MS Study

Project uploaded by:	Pannaga Pavan
Project ID:	IMP_100048
Title:	Carbon Partitioning Metabolomic Studies
Project Description:	Qualitative metabolomic studies in response to very-low CO2 and high CO2 in Microchloropsis gaditana
Research Area:	Biological Sciences
Funding Source:	Department of Biotechnology (DBT)
Project Contributors:	Pannaga Pavan Jutur

Study uploaded by:	Pannaga Pavan
Study ID:	IMS_100041
Title:	Time-course experiment of Microchloropsis gaditana cells supplemented with CO2
Summary:	Experiments were conducted with Microchloropsis gaditana supplemented with very-low CO2 and high CO2. Sampling was done on the following time points: Day 3, 6 and 9.
Publication:
Release Date:	Aug. 26, 2025
Study Type:	Mass Spectrometry (MS)
Data Type:	Untargeted
IEC/IBSC Approval Number :

Sr.No	Sample ID	Sample Name	Organism	Source	Sample Preparation Protocol	Sample Type	Experimental Condition	Time of treatment	Variant/Variety	Gender	Age	Replicates	Storage Conditions	Extraction Protocol	Number of files per sample
1	IMSM_102123	VLC_3	Nannochloropsis gaditana	Algae	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	Plant	Control	Very-low CO2 (300 ppm) for 3 days	Genotype Strain: NIES 2587	NA	NA	NA	NA	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	1
2	IMSM_102124	VLC_6	Nannochloropsis gaditana	Algae	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	Plant	Control	Very-low CO2 (300 ppm) for 6 days	Genotype Strain: NIES 2587	NA	NA	NA	NA	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	1
3	IMSM_102125	VLC_9	Nannochloropsis gaditana	Algae	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	Plant	Control	Very-low CO2 (300 ppm) for 9 days	Genotype Strain: NIES 2587	NA	NA	NA	NA	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	1
4	IMSM_102126	HC_3	Nannochloropsis gaditana	Algae	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	Plant	Treated	High CO2 (30,000 ppm) for 3 days	Genotype Strain: NIES 2587	NA	NA	NA	NA	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	1
5	IMSM_102127	HC_6	Nannochloropsis gaditana	Algae	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	Plant	Treated	High CO2 (30,000 ppm) for 6 days	Genotype Strain: NIES 2587	NA	NA	NA	NA	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	1
6	IMSM_102128	HC_9	Nannochloropsis gaditana	Algae	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	Plant	Treated	High CO2 (30,000 ppm) for 9 days	Genotype Strain: NIES 2587	NA	NA	NA	NA	Quenched cells were resuspended in 1 mL of ice-cold methanol/ethanol/chloroform(2:6:2), followed by sonication of resuspended cells in sonication bath for 15 min. Later, these samples were centrifuged at 10,000×g for 15 min at 4 °C to get rid of cell debris. The supernatant was filtered using a 0.2-µm filter. One hundred microlitres of supernatant was taken and dried under nitrogen stream. The dried leftover was dissolved in 10 µL of freshly prepared methoxyamine hydrochloride solution (40 mg mL−1 in pyridine) and incubated at 30 °C for 90 min with shaking. To the above solution, 90 µL of N-methyl-N-(trimethylsilyl)trifluoroacetamide was added and incubated at 37 °C for 30 min. The samples were centrifuged at 14,000×g for 3 min, and the supernatant was taken for the GC-MS/MS analysis.	1

Sr.No	MS Exp ID	Sample Name/ID	Mass Spectrometer Type	MS Instrument Name	MS Instrument type	MS Ionization Method	Ion Mode/Scan Polarity	Data Transformation (Software/s Used)
1	IME_101441	VLC_3 / IMSM_102123	GCMS	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	EI	Positive	NA
2	IME_101442	VLC_6 / IMSM_102124	GCMS	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	EI	Positive	NA
3	IME_101443	VLC_9 / IMSM_102125	GCMS	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	EI	Positive	NA
4	IME_101444	HC_3 / IMSM_102126	GCMS	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	EI	Positive	NA
5	IME_101445	HC_6 / IMSM_102127	GCMS	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	EI	Positive	NA
6	IME_101446	HC_9 / IMSM_102128	GCMS	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	EI	Positive	NA

Sr.No	First name	Last name	Email	Organization	Designation
1	Pannaga Pavan	Jutur	jppavan@icgeb.res.in	International Centre for Genetic Engineering and Biotechnology	principal_investigator

Sr.No	ftprun ID	MS Exp ID	MS Data Files
1	IMR_102045	IME_101441	VLC-Day-3.mzdata.xml
2	IMR_102046	IME_101442	VLC-Day-6.mzdata.xml
3	IMR_102047	IME_101443	VLC-Day-9.mzdata.xml
4	IMR_102048	IME_101444	HC-Day-3.mzdata.xml
5	IMR_102049	IME_101445	HC-Day-6.mzdata.xml
6	IMR_102050	IME_101446	HC-Day-9.mzdata.xml