Summary of Study ST004054
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 PR002544. The data can be accessed directly via it's Project DOI: 10.21228/M8T269 This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004054 |
| Study Title | Machine learning identifies SLC25A45 as necessary for transport of mitochondrial methylated amino acids and carnitine synthesis |
| Study Summary | Metabolomics profiling of mitochondria purified from SLC25A45 KO vs control HeLa cells to determine the levels of methylated basic amino acids. Mitochondria purified from the KO cells contained less methylated basic amino acids (ADMA and TML) compared to the control ones, consistent with the role of SLC25A45 as necessary for mito transport of methylated basic amino acids. |
| Institute | Rockefeller University |
| Last Name | Khan |
| First Name | Artem |
| Address | 1230 York Ave, New York, NY, USA, 10065 |
| akhan01@rockefeller.edu | |
| Phone | (212) 327-7874 |
| Submit Date | 2025-07-19 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-10-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002544 |
| Project DOI: | doi: 10.21228/M8T269 |
| Project Title: | Machine learning identifies SLC25A45 as necessary for transport of mitochondrial methylated amino acids and carnitine synthesis |
| Project Summary: | Solute carriers (SLCs) regulate cellular and organismal metabolism by transporting small molecules and ions across membranes, yet the physiological substrates of ~20% remain elusive. To address this, we developed a supervised machine learning platform to predict and prioritize gene-metabolite associations. We uncover SLC25A45 as a mitochondrial transporter linked to serum levels of methylated basic amino acids, products of protein catabolism. Mechanistically, SLC25A45 is necessary for the mitochondrial import of methylated basic amino acids, including ADMA and TML, the latter serving as a precursor for carnitine synthesis. In line with this observation, SLC25A45 loss impairs hepatic carnitine synthesis and upregulation of carnitine-containing metabolites under fasted conditions. By facilitating mitochondrial TML import, SLC25A45 connects protein catabolism to carnitine production, sustaining β-oxidation during fasting. Altogether, our study identifies putative substrates for three SLCs and provides a resource for transporter deorphanization. |
| Institute: | Rockefeller University |
| Last Name: | Artem |
| First Name: | Khan |
| Address: | 1230 York Ave, New York, NY, 10065 |
| Email: | akhan01@rockefeller.edu |
| Phone: | (212) 327-7874 |
Subject:
| Subject ID: | SU004200 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype |
|---|---|---|---|
| SA467923 | Sa_1 | HeLa | 25A45_KO |
| SA467924 | Sa_2 | HeLa | 25A45_KO |
| SA467925 | Sa_3 | HeLa | 25A45_KO |
| SA467926 | Sa_4 | HeLa | Control |
| SA467927 | Sa_5 | HeLa | Control |
| SA467928 | Sa_6 | HeLa | Control |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO004193 |
| Collection Summary: | Mitochondria were immunopurified from ~10 mln HeLa cells expressing MITO-TAG by using the magnetic beads conjugated to HA-Antibody. Following three washes in KPBS, 50 μL 80% MeOH were added onto the beads to extract metabolites from the immunopurified mitochondria. Samples were stored at -80°C before loading onto LC-MS. |
| Sample Type: | HeLa cells |
Treatment:
| Treatment ID: | TR004209 |
| Treatment Summary: | No treatment has been done, baseline conditions |
Sample Preparation:
| Sampleprep ID: | SP004206 |
| Sampleprep Summary: | 80% MeOH extract of immunopurified mitochondria were centrifuged at 4C, max speed (>14000 g), supernatant transferred into a vial for the LC-MS analysis. |
Combined analysis:
| Analysis ID | AN006701 |
|---|---|
| Chromatography ID | CH005091 |
| MS ID | MS006400 |
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | EMD Millipore |
| Column | SeQuant ZIC- pHILIC (150 x 2.1 mm, 5 μm) |
| MS Type | EI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Orbitrap IQ-X Tribrid |
| Ion Mode | UNSPECIFIED |
| Units | m/z |
Chromatography:
| Chromatography ID: | CH005091 |
| Instrument Name: | EMD Millipore |
| Column Name: | SeQuant ZIC- pHILIC (150 x 2.1 mm, 5 μm) |
| Column Temperature: | 40°C |
| Flow Gradient: | The gradient (vol/vol) used was as follows: 0–22 min, linear gradient from 90% to 40% B; 22–24 min, held at 40% B; 24–24.1 min, returned to 90% B; 24.1–30 min, equilibrated at 90% B at a flow rate of 150 μl/min. |
| Flow Rate: | flow rate of 150 μL/min. |
| Solvent A: | 100% Water; 20 mM Ammonium carbonate; 0.1% Ammonium hydroxide (pH 9.3) |
| Solvent B: | 100% Acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS006400 |
| Analysis ID: | AN006701 |
| Instrument Name: | Thermo Orbitrap IQ-X Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | EI |
| MS Comments: | The IQ-X Tribrid was operated in full-scan polarity-switching mode with a spray voltage of +3 kV and -2.5 kV, sheath gas at 40, auxiliary gas at 15, sweep gas at 1, an ion-transfer tube temperature of 275°C, and a probe heater temperature of 350°C. Samples were analyzed with a resolution of 120,000, an AGC target of 1.2 × 10⁵, a maximum injection time of 246 ms, and two mass ranges of 55–400 Th and 375–875 Th. Both mass spectrometers were externally calibrated every three days or weekly using Pierce Calibration Solution (Thermo Fisher Scientific). Sample injections were randomized. |
| Ion Mode: | UNSPECIFIED |
