Category:LBS/Search: Difference between revisions

Latest revision as of 04:25, 25 January 2023

Search from Structure

Search from Sphingolipid Major Series
Search from Specific Sugars

Search from the non-reducing end pattern (click "Show" to expand the table)

Name	Structure
	GalNAc_α1-3(Fuc_α1-2)Gal_β1-3GlcNAc_β1-3-R
	Gal_α1-3(Fuc_α1-2)Gal_β1-3GlcNAc_β1-3-R
	Fuc_α1-2Gal_β1-3GlcNAc_β1-3-R
	Gal_β1-3(Fuc_α1-4)GlcNAc_β1-3-R
	Fuc_α1-2Gal_β1-3(Fuc_α1-4)GlcNAc_β1-3-R
	NeuAc_α2-3Gal_β1-3(Fuc_α1-4)GlcNAc_β1-3-R
	Gal_β1-4(Fuc_α1-3)GlcNAc_β1-3-R
	Fuc_α1-2Gal_β1-4(Fuc_α1-3)GlcNAc_β1-3-R
	NeuAc_α2-3Gal_β1-4(Fuc_α1-3)GlcNAc_β1-3-R
	GalNAc_α1-3GalNAc_β1-3Gal_α1-4Gal_β1-4Glc_β1-R
	GalNAc_β1-3Gal_α1-4Gal_β1-4Glc_β1-R

Search from the sugar sequence (List allchains)

-

Advanced search
Non-reducing end

loading...

Search From Mass

Glycosphingolipid Mass Calculator for MS Analysis

Exact Mass	Nominal Mass	Formula

Carbohydrates

Hexose

HexNAc

NeuAc

NeuGc

Fucose

HexA

Fatty Acids

Carbon No.

Unsaturation

Hydroxy group

Polarity

Long Chain Bases

Carbon No.

Unsaturation

Hydroxy group

Adduct Ions

Na

K

Ammonium

Modification

Sulfate

Phosphate

Methyl

Acetyl

Lactone

Examples

Ganglioside GM1 of FA 18:0, LCB d20:1 (LBSG2005105)

Carbohydrates [3 Hexose, 1 HexNAc, 1 NeuAc]
Fatty acid [18 carbons, 0 unsaturation, 0 hydroxy group]
Long chain base [20 carbons, 1 unsaturation, 2 hydroxy groups]

Sulfatide of FA 24:1, LCB d18:1 (LBSG1001005)

Carbohydrates [1 Hexose, 0 HexNAc, 0 NeuAc]
Fatty acid [24 carbons, 1 unsaturation, 0 hydroxy group]
Long chain base [18 carbons, 1 unsaturation, 2 hydroxy groups]
Modification [Sulfate: 1]

Lactotetraosylceramide of FA 16:0, LCB t18:0 (LBSG3B04001)

Carbohydrates [3 Hexose, 1 HexNAc, 0 NeuAc]
Fatty acid [16 carbons, 0 unsaturation, 1 hydroxy group]
Long chain base [18 carbons, 0 unsaturation, 3 hydroxy groups]

This category currently contains no pages or media.

