES BR3 IS IDA-2S.elongatus PCC 11801
SA21461311801 ES BR3 IS IDA-3S.elongatus PCC 11801
SA21461411801 ES BR1 IS IDA-1S.elongatus PCC 11801
SA21461511801 ES BR2 IS IDA-3S.elongatus PCC 11801
SA21461611801 ES BR3 IS IDA-1S.elongatus PCC 11801
SA21461711801 ES BR1 IS IDA-2S.elongatus PCC 11801
SA21461811801 ES BR2 IS IDA-1S.elongatus PCC 11801
SA21461911801 ES BR1 IS IDA-3S.elongatus PCC 11801
SA21462011801 ES BR2 IS IDA-2S.elongatus PCC 11801
SA21462111802 ES BR3 IS IDA-1S.elongatus PCC 11802
SA21462211802 ES BR3 IS IDA-2S.elongatus PCC 11802
SA21462311802 ES BR3 IS IDA-3S.elongatus PCC 11802
SA21462411802 ES BR2 IS IDA-3S.elongatus PCC 11802
SA21462511802 ES BR1 IS IDA-1S.elongatus PCC 11802
SA21462611802 ES BR1 IS IDA-2S.elongatus PCC 11802
SA21462711802 ES BR1 IS IDA-3S.elongatus PCC 11802
SA21462811802 ES BR2 IS IDA-1S.elongatus PCC 11802
SA21462911802 ES BR2 IS IDA-2S.elongatus PCC 11802
Showing results 1 to 18 of 18

Collection:

Collection ID:CO002324
Collection Summary:Experiments were carried out by growing Synechococcus elongatus PCC 11801 and PCC 11802 cells in shake flask under continuous light conditions. The light intensity was ~300-350 µmole photons m-2 s-1. Twenty mL of culture was collected at OD730 of ~0.5-0.6. Samples were quenched with methanol and extracted using the methanol-chloroform-water method. Extracts were stored at -80°C till LCMS analysis. LCMS analysis was done in the negative ion mode using the information-dependent acquisition (IDA) method.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR002343
Treatment Summary:The metabolites were extracted using a methanol-chloroform-water method described in the Metabolite Extraction Protocol file of the collection data.

Sample Preparation:

Sampleprep ID:SP002337
Sampleprep Summary:One aliquot of the metabolite extract of each sample were reconstituted in 100µL 50:50 methanol-water and filtered using nylon syringe filters to remove any particulate matter. The metabolite extract of each test sample was mixed with equal volume of an extract of the PCC 11801 WT biomass that is fully labeled with 13C isotopic carbon by growing for ~5 generations in the presence of NaH13CO3 in modified BG-11 medium. 13C-labeled biomass of PCC 11801 that acted as an internal standard. The injection volume was 6 µL. The peak areas corresponding to the 12C and 13C monoisotopic peak for the metabolites of interest were quantified using MultiQuant 3.0.1 (SCIEX, Framingham, MA). The relative quantification of metabolites was done using isotopic ratio method by normalizing area under the peak for monoisotopic m/z of a particular metabolite by its respective highest possible isotopologue present in the internal standard giving area ratio.
Processing Storage Conditions:On ice
Extract Storage:-80℃

Combined analysis:

Analysis ID AN003665
Analysis type MS
Chromatography type Reversed phase
Chromatography system Shimadzu 20AD
Column Phenomenex Synergi Hydro RP 100 A (100 x 2mm,2.5um)
MS Type ESI
MS instrument type QTOF
MS instrument name ABI Sciex 5600+ TripleTOF
Ion Mode NEGATIVE
Units Area Ratios

Chromatography:

Chromatography ID:CH002715
Instrument Name:Shimadzu 20AD
Column Name:Phenomenex Synergi Hydro RP 100 A (100 x 2mm,2.5um)
Flow Gradient:The gradient method used is as follows: 0% B (0.01 min), 0% B (2 min), 35% B (8 min), 35% B (10.5 min), 90% B (15.50 min), 90% B (20.5 min), 0% B (22 min), and 0% B (30 min)
Flow Rate:0.3 mL/minute
Solvent A:100% water; 15 mM acetic acid; 10 mM tributylamine
Solvent B:100% methanol
Chromatography Type:Reversed phase

MS:

MS ID:MS003416
Analysis ID:AN003665
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The peak areas corresponding to the 12C and 13C monoisotopic peak for the metabolites of interest were quantified using MultiQuant 3.0.1 (SCIEX, Framingham, MA). The relative quantification of metabolites was done using isotopic ratio method by normalizing area under the peak for monoisotopic m/z of a particular metabolite by its respective highest possible isotopologue present in the internal standard giving area ratio.
Ion Mode:NEGATIVE
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