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Split_Ratio_Calculator.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
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<meta property='og:title' content='Isotope Calculation Gadgets'>
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<meta name="description" content="Isotope Calculation Gadgets" />
<title>Isotope Calculation Gadgets</title>
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<h1 class="header-logo">
<a href=".">Isotope Calculation Gadgets</a>
</h1>
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<ul class="header-nav-list">
<li class="header-nav-item"><a href="index.html#About">About</a></li>
<li class="header-nav-item"><a href="index.html#Overview">Overview</a></li>
<li class="header-nav-item"><a href="index.html#Imprementation">Imprementation</a></li>
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<article class="article">
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<h2 class="article-title">Split Ratio Calculator</h2>
<p class="article-img">
<img src="img/Split_ratio_calculator.png" alt="">
</p>
<div class="article-body">
<p>
This gadget can calculate flux split ratio of the glycolysis (Embden-Meyerhof pathway, EMP) and the pentose phosophate pathway (PPP) based on the labeling data obtained from [1-<sup>13</sup>C]glucose tracing experiments.
</p>
<h3 class="article-info-title">Preparation</h3>
<p>
Perform tracer experiments using 100% [1-<sup>13</sup>C]glucose. Other labeled glucose are not supported in this gadget.
</p>
<p>
Obtain natural isotope-subtracted labeling data by using <a href="./Natural_Isotope_Subtractor.html">"Natural Isotope Subtractor".</a>
</p>
<h3 class="article-info-title">Procedure</h3>
<p>
Start Garuda and open the “Split Ratio Calculator”. Choose "Subtracted labeling.csv" generated by <a href="./Natural_Isotope_Subtractor.html">"Natural Isotope Subtractor"</a> as input file and click the "Launch" button.
</p>
<img src="img/src_start_screen.png">
<div class ="note">
<h4>Note:</h4>
<li>
After running "Natural Isotopes Subtractor", the generated data can be transfer smoothly to "Average Labeling Calculator" by clicking the "Discover" button.
</li>
<img src="img/data_transfer.png">
</div>
<p>
Select "Mammalian cells" or "Microbial cells" depending on the species to be analyzed.
</p>
<p>
Make sure that your experimental conditions meet the conditions indicated in the warning.
</p>
<p>
Write an appropriate fragment name depending on the species to be analyzed.
</p>
<p>
<div class ="note">
<h4>For mammalian cells</h4>
<li>
Choose a fragment name of 3PG or PEP containing 1st to 3rd carbons.
Employment of either pyruvate, alanine, or lactate is not recommeneded due to occurrence of labeling dilution via glutaminolysis.
</li>
<h4>For bacterial cells</h4>
<li>
Choose a fragment names of either alanine, pyruvate, or lactate contatinig 1st to 3rd, and 2nd to 3rd carbons.
</li>
</div>
<div class ="note">
<h4>Note:</h4>
<li>
A split ratio of glycolysis and the pentose phosphate pathway can be calculated based on the following atom mapping.
When [1-<sup>13</sup>C]glucose is metabolized via the glycolysis, the lower glycolytic metabolites are labeled with M : M+1 = 1 : 1, whereas when metabolized via PPP, the first <sup>13</sup>C atom of glucose is desorbed as CO2 and the downstream metabolites are unlabeled.
Some bacteria has another brach, the Entner-Doudroff pathway.
The split ratio of this pathway can be investigated by measring two fragment ions containig 1st to 3rd, and 2nd to 3rd carbons because <sup>13</sup>C position of lower glycolytic metabolites is defferent from that produced via glycolysis.
</li>
<img src="img/atom_mapping.png">
<img src="img/split_ratio_formula.png" style="display: block; margin: auto;">
</div>
<p>
A file is generated and it can be saved by double click.
<div class ="note">
<h4>Note:</h4>
<li>
If the calculated values are negative, a warning message will appear. This is due to errors in <sup>13</sup>C-labeling measurements.
</li>
</div>
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<p>Return to <a href="./index.html#Gadgets">How to use</a></p>
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