Category:LBS/Search: Difference between revisions

Latest revision as of 04:25, 25 January 2023

Search from Structure

Search From Mass

Navigation

Tools

@@ Line 1: / Line 1: @@
-==Search Page==
+=={{Bilingual|構造から探す|Search from Structure}}==
+<ul>
+<li> [[:Category:LBS#SphingolipidClass|Search from Sphingolipid Major Series]]
-{{#formtag:form|action="/wiki/Category:LBS/Search" method="post"|
+<li> [[:Category:LBS#SphingolipidSugar|Search from Specific Sugars]]
-{{#formtag:fieldset||
-{{#formtag:legend||Carbohydrate Structure}}
+<li> Search from the non-reducing end pattern (click "Show" to expand the table)
+<table class="wikitable collapsible collapsed" style="text-align:right; background-color:white; margin-left: 1.5em">
+ <tr><th>Name</th><th width="300px">Structure</th></tr>
+ <tr><td>{{#volatile:ListMol/LBS|Blood group A|Structure=GalNAca1-3\(Fuca1-2\)Galb1-3GlcNAcb1-3}}</td><td>{{#invoke:LBS|FormatSugar|GalNAca1-3(Fuca1-2)Galb1-3GlcNAcb1-3-R}}</td></tr>
+ <tr><td>{{#volatile:ListMol/LBS|Blood group B|Structure=Gala1-3\(Fuca1-2\)Galb1-3GlcNAcb1-3}}</td>   <td>{{#invoke:LBS|FormatSugar|Gala1-3(Fuca1-2)Galb1-3GlcNAcb1-3-R}}</td></tr>
+ <tr><td>{{#volatile:ListMol/LBS|Blood group H|Structure=Fuca1-2Galb1-3GlcNAcb1-3}}</td>              <td>{{#invoke:LBS|FormatSugar|Fuca1-2Galb1-3GlcNAcb1-3-R}}</td></tr>
+ <tr><td>{{#volatile:ListMol/LBS|Lewis <sup>a</sup>|Structure=Galb1-3\(Fuca1-4\)GlcNAcb1-3}}</td>                <td>{{#invoke:LBS|FormatSugar|Galb1-3(Fuca1-4)GlcNAcb1-3-R}}</td></tr>
+ <tr><td>{{#volatile:ListMol/LBS|Lewis <sup>b</sup>|Structure=Fuca1-2Galb1-3\(Fuca1-4\)GlcNAcb1-3}}</td>         <td>{{#invoke:LBS|FormatSugar|Fuca1-2Galb1-3(Fuca1-4)GlcNAcb1-3-R}}</td></tr>
+ <tr><td>{{#volatile:ListMol/LBS|sialyl-Lewis<sup>a</sup>|Structure=NeuAca2-3Galb1-3\(Fuca1-4\)GlcNAcb1-3}}</td> <td>{{#invoke:LBS|FormatSugar|NeuAca2-3Galb1-3(Fuca1-4)GlcNAcb1-3-R}}</td></tr>
+ <tr><td>{{#volatile:ListMol/LBS|Lewis <sup>x</sup>, SSEA-1|Structure=Galb1-4\(Fuca1-3\)GlcNAcb1-3}}</td>        <td>{{#invoke:LBS|FormatSugar|Galb1-4(Fuca1-3)GlcNAcb1-3-R}}</td></tr>
+ <tr><td>{{#volatile:ListMol/LBS|Lewis <sup>y</sup>|Structure=Fuca1-2Galb1-4\(Fuca1-3\)GlcNAcb1-3}}</td>         <td>{{#invoke:LBS|FormatSugar|Fuca1-2Galb1-4(Fuca1-3)GlcNAcb1-3-R}}</td></tr>
+ <tr><td>{{#volatile:ListMol/LBS|sialyl-Lewis <sup>x</sup>|Structure=NeuAca2-3Galb1-4\(Fuca1-3\)GlcNAcb1-3}}</td><td>{{#invoke:LBS|FormatSugar|NeuAca2-3Galb1-4(Fuca1-3)GlcNAcb1-3-R}}</td></tr>
+ <tr><td>{{#volatile:ListMol/LBS|Forssman antigen|Structure=GalNAca1-3GalNAcb1-3Gala1-4Galb1-4Glcb1}}</td>       <td>{{#invoke:LBS|FormatSugar|GalNAca1-3GalNAcb1-3Gala1-4Galb1-4Glcb1-R}}</td></tr>
+ <tr><td>{{#volatile:ListMol/LBS|P antigen|Structure=GalNAcb1-3Gala1-4Galb1-4Glcb1}}</td>                        <td>{{#invoke:LBS|FormatSugar|GalNAcb1-3Gala1-4Galb1-4Glcb1-R}}</td></tr>
+</table>
+<li> Search from the sugar sequence [[Persist:ListAllChains|(List allchains)]] {{#formtag:fieldset||
 <table>
   <tr>
-   <td></td>
+   <td>{{#formtag:select|name="nre" id="nre" |<option value="^">NR end</option><option value=".*" selected="yes">any</option>}}</td>
-   <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none"></label>{{#formtag:input|type="radio" name="reducing" value="reducing" id="reducing"}}<label for="reducing"></label></td>
+   <td>{{#formtag:select|name="4th" id="4th"|<option value="((Glc)|(Gal)|(Man)|(Ino))[abfp0-9]*-.">Hexose</option><option value="((GlcNAc)|(GalNAc))[abfp0-9]*-.">HexNAc</option><option value="((GlcA)|(GalA))[abfp0-9]*-.">HexA</option><option value="[^-]*Fuc[^-]*-.">Fucose</option><option value="[^-]*NeuAc[^-]*-.">NeuAc</option><option value="[^-]*NeuGc[^-]*-.">NeuGc</option><option value="[^-]*-.">Others</option><option value="" selected="yes">none</option>}}</td>
