Summary of Study ST002515

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 PR001620. The data can be accessed directly via it's Project DOI: 10.21228/M89B04 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	ST002515
Study Title	Time course 2: Acetate quantification from growth of Eggerthella lenta in defined media
Study Type	Untargeted LC-MS
Study Summary	This dataset contains targeted metabolomics analysis of carboxylic acids in supernatants from 3 strains of Eggerthella lenta grown in defined EDM1 media with varying acetate concentrations.
Institute	University of California, San Francisco
Last Name	Noecker
First Name	Cecilia
Address	513 Parnassus Ave HSW1501, San Francisco, CA 94143
Email	cecilia.noecker@ucsf.edu
Phone	415-502-3264
Submit Date	2023-03-21
Raw Data Available	Yes
Raw Data File Type(s)	d, mzML
Analysis Type Detail	LC-MS
Release Date	2023-04-10
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP002621
Sampleprep Summary:	Samples (20 μL) were first mixed with an internal standard solution (30 μL; 1 mM phenylpropionate-d9) in a V-bottomed, poly(propylene), 96-well plate, and extracted by mixing with 3 sample volumes of extraction solution (75% acetonitrile:25% methanol). The plate was covered with a lid and centrifuged at 5,000 rcf for 15 min at 4 °C. Supernatant was collected for derivatization before subjecting to LC–MS analysis. Samples were processed using a derivatization method targeting compounds containing a free carboxylic acid. Extracted samples were mixed with 3-nitrophenylhydrazine (NPH; 200 mM in 50% acetonitrile) and N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide (120 mM in 6% pyridine) at a 2:1:1 ratio. The plate was sealed with a plastic sealing mat (Thermo Fisher Scientific, #AB-0566) and incubated at 40 °C, 600 rpm in a thermomixer for 60 min to derivatize the carboxylate-containing compounds. The reaction mixture was quenched with 0.02% formic acid in 10% acetonitrile:water before LC–MS.

Sampleprep ID:

SP002621

Sampleprep Summary:

Samples (20 μL) were first mixed with an internal standard solution (30 μL; 1 mM phenylpropionate-d9) in a V-bottomed, poly(propylene), 96-well plate, and extracted by mixing with 3 sample volumes of extraction solution (75% acetonitrile:25% methanol). The plate was covered with a lid and centrifuged at 5,000 rcf for 15 min at 4 °C. Supernatant was collected for derivatization before subjecting to LC–MS analysis. Samples were processed using a derivatization method targeting compounds containing a free carboxylic acid. Extracted samples were mixed with 3-nitrophenylhydrazine (NPH; 200 mM in 50% acetonitrile) and N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide (120 mM in 6% pyridine) at a 2:1:1 ratio. The plate was sealed with a plastic sealing mat (Thermo Fisher Scientific, #AB-0566) and incubated at 40 °C, 600 rpm in a thermomixer for 60 min to derivatize the carboxylate-containing compounds. The reaction mixture was quenched with 0.02% formic acid in 10% acetonitrile:water before LC–MS.