Category:LBS/Search: Difference between revisions

Revision as of 04:07, 27 August 2018

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
1=Structure=GalNAca1-3\(Fuca1-2\)Galb1-3GlcNAcb1-3\|Blood group A	GalNAc_α1-3(Fuc_α1-2)Gal_β1-3GlcNAc_β1-3-R
1=Structure=Gala1-3\(Fuca1-2\)Galb1-3GlcNAcb1-3\|Blood group B	Gal_α1-3(Fuc_α1-2)Gal_β1-3GlcNAc_β1-3-R
1=Structure=Fuca1-2Galb1-3GlcNAcb1-3\|Blood group H	Fuc_α1-2Gal_β1-3GlcNAc_β1-3-R
1=Structure=Galb1-3\(Fuca1-4\)GlcNAcb1-3\|Lewis ^a	Gal_β1-3(Fuc_α1-4)GlcNAc_β1-3-R
1=Structure=Fuca1-2Galb1-3\(Fuca1-4\)GlcNAcb1-3\|Lewis ^b	Fuc_α1-2Gal_β1-3(Fuc_α1-4)GlcNAc_β1-3-R
1=Structure=NeuAca2-3Galb1-3\(Fuca1-4\)GlcNAcb1-3\|sialyl-Lewis^a	NeuAc_α2-3Gal_β1-3(Fuc_α1-4)GlcNAc_β1-3-R
1=Structure=Galb1-4\(Fuca1-3\)GlcNAcb1-3\|Lewis ^x, SSEA-1	Gal_β1-4(Fuc_α1-3)GlcNAc_β1-3-R
1=Structure=Fuca1-2Galb1-4\(Fuca1-3\)GlcNAcb1-3\|Lewis ^y	Fuc_α1-2Gal_β1-4(Fuc_α1-3)GlcNAc_β1-3-R
1=Structure=NeuAca2-3Galb1-4\(Fuca1-3\)GlcNAcb1-3\|sialyl-Lewis ^x	NeuAc_α2-3Gal_β1-4(Fuc_α1-3)GlcNAc_β1-3-R
1=Structure=GalNAca1-3GalNAcb1-3Gala1-4Galb1-4Glcb1\|Forssman antigen	GalNAc_α1-3GalNAc_β1-3Gal_α1-4Gal_β1-4Glc_β1-R
1=Structure=GalNAcb1-3Gala1-4Galb1-4Glcb1\|P antigen	GalNAc_β1-3Gal_α1-4Gal_β1-4Glc_β1-R

Search from the sugar sequence

-

{{#persist:ListAllChains|List allchains|ListAllChains|0|dummy|;}}

Advanced search
Non-reducing end

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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

