Summary of Study ST000614

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 PR000449. The data can be accessed directly via it's Project DOI: 10.21228/M8161N This work is supported by NIH grant, U2C- DK119886.


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Study IDST000614
Study TitleTobacco-specific carcinogens in Bladder Cancer
Study SummarySmoking induced methylation plays a critical role in the accumulation of methylated metabolites, DNA adducts damage and altered metabolism in BCa. These deregulated metabolites can be detected non-invasively and can be used as causal biomarkers that can predict the risk of developing BCa in smokers
Baylor College of Medicine
Last NamePutluri
First NameNagireddy
AddressOne Baylor Plaza
Submit Date2017-05-23
Analysis Type DetailLC-MS
Release Date2018-12-11
Release Version1
Nagireddy Putluri Nagireddy Putluri application/zip

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Sample Preparation:

Sampleprep ID:SP000644
Sampleprep Summary:All the tissues and urine samples used for this study were stored in -140oC. 50 mg of tissue was used for the extraction. For cell lines, 3 x106 cell pellets were thawed at 4 °C and subjected to three freeze-thaw cycles, freezing in liquid nitrogen and thawing on ice, to rupture the cell membranes. The extraction step start with 750 µL ice-cold methanol:water (4:1) containing 20 µL spiked internal standards was added to each cell pellet or tissue sample. Ice-cold chloroform and water was added in a 3:1 ratio for a final proportion of 1:4:3:1 water:methanol:chloroform:water. The organic (methanol and chloroform) and aqueous layers dried and re suspended with 50:50 methonal: water. The extract was deproteinized using a 3-kDa molecular filter (Amicon Ultracel-3K Membrane; Millipore Corporation, Billerica, MA) and the filtrate was dried under vacuum (Genevac EZ-2plus; Gardiner, Stone Ridge, NY). Prior to mass spectrometry, the dried extracts were resuspended in identical volumes of injection solvent composed of 1:1 water:methanol and subjected to liquid chromatography-mass spectrometry. 50 ul of urine was used for sample preparation. Internal standard was spiked into raw sample. Then it was processed through Amicon 3k filter. After that, 50 ul of urine sample was diluted with 450 solvent ( methanol water =50:50 v/v) and subjected to LC/MS analysis. The injection volume was 10 ul.