Summary of Study ST001119
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 PR000750. The data can be accessed directly via it's Project DOI: 10.21228/M8QX2G This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST001119 |
| Study Title | Quantification of microenvironmental metabolites in murine cancers reveals determinants of tumor nutrient availability |
| Study Summary | Cancer cell metabolism is heavily influenced by microenvironmental factors, including nutrient availability. Therefore, knowledge of microenvironmental nutrient levels is essential to understand tumor metabolism. To measure the extracellular nutrient levels available to tumors, we developed a quantitative metabolomics method to measure the absolute concentrations of >118 metabolites in plasma and tumor interstitial fluid, the extracellular fluid that perfuses tumors. Comparison of nutrient levels in tumor interstitial fluid and plasma revealed that the nutrients available to tumors differ from those present in circulation. Further, by comparing interstitial fluid nutrient levels between autochthonous and transplant models of murine pancreatic and lung adenocarcinoma, we found that tumor type, anatomical location and animal diet affect local nutrient availability. These data provide a comprehensive characterization of the nutrients present in the tumor microenvironment of widely used models of lung and pancreatic cancer and identify factors that influence metabolite levels in tumors. |
| Institute | University of Chicago |
| Last Name | Muir |
| First Name | Alexander |
| Address | 929 E 57th St. W GCIS 306, Chicago, Illinois, 60637, USA |
| muir.alexander@gmail.com | |
| Phone | 5104950975 |
| Submit Date | 2019-01-03 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-03-06 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN001830 | AN001831 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | HILIC | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 | Thermo Dionex Ultimate 3000 |
| Column | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) | SeQuant ZIC-pHILIC (150 x 2.1mm,5um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | micromoles/L | micromoles/L |
MS:
| MS ID: | MS001691 |
| Analysis ID: | AN001830 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | LC/MS analysis was performed using a QExactive orbitrap mass spectrometer using an Ion Max source and heated electrospray ionization (HESI) probe coupled to a Dionex Ultimate 3000 UPLC system (Thermo Fisher Scientific, Waltham, MA). External mass calibration was performed every 7 days. 2μL of each sample was injected onto a ZIC-pHILIC 2.1 × 150 mm analytical column equipped with a 2.1 × 20 mm guard column (both 5 μm particle size, EMD Millipore). The autosampler and column oven were held at 4°C and 25°C, respectively. Buffer A was 20 mM ammonium carbonate, 0.1% ammonium hydroxide; buffer B was acetonitrile. The chromatographic gradient was run at a flow rate of 0.150 mL/min as follows: 0-20 min: linear gradient from 80% to 20% B; 20-20.5 min: linear gradient from 20% to 80% B; 20.5-28min: hold at 80% B. The mass spectrometer was operated in full scan, polarity-switching mode with the spray voltage set to 3.0 kV, the heated capillary held at 275°C, and the HESI probe held at 350°C. The sheath gas flow rate was set to 40 units, the auxiliary gas flow was set to 15 units, and the sweep gas flow was set to 1 unit. The MS data acquisition was performed in a range of 70-1000 m/z, with the resolution set to 70,000, the AGC target at 1e6, and the maximum injection time at 20 msec. Metabolite identification and quantification was performed with XCalibur 2.2 software (Thermo Fisher Scientific, Waltham, MA) using a 5ppm mass accuracy and a 0.5 min. retention time window. For metabolite identification, external standard pools were used for assignment of metabolites to peaks at given m/z and retention time, and to determine the limit of detection for each metabolite (see Supplementary File 1 for the m/z, retention time and limit of detection for each metabolite analyzed). Metabolite quantification was performed by two separate methods. Where internal standards were available, first, comparison of the peak areas of the stable isotope labeled internal standards with the external standard pools allowed for quantification of the concentration of labeled internal standards in the extraction buffer. Subsequently, we compared the peak area of a given metabolite in the TIF and plasma samples with the peak area of the internal standard to quantitate the concentration of that metabolite in the TIF or plasma sample. 