Molecular Weight of Biomass

[abhishek@NCL,Pune]

What is the molecular weight of Biomass in E.coli Core model and how
it is calculated from the Biomass Equation in the model? please
explain !!
Thanks in Advance

[김승희]

is it necessary to put the molecular weight of Biomass in Cobra?

Can Cobra calculate the molecular weight?

2012/1/7 abhishek@NCL,Pune <abhishekgu...@gmail.com>

[Erlon Mendes]

Molecular Weight of Biomass is expressed in carbo-mol. Is a common approach
in Stoichiometry of Microbial Systems.

Erlon

-----Mensagem original-----
De: cobra-...@googlegroups.com [mailto:cobra-...@googlegroups.com]
Em nome de abhishek@NCL,Pune
Enviada em: sábado, 7 de janeiro de 2012 10:00
Para: COBRA Toolbox
Assunto: Molecular Weight of Biomass

[Ronan Fleming]

function N=numAtomsOfElementInFormula(formula,element)
% returns the number of atoms of a single element in a formula
%
% INPUT
% formula formula in format Element then NumberOfAtoms with no spaces
% element Abbreviation of element e.g. C or Mg
%
% OUTPUT
% N number of atoms of this element in the formula provided
%
% Ronan Fleming 9 March 09
% Ronan Fleming 21 July 09 handles formulae with same first letter for
% element e.g.C & Co in 'C55H80CoN15O11'
% Ronan Fleming 18 Sept 09 handles composite formulae like
C62H90N13O14P.C10H11N5O3.Co
% Hulda SH 7 July 2011 Simplified and generalized code. Now handles most or
% all exceptional formulas.

--
--
Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
-----------------------------------------------------------------
Independent Group Leader,
Center for Systems Biology,
University of Iceland,
Sturlugata 8,
101 Reykjavik,
Iceland.
http://www.hi.is/~rfleming
http://systemsbiology.hi.is/
Ph:  +354 618 6245
-----------------------------------------------------------------

[Ronan Fleming]

Probably this function is more suitable:

function M=getMolecularMass(formulae,isotopeAbundance)
% get mono-isotopic exact molecular mass for a single formula or a cell array of
% formulae using the atomic weight for each element from NIST
% http://physics.nist.gov/PhysRefData/Compositions/
%
% An atomic weight of an element from a specified source is the ratio of
% the average mass per atom of the element to 1/12 of the mass of an
% atom of 12C.
%
% Note the term "relative atomic mass" is usually reserved for the mass of a
% specific nuclide (or isotope), while "atomic weight" is usually used for the
% weighted mean of the relative atomic mass over all the atoms in the
% sample (polyisotopic mass).
%
%
% If the ratio of the different isotopes are known exactly, this may be
% provided in the m x 2 cell array of m isotopes, i.e. isotopeAbundance.
%
% By default, this script gives the molecular mass assuming monoisotopic
% exact mass.
%
% INPUT
% formula single formula or a cell array of formulae
%
% OPTIONAL INPUT
% isotopeAbundance {(1),0}
% 1 = monoisotopic exact mass
% i.e. only uses naturally predominant isotope
% of each element.
% 0 = polyisotopic inexact mass
% i.e. uses all isotopes of each element weighted
% by natural abundance
%
% or
%
% m x 2 cell arrray with user defined isotope abundance
% isotopeAbundance{i,1}= 'Atomic_Symbol';
% isotopeAbundance{i,2}= Mass_Number;
% isotopeAbundance{i,3}= abundance;
% (where sum of abundances of all isotopes of an element
% must be one)
%
% e.g. Carbon, all as C13
% isotopeAbundance{i,1}= 'C'
% isotopeAbundance{i,2}= 12;
% isotopeAbundance{i,3}= 0;
% isotopeAbundance{i+1,1}= 'C'
% isotopeAbundance{i+1,2}= 13;
% isotopeAbundance{i+1,3}= 1;
% isotopeAbundance{i+2,1}= 'C'
% isotopeAbundance{i+2,2}= 14;
% isotopeAbundance{i+2,3}= 0;
%
% OUTPUT
% M molecular mass(es) in (gram/Mol)
%
% Exact mass check:
% If you want to double check that the mass given by this script is correct
% then compare it to either
% (1) OpenBabel: echo "InChIstring"|babel -iinchi - -oreport
% or
% (2) http://www.sisweb.com/referenc/tools/exactmass.htm
% Please report any errors as these are critical for use of this script
% with mass spec machines.
%
% Ronan Fleming 9 March 09 ronan.mt...@gmail.com
% 15 Sept 09 Support for non-natural isotope distributions