Cell Metabolism Laboratory

Justin Cross (Core Facility Head)

Email(s)

crossj@mskcc.org

Cross Lab
The Cell Metabolism Laboratory is part of the Donald B. and Catherine C. Marron Cancer Metabolism Center and helps investigators characterize biological systems through the direct measurement of the small molecule constituents. Our primary areas of focus are cancer cell metabolism and understanding the host / gut microbiome interaction.

We use a range of complementary GC-MS and LC-MS analytical platforms and help investigators conduct studies from the experimental design stage, through data acquisition, data analysis and interpretation. We also provide access to non-MS technologies for measurement of nutrient and oxygen consumption.

Technologies

Nutrient Consumption

Our YSI 7000 enzymatic analyzer measures glucose, glutamine, and lactate levels in cell culture media and is used to determine cellular nutrient consumption rates.

Oxygen Consumption

Seahorse XFe96 and XFp Extracellular Flux Analyzers are available for the measurement of oxygen consumption and extracellular acidification.

Cell Growth and Viability

The ACEA xCELLigence MP provides the real-time measurements of cell proliferation and viability. A hypoxia chamber is also available for maintaining cells in low oxygen.

Sample Preparation

A variety of instruments and protocols are available for the homogenization of extraction of metabolites and lipids from cells, cell culture media, tissue, serum/plasma, urine and fecal material. A Gerstel MPS instrument is used to automate chemical derivatizations.

 Vials on the autosampler of a mass spec

Gas Chromatography–Mass Spectrometry – Targeted

2 Agilent GC-MS systems with 5975 mass selective detectors are used to measure derivatized organic acids, amino acids, fatty acid methyl esters and short chain fatty acids, by relative and absolute quantitation, and using EI and CI ionization.

Liquid Chromatography–Mass Spectrometry – Targeted

The laboratory uses an Agilent 6230 time-of-flight (TOF) and 6545 Q-TOF LC-MS instruments for the relative quantitation of polar metabolites from cells, plasma and tissue extracts. Dedicated chromatographic methods are used for distinct chemical classes of metabolites including reverse phase, HILIC and ion pair methods. Our Thermo Vantage triple quadrupole LC-MS is used for the targeted quantitation of metabolites, including Acyl CoA profiling, cyclic nucleotides and modified DNA bases.

Untargeted metabolite profiling

Our Agilent 6550 LC Q-TOF and Agilent 7200 GC Q-TOF instruments are used for microbiome-related and lipidomic metabolite profiling. We use recursive feature finding workflows and multivariate statistical strategies in the analysis of large metabolomics datasets. We also integrate data from other ‘omic scale technologies, such as gene expression data and 16S ribosomal profiling of microbial communities, in order to generate hypotheses and inform future targeted experiments.

Isotope Tracing and Flux Measurements

Stable isotope tracing experiments using 13C, 2H and 15N stable isotope tracing, local flux calculations and IROA analysis are undertaken on a collaborative basis.

Analytical Pharmacology

Our AB SCIEX API 4000 with Shimadzu HPLC, fluorescence and UV detection is used for targeted quantitation small molecule pharmaceuticals. We generate supporting data for stage phase I/II clinical trials including DMPK studies, drug metabolite identification and bioavailability studies.