Revision as of 04:07, 27 August 2018

Search from Structure

Search From Mass

Navigation

Tools

@@ Line 1: / Line 1: @@
 {{#includejs:LBSSearch.js}}
-{{#includejs:CalculateMass.js|calculateF2M|calc_formula|calc_mass}}
+<!---{{#includejs:CalculateMass.js|calculateF2M|calc_formula|calc_mass}}--->
 {{#includejs:GlycosphingolipidMassCalculator.js}}
-{{#includejs:AdvancedLBSSearch.js}}
+=={{Bilingual|構造から探す|Search from Structure}}==
+<ul>
+<li> [[:Category:LBS#SphingolipidClass|Search from Sphingolipid Major Series]]
-<span style="color: red; font-size: x-large">under construction</span>
+<li> [[:Category:LBS#SphingolipidSugar|Search from Specific Sugars]]
-<!--DEFINITIONS-->
+<li> Search from the non-reducing end pattern (click "Show" to expand the table)
-{{#def:Hexose|Glc..-.~Galf?..-[1-9/]+~Man..-.}}
-{{#def:HexNAc|GlcNAc([1-6]Me)?..-.~GalNAc([1-6]Me)?..-.}}
-{{#def:HexA|GlcA([1-6]Me)?..-.|GalA([1-6]Me)?..-.}}
-{{#def:Fucose|([1-6]-Deoxy-)?Fuc([1-6]Me)?
-{{def:NeuAc|([4-9]-Deoxy-|8-Epi-|Taurine-|C[1-9]-)?NeuAc([1-9]Me|[1-9]Methoxy)?}}
-{{def:NeuGc|([4-9]-Deoxy-|8-Epi-|Taurine-|C[1-9]-)?NeuGc([1-9]Me|[1-9]Methoxy)?}}
-==Search from Structure==
-<!--
-{{#formtag:fieldset||
-{{#formtag:legend||Sphingolipid Major Series}}
-<table>
- <tr>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">Gala</label></td>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">Spirometo</label></td>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">Ganglio</label></td>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">Isoganglio</label></td>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">Lactoganglio</label></td>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">Ganglio a-series</label></td>
- </tr>
- <tr>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">SM/CPE/CAEP</label></td>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">Spirometo</label></td>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">GIPC GlcN</label></td>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">GIPC GlcA</label></td>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">GIPC Man</label></td>
-  <td>{{#formtag:input|type="radio" name="none" value="none" id="none"}}<label for="none">Others</label></td>
- </tr>
-</table>
-}}
--->
-<div style="margin-left: 1.5em">
-[[:Category:LBS#Sphingolipid_.E3.82.B9.E3.83.95.E3.82.A3.E3.83.B3.E3.82.B4.E8.84.82.E8.B3.AA|Search by Sphingolipid Major Series]]<br />
-[[:Category:LBS#Second_.28s2.29_Code_for_subsequent_sugars|Search by Specific Sugars]]<br />
-</div>
-{{#formtag:fieldset||
-{{#formtag:legend||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>Structure</th></tr>
+  <tr><th>Name</th><th width="300px">Structure</th></tr>
   <tr><td>[[Volatile:ListMol/LBS|1=Structure=GalNAca1-3\(Fuca1-2\)Galb1-3GlcNAcb1-3|Blood group A]]</td><td>{{LBS/FormatSugar|GalNAca1-3(Fuca1-2)Galb1-3GlcNAcb1-3-R}}</td></tr>
   <tr><td>[[Volatile:ListMol/LBS|1=Structure=Gala1-3\(Fuca1-2\)Galb1-3GlcNAcb1-3|Blood group B]]</td>   <td>{{LBS/FormatSugar|Gala1-3(Fuca1-2)Galb1-3GlcNAcb1-3-R}}</td></tr>
@@ Line 68: / Line 29: @@
 </table>
-{{#formtag:fieldset||
+<li> Search from the sugar sequence {{#formtag:fieldset||
-{{#formtag:legend||Search from the polysaccharide sequence}}
 <table>
   <tr>
-   <td>{{#formtag:select|name="nre" id="nre"|<option value="">(Non-reducing end)</option><option value=".*" selected="yes">(any)</option>}}</td>
+   <td>{{#formtag:select|name="nre" id="nre" |<option value="^">NR end</option><option value=".*" selected="yes">any</option>}}</td>
-   <td>{{#formtag:select|name="4th" id="4th"|<option value="Gala[1-9]?-.">Galα-</option><option value="Galb[1-9]?-.">Galβ-</option><option value="Glcb.-.">Glcβ-</option><option value="Manb[1-9]?-.">Manβ-.</option><option value="GalNAcb[1-9]?-.">GalNAcβ-</option><option value="GlcNAcb[1-9]?-.">GlcNAcβ-</option><option value="Glc[AN].[1-9]?-.">GlcN/GlcA-</option><option value="Neu[AG]c[1-9]?α2-.">NeuAc/NeuGc-</option><option value="Ins-P-">Ins-P-</option><option value="[^-]*-[1-9]?">Others</option><option value="" selected="yes">(none)</option>}}</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="3rd" id="3th"|<option value="Gala[1-9]?-.">Galα-</option><option value="Galb[1-9]?-.">Galβ-</option><option value="Glcb.-.">Glcβ-</option><option value="Manb[1-9]?-.">Manβ-.</option><option value="GalNAcb[1-9]?-." selected="yes">GalNAcβ-</option><option value="GlcNAcb[1-9]?-.">GlcNAcβ-</option><option value="Glc[AN].[1-9]?-.">GlcN/GlcA-</option><option value="Neu[AG]c[1-9]?α2-.">NeuAc/NeuGc-</option><option value="Ins-P-">Ins-P-</option><option value="[^-]*-[1-9]?">Others</option><option value="">(none)</option>}}</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="Gala[1-9]?-.">Galα-</option><option value="Galb[1-9]?