+  <td>-</td>
+  <td>{{#formtag:select|name="3th" id="3th"|<option value="((Glc)|(Gal)|(Man)|(Ino))[abfp0-9]*-.">Hexose</option><option value="((GlcNAc)|(GalNAc))[abfp0-9]*-.">HexNAc</option><option value="((GlcA)|(GalA))[abfp0-9]*-.">HexA</option><option value="[^-]*Fuc[^-]*-.">Fucose</option><option value="[^-]*NeuAc[^-]*-." selected="yes">NeuAc</option><option value="[^-]*NeuGc[^-]*-.">NeuGc</option><option value="[^-]*-.">Others</option><option value="">none</option>}}</td>
+  <td>-</td>
+  <td>{{#formtag:select|name="2nd" id="2nd"|<option value="((Glc)|(Gal)|(Man)|(Ino))[abfp0-9]*-." selected="yes">Hexose</option><option value="((GlcNAc)|(GalNAc))[abfp0-9]*-.">HexNAc</option><option value="((GlcA)|(GalA))[abfp0-9]*-.">HexA</option><option value="[^-]*Fuc[^-]*-.">Fucose</option><option value="[^-]*NeuAc[^-]*-.">NeuAc</option><option value="[^-]*NeuGc[^-]*-.">NeuGc</option><option value="[^-]*-.">Others</option><option value="">none</option>}}</td>
+<td>-</td>
+  <td>{{#formtag:select|name="1st" id="1st"|<option value="((Glc)|(Gal)|(Man)|(Ino))[abfp0-9]*-" selected="yes">Hexose</option><option value="((GlcNAc)|(GalNAc))[abfp0-9]*-">HexNAc</option><option value="((GlcA)|(GalA))[abfp0-9]*-">HexA</option><option value="[^-]*Fuc[^-]*-">Fucose</option><option value="[^-]*NeuAc[^-]*-">NeuAc</option><option value="[^-]*NeuGc[^-]*-">NeuGc</option><option value="[^-]*-">Others</option><option value="">none</option>}}</td>
+  <td>-</td>
+  <td>{{#formtag:select|name="re" id="re" |<option value="((Cer)|(Sph))">Cer/Sph</option><option value=".+">any</option>}}</td>
+  <td>&nbsp;</td>
+  <td>{{#formtag:input|name="cals" type="button" value="SEARCH" disabled="true" id="sequence_search_button"}}</td>
   </tr>
 </table>
 }}
+<div id="PolySeqResult" style="height: 400px; overflow: scroll; resize: vertical; display: none"></div>
+{{#formtag:fieldset||
+{{#formtag:legend||Advanced search}}
+{{#formtag:input|type="text" size="60" name="1" id="advanced_polysaccharide_sequence"}}
+{{#formtag:input|type="button" disabled="true" id="advanced_search_button" value="SEARCH"}}<br />
+{{#formtag:input|type="checkbox" id="advanced_search_nre"}}{{#formtag:label|for="advanced_search_nre"|Non-reducing end}}
+}}
+<div id="loading">[[File:loading.gif]] loading...</div>
+<div id="AdvResult" style="height: 400px; overflow: scroll; display: none"></div>
+</ul>
+<!---
+==All Polysaccharide Sequences==
+{{#persist:ListMainchain|List mainchains|ListMainchain|0|dummy|;}}
+--->
+=={{Bilingual|質量から探す|Search From Mass}}==
+<!---
+{{#formtag:input|name="cals" type="button" value="SEARCH" disabled="yes" onclick="calculateF2M()"}}
+{| class="wikitable" style="float:right;"
+|
 {{#formtag:fieldset|id="formula"|
 {{#formtag:legend||Mass calculator}}
   <table>
    <tr>
-    <td>Formula</td>
+    <td style="border: none">Formula<br/>&nbsp;</td>
-    <td>{{#formtag:input|name="calc_formula" id="calc_formula" type="text" placeholder="C6H12O6"}} {{#formtag:input|name="cals" type="button" value="calc" onclick="calculateF2M()"}}</td>
+    <td style="border: none">{{#formtag:input|name="calc_formula" id="calc_formula" type="text" size="15" value="C6H12O6"}}{{#formtag:input|name="cals" type="button" value="calc" id="calculateF2M"}} <br/>&nbsp;&nbsp; &rarr;
-   <td>&rarr;</td>
+    {{#formtag:input|name="calc_mass" id="calc_mass" type="text" size="15" }}</td>
-    <td>{{#formtag:input|name="calc_mass" id="calc_mass" type="text"}}</td>
    </tr>
   </table>
 }}
+|}
+{{#formtag:fieldset||
