Study Data


Go back (Print Records)

MS Study

Project uploaded by: Dr. Rajnish Prakash
Project ID: IMP_100041
Title: Metabolite identification of B. subtilis RNC-6 at pH 4.0
Project Description: Bacterial metabolomics has gained a significant interest as bacteria serve to provide a better subject or model at systems level. Depending on the type of samples and research objective, each step must be at optimal conditions which are significantly important in determining the final output. To date, there are no standardized nor single designated protocols that have been established for a specific bacteria strain for untargeted and targeted approaches. In this paper, we tried to identify the metabolites of probiotics B. subtilis RNC-6 at pH 4.0
Research Area: Biological Sciences
Funding Source: JAYPEE INSTITUTE OF INFORMATION TECHNOLOGY, NOIDA
Project Contributors: JAYPEE INSTITUTE OF INFORMATION TECHNOLOGY, NOIDA

Study uploaded by: Dr. Rajnish Prakash
Study ID: IMS_100036
Title: Metabolite identification of B. subtilis RNC-6 at pH 4.0
Summary: Extracted metabolites from bacterial cell pellet in 80% methanol containing 0.1% formic acid, followed by brief vortexing and sonication. The samples were then incubated at -20°C for 2 hours. The extract was centrifuged at 13,000 rpm for 10 minutes at 4°C to separate the metabolites. Supernatant containing metabolites was filtered using 0.2-micron syringe filter. Finally, 10 µL of the prepared sample was injected into the machine for analysis. All LC/MS experiments were carried out using the Dionex Ultimate 3000 UHPLC (Thermo Scientific, MA) system equipped with a binary solvent delivery manager and a sample manager, coupled with a Thermo Orbitrap Exploris mass spectrometer operating in positive (ESI +) and negative (ESI−) electrospray ionization mode (Thermo Fisher Scientific, Sunnyvale, CA, USA), separately. Separation was achieved with solvent A (Water + 0.1% (v/v) formic acid) and solvent B (Acetonitrile + 0.1% (v/v) formic acid) with the following gradient at a flow rate of 0.35 mL/min: 0 min (2% B), 0–2 min (2% B), 2–5 min (2-20% B), 5–9 min (20 – 100 % B) , 9–13 min (100% B),13-13.1(2%B) and 13.1-16min(2%B). The injection volume was 10 μL and the analysis time was 16 min. The mass spectrometric data were collected using a Thermo Orbitrap Exploris mass spectrometer. All samples were processed and RAW files generated were analysed using MSDIAL-5 software. For compound consolidation, Mass Tolerance was set 10 ppm at MS1 and 25 ppm at MS2 level. Metabolite annotation was performed using High quality database from Mass Bank. Both positive and negative mode analysis was performed separately, which was combined at later stage and duplicates were removed. Total metabolites identified in 4pH sample were 540 and uniquely found metabolites in 4pH sample were 89.
Publication:
Release Date: Dec. 16, 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_101979 RNC-6_Ph4 B. subtilis Cultured cells Extracted metabolites were re-dissolved in 80% methanol containing 2% formic acid, followed by brief vortexing and sonication. The samples were then incubated at -20°C for 2 hours. The extract was centrifuged at 13,000 rpm for 10 minutes at 4°C to separate the metabolites. Supernatant containing metabolites was filtered using 0.2-micron syringe filter. Bacterial Sample Metabolite identification of B. subtilis RNC-6 at pH 4.0 NA B. subtilis NA NA NA -80

Extracted metabolites were re-dissolved in 80% methanol containing 2% formic acid, followed by brief vortexing and sonication. The samples were then incubated at -20°C for 2 hours. The extract was centrifuged at 13,000 rpm for 10 minutes at 4°C to separate the metabolites. Supernatant containing metabolites was filtered using 0.2-micron syringe filter.