-." selected="yes">Galβ-</option><option value="Glcb.-.">Glcβ-</option><option value="Manb[1-9]?-.">Manβ-.</option><option value="GalNAcb[1-9]?-.">GalNAcβ-</option><option value="GlcNAcb[1-9]?-.">GlcNAcβ-</option><option value="Glc[AN].[1-9]?-.">GlcN/GlcA-</option><option value="NeuAc[1-9]?α2-.">NeuAc-</option><option value="Ins-P-">Ins-P-</option><option value="[^-]*-[1-9]?">Others</option><option value="">(none)</option>}}</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="1st" id="1st"|<option value="Gala[1-9]?-">Galα-</option><option value="Galb[1-9]?-">Galβ-</option><option value="Glcb.-" selected="yes">Glcβ-</option><option value="NeuAc..-">NeuAc-</option><option value="Ins-P-">Ins-P-</option><option value="[^-]*-[1-9]?">Others</option><option value="">(none)</option>}}</td>
+   <td>{{#formtag:select|name="re" id="re" |<option value="((Cer)|(Sph))">Cer/Sph</option><option value=".+">any</option>}}</td>
-   <td>-</td>
+   <td>&nbsp;</td>
-   <td>{{#formtag:select|name="re"  id="re" |<option value="(Cer~Sph)">Cer/Sph</option><option value=".+">(any)</option>}}</td>
+   <td>{{#formtag:input|name="cals" type="button" value="SEARCH" disabled="true" id="sequence_search_button"}}</td>
+  <td>{{#persist:ListAllChains|List allchains|ListAllChains|0|dummy|;}}</td>
   </tr>
 </table>
-{{#formtag:input|name="cals" type="button" value="SEARCH" id="mainchain"}}
 }}
+<div id="PolySeqResult" style="height: 400px; overflow: scroll; resize: vertical; display: none"></div>
 {{#formtag:fieldset||
-{{#formtag:legend||Polysaccharide sequence (Advanced)}}
+{{#formtag:legend||Advanced search}}
 {{#formtag:input|type="text" size="60" name="1" id="advanced_polysaccharide_sequence"}}
-{{#formtag:input|type="button" id="advanced_search_button" value="SEARCH"}}<br />
+{{#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}}
 }}
-{{#persist:ListMainchain|List mainchain|ListMainchain|0|dummy|;}}
-{{#formtag:fieldset||
+<div id="loading">[[File:loading.gif]] loading...</div>
-{{#formtag:legend||Display setting}}
+<div id="AdvResult" style="height: 400px; overflow: scroll; display: none"></div>
-<table>
+</ul>
- <tr>
-  <td>limit/page</td>
+<!---
-  <td>{{#formtag:select|name="limit_page"|<option>10</option><option>50</option><option>100</option>}}</td>
+==All Polysaccharide Sequences==
-  <td>order</td>
+{{#persist:ListMainchain|List mainchains|ListMainchain|0|dummy|;}}
-  <td>{{#formtag:select|name="table_id"|<option>lipidbank id</option><option>compound name</option>}} {{#formtag:select|name="sort"|<option>ascending</option><option>descending</option>}}</td>
+--->
- </tr>
-</table>
-}}
-==Search From Mass==
+=={{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;"
@@ Line 117: / Line 80: @@
     <td style="border: none">Formula<br/>&nbsp;</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;
-    {{#formtag:input|name="calc_mass" id="calc_mass" type="text" size="4" }}</td>
+    {{#formtag:input|name="calc_mass" id="calc_mass" type="text" size="15" }}</td>
    </tr>
   </table>
 }}
 |}
 {{#formtag:fieldset||
@@ Line 130: / Line 94: @@
 }}
-<!---
 <table>
   <tr>
@@ Line 140: / Line 104: @@
 <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
 --->
-{{#formtag:input|name="cals" type="button" value="SEARCH" disabled="yes" onclick="calculateF2M()"}}
+{|
+|
 <!-- Glycosphingolipid Mass Calculator -->
-<table class="wikitable collapsible collapsed" border=1 cellspacing=0 cellpadding=5 style="font-size: small; ackground-color: white; border-collapse: collapse">
+<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</th></tr>
+  <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">{{#formtag:select|name="cs_average" id="cs_average"|{{#formtag:option|value="false"|Exact}}{{#formtag:option|value="true"|Average}} }} Mass</td><td style="border: none">Nominal Mass</td><td style="border: none">Formula</td></tr>
+     <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>
@@ Line 182: / Line 148: @@
    <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="0" value="0" id="cs_lcb_hydroxygroup" 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">
@@ Line 188: / Line 154: @@
    <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>Ca<br />{{#formtag:input|type="number" min="0" value="0" id="cs_ca" 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">
@@ Line 204: / Line 170: @@
   </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}}
+<table>
+ <tr>
+  <td>limit/page</td>
+  <td>{{#formtag:select|name="limit_page"|<option>10</option><option>50</option><option>100</option>}}</td>
+  <td>order</td>
+  <td>{{#formtag:select|name="table_id"|<option>lipidbank id</option><option>compound name</option>}} {{#formtag:select|name="sort"|<option>ascending</option><option>descending</option>}}</td>
+ </tr>
+</table>
+}}
+--->