+{{#formtag:legend||Precursor Mass (polysaccharide part only)}}
+{{#formtag:input|name="prec_mass" id="prec_mass" type="text" size="10" value="500"}}
+{{#formtag:legend|| &rarr; Product Masses (comma separated)}}
+&nbsp;&nbsp;{{#formtag:input|name="prod_mass" id="prod_mass" type="text" size="10" value="42,72,179"}} (tolerance {{#formtag:input|name="tol_mass" id="tol_mass" type="text" size="3" value="0.1"}})
+}}
+<table>
+ <tr>
+<td>{{#formtag:input|type="checkbox" name="none" value="none" id="none"}}<label for="none">200-400</label></td>
+<td>{{#formtag:input|type="checkbox" name="none" value="none" id="none"}}<label for="none">400-600</label></td>
+<td>{{#formtag:input|type="checkbox" name="none" value="none" id="none"}}<label for="none">600-800</label></td>
+<td>{{#formtag:input|type="checkbox" name="none" value="none" id="none"}}<label for="none">800-1000</label></td>
+<td>{{#formtag:input|type="checkbox" name="none" value="none" id="none"}}<label for="none">1000-1200</label></td>
+<td>{{#formtag:input|type="checkbox" name="none" value="none" id="none"}}<label for="none">1200-1400</label></td>
+</table>
+GM1, 中性、硫酸基のGalCerなど例をいれておく
+--->
+{|
+|
+<!-- Glycosphingolipid Mass Calculator -->
+<table class="wikitable" border=1 cellspacing=0 cellpadding=5 style="font-size: small; background-color: white; border-collapse: collapse">
+ <tr><th colspan="6" style="text-align: center; font-weight: 600">Glycosphingolipid Mass Calculator for MS Analysis</th></tr>
+ <tr>
+  <td colspan="5">
+   <table style="text-align: center">
+    <tr><td style="border: none"><span style="display: none">{{#formtag:select|name="cs_average" id="cs_average"|{{#formtag:option|value="false"|Exact}}{{#formtag:option|value="true"|Average}} }}</span> Exact Mass</td><td style="border: none">Nominal Mass</td><td style="border: none">Formula</td></tr>
+    <tr><td style="border: none">{{#formtag:input|type="text" id="cs_mass" style="width: 12em"}}</td><td style="border: none">{{#formtag:input|type="text" id="cs_nominalmass" style="width: 8em"}}</td><td style="border: none">{{#formtag:input|type="text" id="cs_formula" style="width: 12em"}}</td></tr>
+   </table>
+  </td>
+  <td style="background-color: #ffccff">{{#formtag:input|type="button" value="calculate" style="font-weight: 600; height: 3em" id="calculate_glycosphingolipid_button"}}</td>
+ </tr>
+ <tr style="background-color: #ffcccc">
+  <td rowspan="2" style="background-color: #ffaaaa; font-weight: 600">Carbohydrates</td>
+  <td>Hexose<br />{{#formtag:input|type="number" min="0" value="0" id="cs_hexose" style="width: 3em"}}</td>
+  <td>HexNAc<br />{{#formtag:input|type="number" min="0" value="0" id="cs_hexnac" style="width: 3em"}}</td>
+  <td>NeuAc<br />{{#formtag:input|type="number" min="0" value="0" id="cs_neuac" style="width: 3em"}}</td>
+  <td>NeuGc<br />{{#formtag:input|type="number" min="0" value="0" id="cs_neugc" style="width: 3em"}}</td>
+  <td rowspan="7" style="background-color: white; border-right: 1px solid white; border-bottom: 1px solid white"></td>
+ </tr>
+ <tr style="background-color: #ffcccc">
+  <td>Fucose<br />{{#formtag:input|type="number" min="0" value="0" id="cs_fucose" style="width: 3em"}}</td>
+  <td>HexA<br />{{#formtag:input|type="number" min="0" value="0" id="cs_hexua"  style="width: 3em"}}</td>
+  <td></td>
+  <td></td>
+ </tr>
+ <tr style="background-color: #ccffcc">
+  <td style="background-color: #aaffaa; font-weight: 600">Fatty Acids</td>
+  <td>Carbon No.<br />{{#formtag:input|type="number" min="0" value="0" id="cs_fa_carbonno" style="width: 3em"}}</td>
+  <td>Unsaturation<br />{{#formtag:input|type="number" min="0" value="0" id="cs_fa_unsaturation" style="width: 3em"}}</td>
