| Project ID | IMP_100041 |
| Title | Metabolite identification of B. subtilis RNC-6 at pH 4.0 |
| Uploaded by | Dr. Rajnish Prakash |
| Research Area | Biological Sciences |
| Funding Source | JAYPEE INSTITUTE OF INFORMATION TECHNOLOGY, NOIDA |
| Contributors | JAYPEE INSTITUTE OF INFORMATION TECHNOLOGY, NOIDA |
| 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 |
| Study ID | IMS_100036 |
| Title | Metabolite identification of B. subtilis RNC-6 at pH 4.0 |
| Uploaded by | Dr. Rajnish Prakash |
| Study Type | Mass Spectrometry (MS) |
| Data Type | Untargeted |
| Release Date | Dec. 16, 2025 |
| IEC/IBSC No. | |
| Publication | |
| 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. |
| # | Sample ID | Sample Name | Organism | Source | Sample Type | Experimental Condition | Gender | Age | Replicates | Storage | Files/Sample |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | IMSM_101979 | RNC-6_Ph4 | B. subtilis | Cultured cells | Bacterial Sample | Metabolite identification of B. subtilis RNC-6 at pH 4.0 | NA | NA | NA | -80 | 1 |
| 2 | IMSM_102042 | RNC-6_Ph4 | B. subtilis | Cultured cells | Bacterial Sample(02) | Metabolite identification of B. subtilis RNC-6 at pH 4.0 | NA | NA | NA | -80 | 1 |
| 3 | IMSM_102043 | RNC-6_Ph5 | B. subtilis | Cultured cells | Bacterial Sample | Metabolite identification of B. subtilis RNC-6 at pH 4.0 | NA | NA | NA | -80 | 1 |
| 4 | IMSM_102044 | RNC-6_Ph5 | B. subtilis | Cultured cells | Bacterial Sample(02) | Metabolite identification of B. subtilis RNC-6 at pH 4.0 | NA | NA | NA | -80 | 1 |
| # | MS Exp ID | Sample Name / ID | MS Type | Instrument Name | Instrument Type | Ionization Method | Ion Mode | Software Used |
|---|---|---|---|---|---|---|---|---|
| 1 | IME_101270 | RNC-6_Ph4 / IMSM_102042 | Tandem MS | Orbitrap Exploris | Orbitrap | Electrospray Ionization - ESI | Negative | NA |
| 2 | IME_101271 | RNC-6_Ph5 / IMSM_102043 | Tandem MS | Orbitrap Exploris | Orbitrap | Electrospray Ionization - ESI | Positive | NA |
| 3 | IME_101272 | RNC-6_Ph5 / IMSM_102044 | Tandem MS | Orbitrap Exploris | Orbitrap | Electrospray Ionization - ESI | Negative | NA |
| 4 | IME_101269 | RNC-6_Ph4 / IMSM_101979 | Tandem MS | Orbitrap Exploris | Orbitrap | Electrospray Ionization - ESI | Positive | NA |
| # | First Name | Last Name | Organization | Designation | |
|---|---|---|---|---|---|
| 1 | Dr. Rajnish Prakash | Singh | manasrajnish2008@gmail.com | JAYPEE INSTITUTE OF INFORMATION TECHNOLOGY | scientist |
| # | FTP Run ID | MS Exp ID | MS Data File |
|---|---|---|---|
| 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 |