chemdata:glycocalc

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chemdata:glycocalc [2014/03/07 15:14]
lorna
chemdata:glycocalc [2015/10/08 11:40] (current)
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 +===== The NIST Glyco Mass Calculator =====
  
  
-**__The NIST Glyco Mass Calculator __ ** +[[:​chemdata:​team:​lorna|M. Lorna A. De Leoz]] and [[:​chemdata:​team:​sstein|Stephen E. Stein]], ​Mass Spectrometry Data Center
  
  
-**AUTHORS:​** [[:​chemdata:​team:​lorna|Maria Lorna ADe Leoz]] ​and [[:​chemdata:​team:​sstein|Stephen EStein]]Mass Spectrometry Data Center+The Glyco MS Calculator is a tool to help calculate the masses and elemental compositions of glycoforms (e.g. glycans, glycopeptides) ​and their common ionsThe user inputs the number of residues in the glycan and the program calculates for the masses and elemental composition of the glycan. It also calculates for the derivatized massese.g. permethylated or 2-AB labeled, of the glycan. Then, it generates the monoisotopic masses of molecular ion adducts often observed in ESI mass spectra.
  
  
-**File Format  ** MS Excel 2010macro-enabled+[[http://​www.nist.gov/​customcf/​glyco-mass-calc/​|Launch]] the  online calculator or {{:​chemdata:​glycomscalculator.zip|download}} ​ the Excel 2010 file (macro-enabled).
  
  
-**DESCRIPTION:​**  +For suggestions,​ inquiries, and comments, please contact ​DrLorna De Leoz at lorna.deleoz@nist.gov or (301) 975-6731.
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-The Glyco MS Calculator is a tool to aid in the analysis of glycoforms, e.g. glycans and glycopeptides. ​ The user inputs the number of residues in the glycan and the program calculates for the masses and elemental composition of the glycan. ​ It also calculates for the derivatized masses, e.g. permethylated or 2-AB labeled, of the glycan. ​ Then, it generates the monoisotopic masses of molecular ion adducts often observed in ESI mass spectra. Download [[:​chemdata:​glycocalc|here.]] (122.79 KiB, 4w ago, 1 download) +
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-**HOW TO USE:**  +
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-    - Enter the number of residues in the blue boxes in Table 1 (B9-12). ​ Press Clear All in B13 if you need to reset the values. +
-    - Tables 1 and 2 will be automatically populated based on the number of residues inputted. ​ To populate Table 3, click on the desired derivatization or reducing end type in Table 2.  Choose one from I18-I27. +
-    - The common monoisotopic masses will be shown in G33-G84 in Table 3. +
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-**EXAMPLE:​**  +
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-Find the exact masses of the ions of glycan **G2FB **      in **native/​underivatized** ​     form. +
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-{{:​chemdata:​glycan.png?​90x165 ​ }}**1. ​ Enter the number of residues:**  +
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-Sialic Acid (B9) = 0     \\ Hexose (B10) = 5     \\ N-acetylhexosamine (B11) = 5     \\ Fucose (B12) = 1 +
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-**2.  Tables 1 and 2 will be automatically filled up.**  +
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-Examples: ​    \\ Underivatized Elemental Composition (Table 1, E13-H13) = C76H125N5O54 ​    \\ Underivatized Glycan Monoisotopic Mass (Table 2, C18) = 1989.7295 ​    \\ Permethylated Glycan Monoisotopic Mass  (Table 2, C20) = 2466.2616 +
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-**3.  Press the "​Native"​ button in (Table 2, I18) and Table 3 will be automatically populated with the ions for native/​underivatized G2FB.  In Table 3, the mass of the parent ion (G30) = 1989.7295 and the rest of the table will be populated with native mass values. ​ **  +
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-Examples: ​    \\ [M + 3H]<​sup>​3+ </​sup>​ (G34) = //​m/​z// ​     1717.2939 ​    \\ [M + 2Na]<​sup>​2+ </​sup>​ (G43) = //​m/​z// ​     2597.4192 +
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-**OTHER INFORMATION:​**  +
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-    - Color key:  blue boxes accept user inputs, pink boxes are monoisotopic masses of the glycan, green boxes are the monoisotopic masses of the ions. +
-    - Exact masses for the elements, monosaccharide residues, and compounds are listed in the Constants tab.  Sources: NIST Physical Reference Data, Atomic Weights and Isotopic Compositions with Relative Atomic Masses, [[http://​www.nist.gov/​pml/​data/​comp.cfm|http://​www.nist.gov/​pml/​data/​comp.cfm]],​ accessed 12/9/2013; Carbocalc by IonSource, [[http://​www.ionsource.com/​Card/​carbo/​carbocalc.xls|www.ionsource.com/​Card/​carbo/​carbocalc.xls]]‎,​ accessed 12/​9/​2013. +
-    - For glycopeptides,​ the peptide mass is inputted in B25.  Other derivatizations can be inputted either as exact mass (B26) or elemental composition (E27-H27). +
-    - For suggestions,​ inquiries, and comments, please contact ​[[marialorna.deleoz@nist.gov|marialorna.deleoz@nist.gov]] or [[stephen.stein@nist.gov|stephen.stein@nist.gov]]. +
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-**SOURCES:​**  +
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-    ​**Mass Spectrometry Adduct Calculator **      by Tobias Kind from the Fiehn Lab of University of California-Davis,​ [[http://​fiehnlab.ucdavis.edu/​staff/​kind/​Metabolomics/​MS-Adduct-Calculator/​|http://​fiehnlab.ucdavis.edu/​staff/​kind/​Metabolomics/​MS-Adduct-Calculator/​]],​ accessed 12/​9/​2013. +
-    - **GlycanMass** ​     by the Swiss Institute of Bioinformatics,​ [[http://​web.expasy.org/​glycanmass/​|http://​web.expasy.org/​glycanmass/​]],​ accessed 12/​9/​2013. +
-    - **Carbocalc** ​     by IonSource, [[http://​www.ionsource.com/​Card/​carbo/​carbocalc.xls|www.ionsource.com/​Card/​carbo/​carbocalc.xls]]‎,​ accessed 12/9/2013. +
  
chemdata/glycocalc.txt · Last modified: 2015/10/08 11:40 (external edit)