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MB Sample ID: SA124543
| Local Sample ID: | 07_C1-1_SI_allogenic_42days_170427_UKy_GCH_rep1-polar-ICMS_A |
| Subject ID: | SU001546 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001546 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 07_C1-1_SI_allogenic_42days_170427_UKy_GCH_rep1-polar-ICMS_A | SA124543 | FL015071 | allogenic | Treatment Protocol |
Collection:
| Collection ID: | CO001541 |
| Collection Summary: | Mouse is sacrificed and tissues are harvested. |
| Collection Protocol ID: | mouse_tissue_collection |
| Sample Type: | Multiple tissues |
Treatment:
| Treatment ID: | TR001561 |
| Treatment Summary: | Mouse with allogenic bone marrow transplant. Fed with semi-liquid diet supplemented with fully labeled glucose for 24 hours before harvest. Mouse with no treatment. Fed with semi-liquid diet supplemented with fully labeled glucose for 24 hours before harvest. Mouse with syngenic bone marrow transplant. Fed with semi-liquid diet supplemented with fully labeled glucose for 24 hours before harvest. |
| Treatment Protocol ID: | allogenic naive syngenic |
Sample Preparation:
| Sampleprep ID: | SP001554 |
| Sampleprep Summary: | Before going into the IC-FTMS the frozen sample is reconstituted in water. Polar extraction from homogenate, lypholized, and frozen. Frozen tissue is ground in a SPEX grinder under liquid nitrogen to homogenize the sample. Tissue is frozen in liquid nitrogen to stop metabolic processes. Protein extraction and quantification. |
| Sampleprep Protocol ID: | polar_extraction; IC-FTMS_preparation; tissue_quench; frozen_tissue_grind; protein_extraction |
| Sampleprep Protocol Filename: | 4B_Extract_Polar_Lipid_Prot_Fan_070417.pdf 4D_17Jun4_Fan_Prot_Quant.pdf |
Combined analysis:
| Analysis ID | AN002448 |
|---|---|
| Analysis type | MS |
| Chromatography type | Ion exchange |
| Chromatography system | Thermo Dionex ICS-5000+ |
| Column | Dionex IonPac AS11-HC (250 x 2mm,4um) |
| MS Type | ESI |
| MS instrument type | IC-FTMS |
| MS instrument name | Orbitrap Fusion |
| Ion Mode | NEGATIVE |
| Units | abundance & normalized peak area |
Chromatography:
| Chromatography ID: | CH001793 |
| Chromatography Summary: | Targeted IC |
| Instrument Name: | Thermo Dionex ICS-5000+ |
| Column Name: | Dionex IonPac AS11-HC (250 x 2mm,4um) |
| Chromatography Type: | Ion exchange |
MS:
| MS ID: | MS002271 |
| Analysis ID: | AN002448 |
| Instrument Name: | Orbitrap Fusion |
| Instrument Type: | IC-FTMS |
| MS Type: | ESI |
| MS Comments: | ICMS Analytical Experiment with detection of compounds by comparison to standards. Thermo RAW files are loaded into TraceFinder and peaks are manually curated. The area under the chromatograms is then exported to an Excel file. The area is then corrected for natural abundance. The natural abundance corrected area is then used to calculate the concentration of each compound for each sample. This calculation is done using standards. The first sample ran on the ICMS is a standard that has known concentrations of certain compounds. Then a number of samples are ran (typically 3-4) followed by another standard. The equation to calculate the concentration is "intensity in sample"/("intensity in first standard" + (("intensity in second standard" - "intensity in first standard")/# of samples) * "known concentration in standard", where the "intensity" is the aforementioned natural abundance corrected area, and the unlabeled intensity from the standard is used for all isotopologues of the compound. The reconstitution volume is simply the volume that the polar part of the sample was reconstituted to before going into the ICMS. The injection volume is how much of the reconstitution volume was injected into the ICMS. The protein is how much protein was in the entire sample (not only the small portion that was aliquoted for the ICMS). The polar split ratio is the fraction of the polar part of the sample that was aliquoted for the ICMS. This is calculated by dividing the weight of the polar aliquot for ICMS by the total weight of the polar portion of the sample. The protein normalized concentration is calculated using the equation, concentration * (reconstitution volume / 1000 / polar split ratio / protein). |
| Ion Mode: | NEGATIVE |