+  <td>Hydroxy group<br />{{#formtag:input|type="number" min="0" value="0" id="cs_fa_hydroxygroup" style="width: 3em"}}</td>
+  <td rowspan="3" style="background-color: #ccffff">Polarity<br />{{#formtag:select|name="cs_polarity" id="cs_polarity"|{{#formtag:option|value="NON"|NON}}{{#formtag:option|value="NEG"|NEG}}{{#formtag:option|value="POS"|POS}} }}<br /><div id="div_charge" style="display: none">Charge<br />{{#formtag:input|type="number" min="1" value="1" id="cs_charge" style="width: 3em"}}</div>
+  </td>
+ </tr>
+ <tr style="background-color: #ccccff">
+  <td style="background-color: #aaaaff; font-weight: 600">Long Chain Bases</td>
+  <td>Carbon No.<br />{{#formtag:input|type="number" min="5" value="5" id="cs_lcb_carbonno" style="width: 3em"}}</td>
+  <td>Unsaturation<br />{{#formtag:input|type="number" min="0" value="0" id="cs_lcb_unsaturation" style="width: 3em"}}</td>
+  <td>Hydroxy group<br />{{#formtag:input|type="number" min="2" value="2" id="cs_lcb_hydroxygroup" style="width: 3em"}}</td>
+ </tr>
+ <tr style="background-color: #ccccaa">
+  <td style="background-color: #aaaa88; font-weight: 600">Adduct Ions</td>
+  <td>Na<br />{{#formtag:input|type="number" min="0" value="0" id="cs_na" style="width: 3em"}}</td>
+  <td>K<br />{{#formtag:input|type="number" min="0" value="0" id="cs_k" style="width: 3em"}}</td>
+  <td>Ammonium<br />{{#formtag:input|type="number" min="0" value="0" id="cs_nh4" style="width: 3em"}}</td>
+ </tr>
+ <tr style="background-color: #cccccc">
+  <td rowspan="2" style="background-color: #aaaaaa; font-weight: 600">Modification</td>
+  <td>Sulfate<br />{{#formtag:input|type="number" min="0" value="0" id="cs_sulfate" style="width: 3em"}}</td>
+  <td>Phosphate<br />{{#formtag:input|type="number" min="0" value="0" id="cs_phosphate" style="width: 3em"}}</td>
+  <td>Methyl<br />{{#formtag:input|type="number" min="-99" value="0" id="cs_methyl" style="width: 3em"}}</td>
+  <td>Acetyl<br />{{#formtag:input|type="number" min="-99" value="0" id="cs_acetyl" style="width: 3em"}}</td>
+ </tr>
+ <tr style="background-color: #cccccc">
+  <td>Lactone<br />{{#formtag:input|type="number" min="0" value="0" id="cs_lactone" style="width: 3em"}}</td>
+  <td></td>
+  <td></td>
+  <td>{{#formtag:input|type="hidden" min="0" value="0" id="cs_nmethylamide" style="width: 3em"}}</td>
+ </tr>
+</table>
+|valign=top|
+<big>Examples</big>
+<table>
+<tr><td>'''Ganglioside GM1 of FA 18:0, LCB d20:1''' ([[LBSG2005105]]) {{#formtag:input|type="button" value="Display" id="ex_ganglioside"}}
+<ul><li>Carbohydrates [3 Hexose, 1 HexNAc, 1 NeuAc]
+<li>Fatty acid [18 carbons, 0 unsaturation, 0 hydroxy group]
+<li>Long chain base [20 carbons, 1 unsaturation, 2 hydroxy groups]
+</ul>
+</td></tr>
+<tr><td>'''Sulfatide of FA 24:1, LCB d18:1''' ([[LBSG1001005]]) {{#formtag:input|type="button" value="Display" id="ex_sulfatide"}}
+<ul><li>Carbohydrates [1 Hexose, 0 HexNAc, 0 NeuAc]
+<li>Fatty acid [24 carbons, 1 unsaturation, 0 hydroxy group]
+<li>Long chain base [18 carbons, 1 unsaturation, 2 hydroxy groups]
+<li>Modification [Sulfate: 1]
+</ul>
+</td></tr>
+<tr><td>'''Lactotetraosylceramide of FA 16:0, LCB t18:0''' ([[LBSG3B04001]]) {{#formtag:input|type="button" value="Display" id="ex_lactotetraosylceramide"}}
+<ul><li>Carbohydrates [3 Hexose, 1 HexNAc, 0 NeuAc]
+<li>Fatty acid [16 carbons, 0 unsaturation, 1 hydroxy group]
+<li>Long chain base [18 carbons, 0 unsaturation, 3 hydroxy groups]
+</ul>
+</td></tr>
+</table>
+|}
+<!---
 {{#formtag:fieldset||
 {{#formtag:legend||Display setting}}
@@ Line 35: / Line 207: @@
 </table>
 }}
+--->
-}}