Name: a strategy for sensitive, large scale quantitative metabolomics
Uploaded: 2014-05-27T13:45:00
Description: Watch this Scientific Journal Video about A Strategy for Sensitive, Large Scale Quantitative Metabolomics at JoVE.com

The authors would like to acknowledge Detlef Schumann, Jennifer Sutton (Thermo Fisher Scientific) and Nathaniel Snyder (University of Pennsylvania) for valuable discussions on mass calibration and data processing.&#160; Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under Award Number R00CA168997. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

1. Preparation of LC-MS Reagents, Establishment of a Chromatography Method, and Establishment of Instrument Operating Procedures
<ol>
	<li>Preparation of LC Solvents
	<ol>
		<li>Prepare 500 ml mobile phases. A is 20 mM ammonium acetate and 15 mM ammonium hydroxide in 3% acetonitrile/water, final pH 9.0;&#160;and B is 100% acetonitrile.</li>
		<li>Loosely cap the bottle, place it in a water bath sonicator, and sonicate for 10 min without extra heating. (This step is to ensure that all of the ammonium salts completely di...

<ol>
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The most critical steps for successful metabolite profiling in cells using this protocol are: 1) controlling the growth medium and careful extraction of the cells; 2) adjusting the LC method based on MS method setup to ensure there are enough (usually at least 10) data points across a peak for quantitation; 3) doing a low mass calibration before running samples; 4) injecting no more than 5 ml to avoid retention time shifting and peak broadening caused by water; and 5) preparing and running samples for comparison in the s...

Metabolomics, defined as an experiment that measures multiple metabolites simultaneously, has been an area of intense interest.&#160; Metabolomics provides a direct readout of molecular physiology and has provided insights into development and disease such as cancer1-4.&#160; Nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS) are among the most commonly used instruments5-9. &#160;NMR, especially has been used for flux experiments since heavy isotope labeled compounds, such as 13C labeled metabolites, are NMR-active10,11. &#160;However, this strategy requires relatively high sample purity and large sample quantity, which limits its applications in metabolomics. &#160;Meanwhile, data collected from NMR needs intensive analysis and compound assignment of complex NMR spectra is difficult.&#160;GC-MS has been widely used for polar metabolites and lipid studies, but it requires volatile compounds and therefore often derivatization of metabolites, which sometimes involves complex chemistry that can be time consuming and introduces experimental noise.
Liquid chromatography (LC) coupled to triple quadrupole mass spectrometry uses the first quadrupole for selecting the intact parent ions, which are then fragmented in the second quadrupole, while the third quadrupole is used to select characteristic fragments or daughter ions. &#160;This method, which records the transition from parent ions to specific daughter ions, is termed multiple reaction monitoring (MRM). &#160;MRM is a very sensitive, specific, and robust method for both small molecule and protein quantitation12-15,21.&#160; However, MRM does have its limitations. To achieve high specificity a MRM method needs to be built for each metabolite. This method consists of identifying a specific fragment and corresponding optimized collision energy, which requires pre-knowledge of the properties of the metabolites of interest, such as chemical structure information. Therefore, with some exceptions involving the neutral loss of common fragments, it is not possible to identify unknown metabolites with this method.&#160;

In the recent years, high-resolution mass spectrometry (HRMS) instruments have been released, such as the LTQ-orbitrap and Exactive series, the QuanTof, and TripleTOF 560016-18,22. HRMS can provide a mass to charge ratio (m/z) of intact ions within an error of a few ppm. Therefore, an HRMS instrument operated by detecting all precursor ions (i.e. full scan mode) can obtain direct structural information from the exact mass and the resulting elemental composition of the analyte, and this information can be used to identify potential metabolites.&#160; Indeed, all information about a compound can be obtained with an exact mass, up to the level of structural isomers. &#160;Also, a full scan method does not require previous knowledge of metabolites and does not require method optimization. &#160;Moreover, since all ions with m/z falling into the scan range can be analyzed, HRMS has a nearly unlimited capacity in terms of the number of metabolites that can be quantified in a single run compared to the MRM method. HRMS is also comparable to a triple quadrupole MRM in quantitative capacity due to the short duty cycle resulting in a comparable number of data points that can be obtained in a full MS scan. Therefore, HRMS provides an alternative approach for quantitative metabolomics. Recently, an improved version of HRMS termed Q-Exactive mass spectrometry (QE-MS) can be operated under the switching between positive and negative modes with sufficiently fast cycle times in a single method, which expands the detection range19.&#160; Here we describe our metabolomics strategy using the QE-MS.&#160; &#160;

<table border="0" cellpadding="0" cellspacing="0" width="600">
	<tbody>
		<tr height="20">
			<td height="20" style="height:20px;width:156px;">Positive calibration mix</td>
			<td style="width:117px;">Thermo Scientific</td>
			<td style="width:120px;">#88323</td>
			<td style="width:207px;">It is light sensitive. Store at 4 &#176;C</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Negative calibration mix</td>
			<td>Thermo Scientific</td>
			<td>#88324</td>
			<td>Store at 4 &#176;C</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Diazinon</td>
			<td style="width:117px;">Sant Cruz Biotechnology</td>
			<td>#C0413</td>
			<td style="width:207px;">It causes eyes irritation, so work in hood. Store at 4 &#176;C</td>
		</tr>
		<tr height="80">
			<td height="80" style="height:80px;">H-ESI needle insert</td>
			<td>Fisher Scientific</td>
			<td>#1303200</td>
			<td style="width:207px;">This could be replaced or cleaned with 5 % Formic acid/water (remove rubber ring) if clogged.</td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Xbridge amide column</td>
			<td>Waters</td>
			<td>#186004860</td>
			<td style="width:207px;">Guard column is recommend to increase column lifetime.</td>
		</tr>
	</tbody>
</table>

a strategy for sensitive, large scale quantitative metabolomics

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. However, current platforms have different limiting factors, such as labor intensive sample preparations, low detection limits, slow scan speeds, intensive method optimization for each metabolite, and the inability to measure both positively and negatively charged ions in single experiments. Therefore, a novel metabolomics protocol could advance metabolomics studies. Amide-based hydrophilic chromatography enables polar metabolite analysis without any chemical derivatization. High resolution MS using the Q-Exactive (QE-MS) has improved ion optics, increased scan speeds (256 msec at resolution 70,000), and has the capability of carrying out positive/negative switching. Using a cold methanol extraction strategy, and coupling an amide column with QE-MS enables robust detection of 168 targeted polar metabolites and thousands of additional features simultaneously.&#160; Data processing is carried out with commercially available software in a highly efficient way, and unknown features extracted from the mass spectra can be queried in databases.

The accuracy of metabolomics data highly depends on the LC-QE-MS instrument performance. To assess whether the instrument is operating in good condition, and whether the method applied is proper, several known metabolite LC peaks are extracted from the total ion chromatography (TIC), as shown in Figure 1. Polar metabolites, including amino acids, glycolysis intermediates, TCA intermediates, nucleotides, vitamins, ATP, NADP+ and so on have good retention on the column and good peak shapes in th...

Watch this Scientific Journal Video about A Strategy for Sensitive, Large Scale Quantitative Metabolomics at JoVE.com

A Strategy for Sensitive, Large Scale Quantitative Metabolomics

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. Utilizing normal-phased liquid chromatography coupled to high-resolution mass spectrometry with polarity switching and a rapid duty cycle, we describe a protocol to analyze the polar metabolic composition of biological material with high sensitivity, accuracy, and resolution.

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. However, current platforms have different limiting ...

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