Metabolomic profiling of primary leukemia samples
Metabolomic profiling results of flash frozen bone marrow samples from a cohort of T-cell acute leukemia samples (n = 22, including ETP-ALL (n = 9) and T-ALL (n = 13), categorized by immunophenotype and genetic alterations) by chromatography-tandem mass spectrometry. Quantitative profiling of 403 named cellular metabolites normalized for sample weight and protein content.
Steps to reproduce
We analyzed leukemic bone marrow samples from ETP-ALL and T-ALL patients . Briefly, we snap froze cell pellets and extracted and prepared them for analysis using standard solvent extraction methods. We split the extracted samples into equal parts for analysis on the GC/MS and LC/MS/MS platforms of Metabolon, Inc (Morrisville, NC). Identification of known chemical entities was based on comparison to metabolomic library entries of purified standards. We first normalized results to protein concentration, log transformed and imputed any missing values with the minimum observed value for each compound. We then used Welch’s two-sample t-test to identify biochemicals that differed significantly between experimental groups. To account for the multiple comparisons, we also calculated an estimate of the false discovery rate (q-value), which indicates the fraction of biochemicals that would meet a given p-value cut-off by random chance.