Summary of Study ST002531

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001627. The data can be accessed directly via it's Project DOI: 10.21228/M8D434 This work is supported by NIH grant, U2C- DK119886.


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.

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Study IDST002531
Study TitleCellular consumption/release of polar metabolites by mPDAC cells cultured in different culture media conditions
Study SummaryWe used quantitative LC-MS metabolite profiling to perform analysis of 108 metabolites that mPDAC cells consume or release while growing in RPMI or TIFM media.
University of Chicago
Last NameApiz Saab
First NameJuan
Address929 E. 57th St.
Submit Date2023-03-24
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-04-13
Release Version1
Juan Apiz Saab Juan Apiz Saab application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR001627
Project DOI:doi: 10.21228/M8D434
Project Title:Pancreatic tumors activate arginine biosynthesis to adapt to myeloid-driven amino acid stress
Project Summary:Nutrient stress in the tumor microenvironment requires cancer cells to adopt adaptive metabolic programs to maintain survival and proliferation. Therefore, knowledge of microenvironmental nutrient levels and how cancer cells cope with such nutrition is critical to understand the metabolism underpinning cancer cell biology. Previously, we performed quantitative metabolomics of the interstitial fluid (the local perfusate) of murine pancreatic ductal adenocarcinoma (PDAC) tumors to comprehensively characterize nutrient availability in the microenvironment of these tumors (Sullivan et al., 2019a). Here, we develop Tumor Interstitial Fluid Medium (TIFM), a cell culture medium that contains nutrient levels representative of the PDAC microenvironment, enabling study of PDAC metabolism under physiological nutrition. We show that PDAC cells cultured in TIFM, compared to standard laboratory models, adopt a cellular state more similar to PDAC cells in tumors. Further, using the TIFM model we identified arginine biosynthesis as a metabolic adaptation PDAC cells engage to cope with microenvironmental arginine starvation driven by myeloid cells in PDAC tumors. Altogether, these data show that nutrient availability in tumors is an important determinant of cancer cell metabolism and behavior, and cell culture models that incorporate physiological nutrient availability have improved fidelity and enable the discovery of novel cancer metabolic phenotypes.
Institute:University of Chicago
Last Name:Apiz Saab
First Name:Juan
Address:929 E. 57th St.


Subject ID:SU002631
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090


Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Media Collection_Time
SA25470820221116_QE2_JAS_Job2640_64RPMI Day_1
SA25470920221116_QE2_JAS_Job2640_69RPMI Day_1
SA25471020221116_QE2_JAS_Job2640_68RPMI Day_1
SA25471120221116_QE2_JAS_Job2640_65RPMI Day_1
SA25471220221116_QE2_JAS_Job2640_66RPMI Day_1
SA25471320221116_QE2_JAS_Job2640_67RPMI Day_1
SA25471420221116_QE2_JAS_Job2640_75RPMI Day_2
SA25471520221116_QE2_JAS_Job2640_74RPMI Day_2
SA25471620221116_QE2_JAS_Job2640_71RPMI Day_2
SA25471720221116_QE2_JAS_Job2640_70RPMI Day_2
SA25471820221116_QE2_JAS_Job2640_73RPMI Day_2
SA25471920221116_QE2_JAS_Job2640_72RPMI Day_2
SA25472020221116_QE2_JAS_Job2640_87TIFM Day_1
SA25472120221116_QE2_JAS_Job2640_86TIFM Day_1
SA25472220221116_QE2_JAS_Job2640_82TIFM Day_1
SA25472320221116_QE2_JAS_Job2640_85TIFM Day_1
SA25472420221116_QE2_JAS_Job2640_83TIFM Day_1
SA25472520221116_QE2_JAS_Job2640_84TIFM Day_1
SA25472620221116_QE2_JAS_Job2640_93TIFM Day_2
SA25472720221116_QE2_JAS_Job2640_92TIFM Day_2
SA25472820221116_QE2_JAS_Job2640_90TIFM Day_2
SA25472920221116_QE2_JAS_Job2640_88TIFM Day_2
SA25473020221116_QE2_JAS_Job2640_89TIFM Day_2
SA25473120221116_QE2_JAS_Job2640_91TIFM Day_2
Showing results 1 to 24 of 24


Collection ID:CO002624
Collection Summary:100,000-150,000 cells were seeded in 2mL of culture medium in six-well plates with 3 technical replicates per condition per time point and allowed to attach overnight. The following day (day 1), cells were washed twice with 2mL PBS. They were then given 2mL of media, either TIFM or RPMI. An unspent media sample was collected at this time as well and stored at -80 °C. Cell number on day 1 was measured using a Vi-CELL XR Cell Viability Analyzer (Beckman Coulter). 24h later (day 2), 1mL of spent media from cells was collected, centrifuged and stored at -80 °C. Cell number was counted again. Quantification of metabolite levels in unspent (day 1) and day 2 (conditioned media) cell culture media samples was performed.
Sample Type:Cell culture media


Treatment ID:TR002643
Treatment Summary:NA

Sample Preparation:

Sampleprep ID:SP002637
Sampleprep Summary:We extracted metabolites from 5µL of cell culture media samples using 45µL of a 75:25:0.1 HPLC grade acetonitrile:methanol:formic acid extraction mix with labelled stable isotope internal standards. Samples in extraction mix were vortexed for 10 min at 4°C and centrifugated at 15,000x rpm for 10 min at 4°C to pellet insoluble material. 20µL of the soluble polar metabolite supernatant was moved to sample vials for analysis by LC-MS.

Combined analysis:

Analysis ID AN004165
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Dionex Ultimate 3000
Column SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Units Peak area (m/z)


Chromatography ID:CH003084
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Column Temperature:25
Flow Gradient:0–20 min: linear gradient from 80% to 20% B; 20–20.5 min: linear gradient from 20% to 80% B; 20.5–28 min: hold at 80% B
Flow Rate:0.150 mL/min
Solvent A:20 mM ammonium carbonate, 0.1% ammonium hydroxide
Solvent B:100% Acetonitrile
Chromatography Type:HILIC


MS ID:MS003912
Analysis ID:AN004165
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Comments:XCalibur 965 2.2 software (Thermo 966 Fisher Scientific) was used identification and relative quantification for metabolites.