-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathNatural_Isotope_Subtractor.html
159 lines (150 loc) · 7.21 KB
/
Natural_Isotope_Subtractor.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width,initial-scale=1.0,user-scalable=no">
<meta property='og:type' content='website'>
<meta property='og:title' content='Isotope Calculation Gadgets'>
<meta property='og:url' content='URLが入る'>
<meta property='og:description' content='Isotope Calculation Gadgets'>
<meta property="og:image" content="img/ogp.png">
<meta name="description" content="Isotope Calculation Gadgets" />
<title>Isotope Calculation Gadgets</title>
<link rel="preconnect" href="https://fonts.gstatic.com">
<link href="https://fonts.googleapis.com/css2?family=Montserrat:wght@400;700&display=swap" rel="stylesheet">
<link href="https://fonts.googleapis.com/css?family=Material+Icons+Outlined" rel="stylesheet">
<link href="css/ress.css" media="all" rel="stylesheet" type="text/css" />
<link href="css/style.css" media="all" rel="stylesheet" type="text/css" />
<link rel="shortcut icon" href="img/favicon.ico" />
<link rel=”canonical” href=”URLが入る” />
</head>
<body>
<div class="wrapper">
<!-- header -->
<header class="header ">
<div class="inner">
<h1 class="header-logo">
<a href=".">Isotope Calculation Gadgets</a>
</h1>
<nav class="header-nav">
<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>
<li class="header-nav-item"><a href="index.html#Gadgets">How to use</a></li>
<li class="header-nav-item"><a href="index.html#Contact">Contact</a></li>
</ul>
</nav>
</div>
</header>
<!-- /header -->
<main class="content">
<article class="article">
<div class="article-inner">
<h2 class="article-title">Natural Isotope Subtractor</h2>
<p class="article-img">
<img src="img/Natural_isotope_subtractor.png">
</p>
<div class="article-body">
<p>
The "Natural Isotope Subtractor" is a program that removes the effects of natural isotopes from raw mass spectrometry data. This allows the accurate interpretation of intracellular metabolic states from isotopic labeling data.
</p>
<h3 class="article-info-title">Preparation</h3>
<p>
Perform isotope tracing culture experiments.
<div class ="note">
<h4>Note:</h4>
<li>
It is recommended to use substrates labeled with one element (ex. C or N only) to facilitate interpretation of the labeling patterns.
</li>
</div>
</p>
<p>
Analyze isotope-labeled metabolites using mass spectrometry.
</p>
<p>
Perform peak integration for possible isotopomers of target metabolites.
<div class ="note">
<h4>Note:</h4>
<li>
It is necessary to measure the isotopomer peaks corresponding to the maximum number of labeled atoms in the skeleton plus the number of naturally occurring isotopes.
</li>
</div>
</p>
<h3 class="article-info-title">Procedures</h3>
<p>
Paste the peak area data to 1_2_Template.csv file generated by "Isotope Template Generator".
</p>
<img src="img/data_input.png">
<p>
Start Garuda and open the “Natural Isotope Subtractor”.
<div class ="note">
<h4>Note:</h4>
<li>
If you see "Another instance of the Core is already running", click the icon in the lower right corner.
</li>
<p class="article-img2">
<img src="img/garuda_core.png">
</p>
</div>
</p>
<p>
Select the “1_2_Template file.csv” where the measured data was entered and “Chemical formula .csv” used in “Isotope Template Generator”, then click “Launch” button.
</p>
<img src="img/nis_start_screen.png">
<p>
Please choose an appropriate analysis mode (ex. "SIM"). Two files will be generated and it can be saved by double click.
<div class ="note">
<h4>Note:</h4>
<li>
Subtracted labeling.csv is data where the effect of natural isotopes has been removed.
</li>
<li>
Raw labeling.csv is data where the effect of natural isotopes has NOT been removed.
</li>
</div>
<div class ="note">
<h4>Note:</h4>
<li>
If samples are analyzed in its natural state without adding isotope tracers, the ratio of raw mass isotopomer before the removal of natural isotopes should be consistent with the theoretical natural isotope ratio calculated by the "Isotope Template Generator". By comparing these ratios, the analytical method can be validated. This work should be done at least once before conducting isotope labeling experiments. If the difference between the theoretical and the natural ratio is less than 0.01, the labeling fraction of that fragment ion is reliable. If there are overlapping ions, the value may not agree with the theoretical value.
</li>
</div>
</p>
<p>
For further analysis, click "Discover" button and choose a next gadget.
<div class ="note">
<h4>Note:</h4>
<li>
The obtained data can transfer to "Average Labeling Calculator" and "Split_Ratio_Calculator" by clicking "Disocver" button. For data visualization, "Shimadzu MS Data Inport" can be used.
</li>
<p>
<img src="img/nis_output_screen.png">
</p>
</div>
</p>
</div>
<div class="home-link">
<p>Go to <a href="./Average_Labeling_Calculator.html">Average Labeling Calculator</a></p>
</div>
<div class="home-link">
<p>Go to <a href="./Split_Ratio_Calculator.html">Split Ratio Calculator</a></p>
</div>
<div class="home-link">
<p>Return to <a href="./index.html#Gadgets">How to use</a></p>
</div>
</div>
</article>
<div class="page-top" id="js-page-top">
<span class="material-icons-outlined">expand_less</span>
</div>
</main>
<!-- footer -->
<footer class="footer">
<div class="copyright">©Nobuyuki Okahashi</div>
</footer>
<!-- /footer -->
</div>
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script>
<script type='text/javascript' src="js/script.js"></script>
</body>
</html>