70 metabolites were quantitated using this internal standard method (see Supplementary File 1 for the metabolites quantitated with internal standards). For metabolites without internal standards, the peak area of each analyte was normalized to the peak area of a labeled amino acid internal standard that eluted at roughly the same retention time to account for differences in recovery between samples (see Supplementary File 1 for the labeled amino acid paired to each metabolite analyzed without an internal standard). From the normalized peak areas of metabolites in the external standard pools, we generated a standard curve describing the relationship between metabolite concentration and normalized peak area. The standard curves were linear with fits typically at or above r2=0.95. Metabolites which did not meet these criteria were excluded from further analysis. These equations were then used to convert normalized peak areas of analytes in the TIF or plasma samples into analyte concentration in the samples. 74 metabolites were quantitated using this method. The relationship between metabolite concentration and normalized peak area is matrix dependent, and the external standards are prepared in water, which is a different matrix than either TIF or plasma. Therefore, we consider metabolite measurements using this external standard method semi-quantitative. |
| Ion Mode: | POSITIVE |
| MS ID: | MS001692 |
| Analysis ID: | AN001831 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | LC/MS analysis was performed using a QExactive orbitrap mass spectrometer using an Ion Max source and heated electrospray ionization (HESI) probe coupled to a Dionex Ultimate 3000 UPLC system (Thermo Fisher Scientific, Waltham, MA). External mass calibration was performed every 7 days. 2μL of each sample was injected onto a ZIC-pHILIC 2.1 × 150 mm analytical column equipped with a 2.1 × 20 mm guard column (both 5 μm particle size, EMD Millipore). The autosampler and column oven were held at 4°C and 25°C, respectively. Buffer A was 20 mM ammonium carbonate, 0.1% ammonium hydroxide; buffer B was acetonitrile. The chromatographic gradient was run at a flow rate of 0.150 mL/min as follows: 0-20 min: linear gradient from 80% to 20% B; 20-20.5 min: linear gradient from 20% to 80% B; 20.5-28min: hold at 80% B. The mass spectrometer was operated in full scan, polarity-switching mode with the spray voltage set to 3.0 kV, the heated capillary held at 275°C, and the HESI probe held at 350°C. The sheath gas flow rate was set to 40 units, the auxiliary gas flow was set to 15 units, and the sweep gas flow was set to 1 unit. The MS data acquisition was performed in a range of 70-1000 m/z, with the resolution set to 70,000, the AGC target at 1e6, and the maximum injection time at 20 msec. Metabolite identification and quantification was performed with XCalibur 2.2 software (Thermo Fisher Scientific, Waltham, MA) using a 5ppm mass accuracy and a 0.5 min. retention time window. For metabolite identification, external standard pools were used for assignment of metabolites to peaks at given m/z and retention time, and to determine the limit of detection for each metabolite (see Supplementary File 1 for the m/z, retention time and limit of detection for each metabolite analyzed). Metabolite quantification was performed by two separate methods. Where internal standards were available, first, comparison of the peak areas of the stable isotope labeled internal standards with the external standard pools allowed for quantification of the concentration of labeled internal standards in the extraction buffer. Subsequently, we compared the peak area of a given metabolite in the TIF and plasma samples with the peak area of the internal standard to quantitate the concentration of that metabolite in the TIF or plasma sample. 70 metabolites were quantitated using this internal standard method (see Supplementary File 1 for the metabolites quantitated with internal standards). For metabolites without internal standards, the peak area of each analyte was normalized to the peak area of a labeled amino acid internal standard that eluted at roughly the same retention time to account for differences in recovery between samples (see Supplementary File 1 for the labeled amino acid paired to each metabolite analyzed without an internal standard). From the normalized peak areas of metabolites in the external standard pools, we generated a standard curve describing the relationship between metabolite concentration and normalized peak area. The standard curves were linear with fits typically at or above r2=0.95. Metabolites which did not meet these criteria were excluded from further analysis. These equations were then used to convert normalized peak areas of analytes in the TIF or plasma samples into analyte concentration in the samples. 74 metabolites were quantitated using this method. The relationship between metabolite concentration and normalized peak area is matrix dependent, and the external standards are prepared in water, which is a different matrix than either TIF or plasma. Therefore, we consider metabolite measurements using this external standard method semi-quantitative. |
| Ion Mode: | NEGATIVE |
