Description of Molecular Isotopic Distribution Calculator Program

This progrm has been produced by Scientific Instrument Services for use by the scientific community. Copyright 1996-2002 by Scientific Instrument Services. All rights reserved. This program or any of its parts may not be reproduced on another site without the concent of Scientific Instrument Services.

The Formula can input using the standard one or two letter chemical symbols, number of atoms and parenthesizes where applicable. The same atom can be listed more than once and where no quantity is listed it is assumed to be 1. The following examples are all valid:

• C6H6
• C6H5Cl
• CHCl3
• (CH3)2CH2CH2(CH3)2
• CH3C6H12CH3
• COOHCHCH3NH2

The user can input the following information into the program screen:

• Molecular formula of the compound of interest according to the above parameters
• The title and subtitle that will appear on the graphical output
• The mass scale desired in the graphic output. Both low and high mass ranges can be selected. default is 0 and 600.
• The user also has the option of analyzing the data in low (unit mass resolution) or high mass resolution.
• Low mass resolution outputs results in unit mass resolution
• High resolution reports data in x.xxxx digit resolution, which prints out M+1 isotopes separately

The program calculates the exact molecular formula and molecular weights and the isotopic distributions of the molecules. It displays the data in tabular format. It then produces a screen with the numeric data and a graphical presentation of the calculated masses and their relative occurances. The program is based on the binomial theorem for the calculation of the isotopicdistributions of the mass distributions. The accuracy of the relative intensities is extimated to be within 1% of the actual value.

The calculations are performed on out Unix based server. This receives your data, performs the calculations and then returns the data back to your browser as described above. The time for the analysis and calculation of your formula is dependent on the size of your molecule and the number of atoms that are to be calculated. Since the binomial theorem is used the calculations can become quite long with large molecules. Time for analysis can very from 10 seconds to a minute or more for large molecules.

Program Operation

This program consists of 3 separate programs which run together to calculate the molecular weights and isotopic distributions of the molecular formula input by the user.

mass10.pl - Main Control Program - by John J. Manura, Scientific Instrument Services

This program is written in Perl Scripts and provides the following functions:

• Provides the HTML code to produce the main screen and graphs
• Provides the form from which the user inputs:
• The Sample Name and Title to appear in the graphical output
• The Subtitle to appear in the graphical output
• The molecular formula to be analyzed
• The mass range (both upper and lower) to be displayed in the graphical output
• The selection of High or Low mass resolution for the data analysis
• Receies and parses the data input by the user
• Calculates the scalar values to produce the graphic output
• Scales the data to produce the desired X scale of the mass spectrum
• Submits the data to the Java program to calculate the isotopic abundances
• Submits the data to the FLY program to produce the PNG graphic output file
• Prints the final display of all the data for viewing, update or reevaluation

IA.java - Isotopic Abundance Calculator Program - by David J. Manura.

This is a Java application program to calculate the isotopic abundances of the molecule. It is based on the binomial theorem by for the calculation of the isotopicdistributions in the molecule submitted.

This program provides the following functions:

• Receives the raw data from the mass10.pl program
• Checks the formula for validity and errors (number of parenthesis, elements and incorrect input)
• Removes the parenthesis
• Calculates the molecular formula
• Selects if data is to be determined in high or low resolution
• Reads in Element masses, isotopes and relative intensity values to be used in the calculations
• Uses the binomial theorem to calculate the isotopic distribution of all ions and masses
• Determines the most abundant ion
• Normalizes the data to the most abuntant ion
• Rounds off mass intensities to the nearest 0.1 percent intensity
• Sorts data in relative intensity order
• Outputs data back to the mass10.pl program

FLY - PNG Creation Program by Martin Gleeson, http://www.unimelb.edu.au/fly/fly.html

This is a C program that takes the raw data supplied by the mass10.pl program and creates the PNG image of the mass spectrum.

General Information

This program is still under development. It will be constantly improved over the next few weeks to add more features and versatility. If you have any suggestions, we would like to hear from you. Plans are to develop this program further to perform molecular weight calculations of proteins in which you can key in the three letter codes for the amino acids to calculate the molecular weights and isotopes of the proteins. We are open to other suggestions.

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