Summary of Study ST002466

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 PR001592. The data can be accessed directly via it's Project DOI: 10.21228/M8X712 This work is supported by NIH grant, U2C- DK119886.

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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 IDST002466
Study TitleDeciphering the metabolomic differences between two fast-growing cyanobacteria, S.elongatus PCC 11801 and 11802 via 13C-metabolic flux analysis
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, dynamic 13C-labeling experiments were carried out 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. The detailed protocol for experiment can be found in the protocol file.
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 Date2023-01-26
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-07-05
Release Version1
Pramod Wangikar Pramod Wangikar
https://dx.doi.org/10.21228/M8X712
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001592
Project DOI:doi: 10.21228/M8X712
Project Title:Dynamic 13C-labeling and metabolic flux analysis unveils metabolic differences between two fast-growing cyanobacteria S. 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
Contributors:Damini Jaiswal

Subject:

Subject ID:SU002556
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 Time point of 13C labeling (s) SWATH Program
SA247131PCC 11801 0 SEC SWATH1-2 BR20 SWATH 1
SA247132PCC11801 0 SEC SWATH1-1 BR10 SWATH 1
SA247133PCC11802 0 SEC SWATH1-1 BR20 SWATH 1
SA247134PCC11802 0 SEC SWATH1-2 BR20 SWATH 1
SA247135PCC 11801 0 SEC SWATH1-1 BR20 SWATH 1
SA247136PCC 11802 0 SEC SWATH-1 BR10 SWATH 1
SA247137PCC11801 0 SEC SWATH1-2 BR10 SWATH 1
SA247138PCC11802 0 SEC SWATH2-1 BR20 SWATH 2
SA247139PCC11802 0 SEC SWATH2-2 BR20 SWATH 2
SA247140PCC11801 0 SEC SWATH2-1 BR10 SWATH 2
SA247141PCC 11801 0 SEC SWATH2-2 BR20 SWATH 2
SA247142PCC 11802 0 SEC SWATH-2 BR10 SWATH 2
SA247143PCC 11801 0 SEC SWATH2-1 BR20 SWATH 2
SA247144PCC11801 0 SEC SWATH2-2 BR10 SWATH 2
SA247145PCC11802 0 SEC SWATH4-1 BR20 SWATH 4
SA247146PCC 11801 0 SEC SWATH4-1 BR20 SWATH 4
SA247147PCC11801 0 SEC SWATH4-2 BR10 SWATH 4
SA247148PCC11801 0 SEC SWATH4-1 BR10 SWATH 4
SA247149PCC11802 0 SEC SWATH4-2 BR20 SWATH 4
SA247150PCC 11801 0 SEC SWATH4-2 BR20 SWATH 4
SA247151PCC 11801 120 SEC SWATH1-2 BR2120 SWATH 1
SA247152PCC 11801 120 SEC SWATH1-1 BR2120 SWATH 1
SA247153PCC11801 120 SEC SWATH1-2 BR1120 SWATH 1
SA247154PCC 11802 120 SEC SWATH-1 BR1120 SWATH 1
SA247155PCC11802 120 SEC SWATH1-2 BR2120 SWATH 1
SA247156PCC11802 120 SEC SWATH1-1 BR2120 SWATH 1
SA247157PCC11801 120 SEC SWATH1-1 BR1120 SWATH 1
SA247158PCC11802 120 SEC SWATH2-1 BR2120 SWATH 2
SA247159PCC 11801 120 SEC SWATH2-2 BR2120 SWATH 2
SA247160PCC 11802 120 SEC SWATH-2 BR1120 SWATH 2
SA247161PCC11802 120 SEC SWATH2-2 BR2120 SWATH 2
SA247162PCC 11801 120 SEC SWATH2-1 BR2120 SWATH 2
SA247163PCC11801 120 SEC SWATH2-1 BR1120 SWATH 2
SA247164PCC11801 120 SEC SWATH2-2 BR1120 SWATH 2
SA247165PCC11802 120 SEC SWATH4-2 BR2120 SWATH 4
SA247166PCC11802 120 SEC SWATH4-1 BR2120 SWATH 4
SA247167PCC 11801 120 SEC SWATH4-1 BR2120 SWATH 4
SA247168PCC11801 120 SEC SWATH4-1 BR1120 SWATH 4
SA247169PCC 11801 120 SEC SWATH4-2 BR2120 SWATH 4
SA247170PCC11801 120 SEC SWATH4-2 BR1120 SWATH 4
SA247171PCC11802 1800 SEC SWATH1-2 BR21800 SWATH 1
SA247172PCC 11801 1800 SEC SWATH1-2 BR11800 SWATH 1
SA247173PCC11802 1800 SEC SWATH1-1 BR21800 SWATH 1
SA247174PCC 11801 1800 SEC SWATH1-1 BR21800 SWATH 1
SA247175PCC11802 1800 SEC SWATH1-1 BR11800 SWATH 1
SA247176PCC 11801 1800 SEC SWATH1-1 BR11800 SWATH 1
SA247177PCC 11801 1800 SEC SWATH1-2 BR21800 SWATH 1
SA247178PCC 11801 1800 SEC SWATH2-1 BR21800 SWATH 2
SA247179PCC11802 1800 SEC SWATH2-1 BR11800 SWATH 2
SA247180PCC 11801 1800 SEC SWATH2-2 BR21800 SWATH 2
SA247181PCC11802 1800 SEC SWATH2-1 BR21800 SWATH 2
SA247182PCC11802 1800 SEC SWATH2-2 BR21800 SWATH 2
SA247183PCC 11801 1800 SEC SWATH2-1 BR11800 SWATH 2
SA247184PCC 11801 1800 SEC SWATH2-2 BR11800 SWATH 2
SA247185PCC11802 1800 SEC SWATH4-1 BR11800 SWATH 4
SA247186PCC11802 1800 SEC SWATH4-2 BR21800 SWATH 4
SA247187PCC 11801 1800 SEC SWATH4-2 BR11800 SWATH 4
SA247188PCC11802 1800 SEC SWATH4-1 BR21800 SWATH 4
SA247189PCC 11801 1800 SEC SWATH4-2 BR21800 SWATH 4
SA247190PCC 11801 1800 SEC SWATH4-1 BR11800 SWATH 4
SA247191PCC 11801 1800 SEC SWATH4-1 BR21800 SWATH 4
SA247192PCC 11801 180 SEC SWATH1-2 BR2180 SWATH 1
SA247193PCC11802 180 SEC SWATH1-2 BR2180 SWATH 1
SA247194PCC 11801 180 SEC SWATH1-1 BR2180 SWATH 1
SA247195PCC11802 180 SEC SWATH1-1 BR2180 SWATH 1
SA247196PCC 11802 180 SEC SWATH-1 BR1180 SWATH 1
SA247197PCC11801 180 SEC SWATH1-2 BR1180 SWATH 1
SA247198PCC11801 180 SEC SWATH1-1 BR1180 SWATH 1
SA247199PCC11801 180 SEC SWATH2-2 BR1180 SWATH 2
SA247200PCC 11801 180 SEC SWATH2-2 BR2180 SWATH 2
SA247201PCC11801 180 SEC SWATH2-1 BR1180 SWATH 2
SA247202PCC11802 180 SEC SWATH2-1 BR2180 SWATH 2
SA247203PCC11802 180 SEC SWATH2-2 BR2180 SWATH 2
SA247204PCC 11801 180 SEC SWATH2-1 BR2180 SWATH 2
SA247205PCC 11802 180 SEC SWATH-2 BR1180 SWATH 2
SA247206PCC11801 180 SEC SWATH4-1 BR1180 SWATH 4
SA247207PCC 11801 180 SEC SWATH4-1 BR2180 SWATH 4
SA247208PCC 11801 180 SEC SWATH4-2 BR2180 SWATH 4
SA247209PCC11802 180 SEC SWATH4-1 BR2180 SWATH 4
SA247210PCC11801 180 SEC SWATH4-2 BR1180 SWATH 4
SA247211PCC11802 180 SEC SWATH4-2 BR2180 SWATH 4
SA247212PCC11801 300 SEC SWATH1-1 BR1300 SWATH 1
SA247213PCC 11801 300 SEC SWATH1-1 BR2300 SWATH 1
SA247214PCC11801 300 SEC SWATH1-2 BR1300 SWATH 1
SA247215PCC11802 300 SEC SWATH1-2 BR2300 SWATH 1
SA247216PCC11802 300 SEC SWATH1-1 BR2300 SWATH 1
SA247217PCC 11802 300 SEC SWATH-1 BR1300 SWATH 1
SA247218PCC 11801 300 SEC SWATH1-2 BR2300 SWATH 1
SA247219PCC 11801 300 SEC SWATH2-1 BR2300 SWATH 2
SA247220PCC11802 300 SEC SWATH2-2 BR2300 SWATH 2
SA247221PCC 11801 300 SEC SWATH2-2 BR2300 SWATH 2
SA247222PCC11802 300 SEC SWATH2-1 BR2300 SWATH 2
SA247223PCC11801 300 SEC SWATH2-1 BR1300 SWATH 2
SA247224PCC 11802 300 SEC SWATH-2 BR1300 SWATH 2
SA247225PCC11801 300 SEC SWATH2-2 BR1300 SWATH 2
SA247226PCC11801 300 SEC SWATH4-1 BR1300 SWATH 4
SA247227PCC11801 300 SEC SWATH4-2 BR1300 SWATH 4
SA247228PCC11802 300 SEC SWATH4-1 BR2300 SWATH 4
SA247229PCC 11801 300 SEC SWATH4-1 BR2300 SWATH 4
SA247230PCC 11801 300 SEC SWATH4-2 BR2300 SWATH 4
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Collection:

