MS Study

Project uploaded by:	Pannaga Pavan
Project ID:	IMP_100028
Title:	Multi-omics analysis of Aurantiochytrium limacinum
Project Description:	To evaluate temporal changes in the presence of glycerol, time-course metabolite profiling was done in the presence of glycerol and glucose at three different time-points i.e., 0, 48 and 96 h using GCMS.
Research Area:	Biological Sciences
Funding Source:	Department of Biotechnology (DBT)
Project Contributors:	Pannaga Pavan Jutur

Study uploaded by:	Pannaga Pavan
Study ID:	IMS_100022
Title:	Time course GCMS based untargeted metabolomics in the presence of glucose and glycerol
Summary:	Our preliminary analysis identifies that glycerol enhanced DHA accumulation in native isolate Aurantiochytrium limacinum. To evaluate temporal changes in the presence of glycerol, time-course metabolite profiling was done in the presence of glycerol and glucose at three different time-points i.e., 0, 48 and 96 h using GC-MS. We identified nearly 40 metabolites, among which metabolites belonging to pentose phosphate pathway, TCA cycle and amino acid metabolism were significantly differentially regulated which suggests its role in glycerol induced DHA accumulation.
Publication:
Release Date:	March 6, 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_101065	D0_1	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glucose (3% w/v) in YPD medium	0 hours	NA	NA	NA	NA	NA	NA
2	IMSM_101066	D4_Glucose_1	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glucose (3% w/v) in YPD medium	96 hours	NA	NA	NA	NA	NA	NA
3	IMSM_101067	D4_Glucose_2	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glucose (3% w/v) in YPD medium	96 hours	NA	NA	NA	NA	NA	NA
4	IMSM_101068	D4_Glucose_3	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glucose (3% w/v) in YPD medium	96 hours	NA	NA	NA	NA	NA	NA
5	IMSM_101069	D2_Glucose_3	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glucose (3% w/v) in YPD medium	48 hours	NA	NA	NA	NA	NA	NA
6	IMSM_101070	D2_Glucose_1	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glucose (3% w/v) in YPD medium	48 hours	NA	NA	NA	NA	NA	NA
7	IMSM_101071	D0_2	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glucose (3% w/v) in YPD medium	0 hours	NA	NA	NA	NA	NA	NA
8	IMSM_101072	D2_Glucose_2	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glucose (3% w/v) in YPD medium	48 hours	NA	NA	NA	NA	NA	NA
9	IMSM_101073	D0_3	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glucose (3% w/v) in YPD medium	0 hours	NA	NA	NA	NA	NA	NA
10	IMSM_101074	D4_Glycerol_3	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glycerol (3% w/v) in YPD medium	96 hours	NA	NA	NA	NA	NA	NA
11	IMSM_101075	D4_Glycerol_2	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glycerol (3% w/v) in YPD medium	96 hours	NA	NA	NA	NA	NA	NA
12	IMSM_101076	D2_Glycerol_2	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glycerol (3% w/v) in YPD medium	48 hours	NA	NA	NA	NA	NA	NA
13	IMSM_101077	D2_Glycerol_1	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glycerol (3% w/v) in YPD medium	48 hours	NA	NA	NA	NA	NA	NA
14	IMSM_101078	D2_Glycerol_3	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glycerol (3% w/v) in YPD medium	48 hours	NA	NA	NA	NA	NA	NA
15	IMSM_101079	D4_Glycerol_1	Aurantiochytrium limacinum	Cultured cells	Quenched cells resuspended in 1 mL ice-cold methanol/ethanol/chloroform (2:6:2), sonicated for 15 min, centrifuged at 10,000×g for 15 min at 4°C. Supernatant filtered, dried under nitrogen stream, dissolved in methoxamine hydrochloride solution, incubated at 30°C for 90 min, followed by MSTFA derivatization.	Cultured cells	Glycerol (3% w/v) in YPD medium	96 hours	NA	NA	NA	NA	NA	NA

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_100539	D0_1 / IMSM_101065	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
2	IME_100540	D4_Glucose_1 / IMSM_101066	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
3	IME_100541	D4_Glucose_2 / IMSM_101067	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
4	IME_100542	D4_Glucose_3 / IMSM_101068	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
5	IME_100543	D2_Glucose_3 / IMSM_101069	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
6	IME_100544	D2_Glucose_1 / IMSM_101070	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
7	IME_100545	D0_2 / IMSM_101071	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
8	IME_100546	D2_Glucose_2 / IMSM_101072	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
9	IME_100547	D0_3 / IMSM_101073	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
10	IME_100548	D4_Glycerol_3 / IMSM_101074	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
11	IME_100549	D4_Glycerol_2 / IMSM_101075	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
12	IME_100550	D2_Glycerol_2 / IMSM_101076	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
13	IME_100551	D2_Glycerol_1 / IMSM_101077	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
14	IME_100552	D2_Glycerol_3 / IMSM_101078	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - EI	Positive	NA
15	IME_100553	D4_Glycerol_1 / IMSM_101079	GCMS (Gas Chromatography -Mass Spectrometry)	Agilent 7890A\|IMDA_MS_100018	Triple quadrupole	Electron Ionization - 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_101138	IME_100539	D0_1.mzdata.xml
2	IMR_101139	IME_100540	D4_GLU_1.mzdata.xml
3	IMR_101140	IME_100541	D4_GLU_2.mzdata.xml
4	IMR_101141	IME_100542	D4_GLU_3.mzdata.xml
5	IMR_101142	IME_100543	D2_GLU_3.mzdata.xml
6	IMR_101143	IME_100544	D2_GLU_1.mzdata.xml
7	IMR_101144	IME_100545	D0_2.mzdata.xml
8	IMR_101145	IME_100546	D2_GLU_2.mzdata.xml
9	IMR_101146	IME_100547	D0_3.mzdata.xml
10	IMR_101147	IME_100548	D4_GLY_3.mzdata.xml
11	IMR_101148	IME_100549	D4_GLY_2.mzdata.xml
12	IMR_101149	IME_100550	D2_GLY_2.mzdata.xml
13	IMR_101150	IME_100551	D2_GLY_1.mzdata.xml
14	IMR_101151	IME_100552	D2_GLY_3.mzdata.xml
15	IMR_101152	IME_100553	D4_GLY_1.mzdata.xml