 1
2 IMSM_102042 RNC-6_Ph4 B. subtilis Cultured cells Extracted metabolites were re-dissolved in 80% methanol containing 2% formic acid, followed by brief vortexing and sonication. The samples were then incubated at -20°C for 2 hours. The extract was centrifuged at 13,000 rpm for 10 minutes at 4°C to separate the metabolites. Supernatant containing metabolites was filtered using 0.2-micron syringe filter. Bacterial Sample(02) Metabolite identification of B. subtilis RNC-6 at pH 4.0 NA B. subtilis NA NA NA -80

Extracted metabolites were re-dissolved in 80% methanol containing 2% formic acid, followed by brief vortexing and sonication. The samples were then incubated at -20°C for 2 hours. The extract was centrifuged at 13,000 rpm for 10 minutes at 4°C to separate the metabolites. Supernatant containing metabolites was filtered using 0.2-micron syringe filter.

 1
3 IMSM_102043 RNC-6_Ph5 B. subtilis Cultured cells Extracted metabolites were re-dissolved in 80% methanol containing 2% formic acid, followed by brief vortexing and sonication. The samples were then incubated at -20°C for 2 hours. The extract was centrifuged at 13,000 rpm for 10 minutes at 4°C to separate the metabolites. Supernatant containing metabolites was filtered using 0.2-micron syringe filter. Bacterial Sample Metabolite identification of B. subtilis RNC-6 at pH 4.0 NA B. subtilis NA NA NA -80

Extracted metabolites were re-dissolved in 80% methanol containing 2% formic acid, followed by brief vortexing and sonication. The samples were then incubated at -20°C for 2 hours. The extract was centrifuged at 13,000 rpm for 10 minutes at 4°C to separate the metabolites. Supernatant containing metabolites was filtered using 0.2-micron syringe filter.

 1
4 IMSM_102044 RNC-6_Ph5 B. subtilis Cultured cells Extracted metabolites were re-dissolved in 80% methanol containing 2% formic acid, followed by brief vortexing and sonication. The samples were then incubated at -20°C for 2 hours. The extract was centrifuged at 13,000 rpm for 10 minutes at 4°C to separate the metabolites. Supernatant containing metabolites was filtered using 0.2-micron syringe filter. Bacterial Sample(02) Metabolite identification of B. subtilis RNC-6 at pH 4.0 NA B. subtilis NA NA NA -80

Extracted metabolites were re-dissolved in 80% methanol containing 2% formic acid, followed by brief vortexing and sonication. The samples were then incubated at -20°C for 2 hours. The extract was centrifuged at 13,000 rpm for 10 minutes at 4°C to separate the metabolites. Supernatant containing metabolites was filtered using 0.2-micron syringe filter.

 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_101269 RNC-6_Ph4 / IMSM_101979 Tandem MS Orbitrap Exploris Orbitrap Electrospray Ionization - ESI Positive NA
2 IME_101270 RNC-6_Ph4 / IMSM_102042 Tandem MS Orbitrap Exploris Orbitrap Electrospray Ionization - ESI Negative NA
3 IME_101271 RNC-6_Ph5 / IMSM_102043 Tandem MS Orbitrap Exploris Orbitrap Electrospray Ionization - ESI Positive NA
4 IME_101272 RNC-6_Ph5 / IMSM_102044 Tandem MS Orbitrap Exploris Orbitrap Electrospray Ionization - ESI Negative NA

Sr.No First name Last name Email Organization Designation
1 Dr. Rajnish Prakash Singh manasrajnish2008@gmail.com JAYPEE INSTITUTE OF INFORMATION TECHNOLOGY scientist

Sr.No ftprun ID MS Exp ID MS Data Files
1 IMR_101873 IME_101269 22_05_2025_DR_RAJNISH_4PH_POS_VP4948.raw
2 IMR_101874 IME_101270 22_05_2025_DR_RAJNISH_4PH_NEG_VP4948.raw
3 IMR_101875 IME_101271 22_05_2025_DR_RAJNISH_5PH_POS_VP4949.raw
4 IMR_101876 IME_101272 22_05_2025_DR_RAJNISH_5PH_NEG_VP4949.raw