Collection ID:CO002549
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 SWATH methods.
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR002568
Treatment Summary:The metabolites were extracted using a methanol-chloroform-water method described in the Dynamic 13C-labeling of S.elongatus PCC 11801 and 11802 file of the collection data.

Sample Preparation:

Sampleprep ID:SP002562
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 injection volume was 4µL.
Processing Storage Conditions:On ice
Extract Storage:-80℃

Combined analysis:

Analysis ID AN004022
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 Relative Abundance of Isotopologues

Chromatography:

Chromatography ID:CH002972
Instrument Name:Shimadzu 20AD
Column Name:Phenomenex Synergi Hydro RP 100 A (100 x 2mm, 2.5um)
Column Temperature:25
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; 10 mM tributylamine; 15mM acetic acid
Solvent B:100% methanol
Chromatography Type:Reversed phase

MS:

MS ID:MS003769
Analysis ID:AN004022
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The data was acquired with SWATH methods. The details of SWATH methods can be found in the article https://doi.org/10.1016/j.isci.2020.101704. The quantification of MID of metabolites and fragment ions was performed by integrating the area under the curve of precursor and fragment isotopologues using MultiQuant 3.0.1 (Sciex, Framingham, MA) from the Q1 isolation window of the SWATH program, where all the precursor isotopologues of the respective metabolite were present. The peak areas were used to estimate precursor and product MID: mi=Mi/(∑(j=0)^n Mj ) where mi and Mi represent the normalized relative and unnormalized isotopologue abundance for each precursor/fragment ion in which i 13C atoms are incorporated, and n represents the number of carbon.
Ion Mode:NEGATIVE
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