Program emass calculates accurate masses and intensities of isotopic
peaks.

Rockwood, A.L. and Haimi, P.: "Efficient calculation of Accurate 
Masses of Isotopic Peaks",
Journal of The American Society for Mass Spectrometry
JASMS 03-2263, in press


Build instructions:
-------------------

In Linux/Unix systems with gcc and gnu make, type "make".
In Microsoft Windows systems with Visual Studio 7.0 or greater, open
the project file emass.vcproj from Visual Studio and select build
solution from build -menu.


Using:
------

Program emass reads the isotope distributions of elements from a file
called "ISOTOPE.DAT", which must reside in the directory where the
program is started.

The program takes the molecular formula and optionally the charge of
the molecule from standard input (typically the keyboard). The charge 
must be separated from the formula by a comma. The program prints the 
masses and intensities of the isotopic peaks to the standard output 
(typically the screen). The molecular formula may contain parentheses 
and spaces. 

Examples of valid inputs:

H2O
CH3 (CH2)5 COO, -1
HOCH2 HCNH3, 1

Input is terminated by pressing the enter key on the keyboard. Output 
is displayed on the screen. For example if the input is:

C2H6

then the output would appear on the screen as

formula: C2H6 charge : 0 limit: 0.000000e+000
30.046948 100.000000
31.050416 2.328797
32.054076 0.014579
33.060123 0.000012

If the charge is left unspecified or is specified as zero then the 
output is in the form of mass, abundance pairs. If a non-zero charge 
is specified then the output is in the form of m/z ratio, abundance 
pairs. The calculated result takes the electron mass into account.

To generate an output file rather than a screen-based output please 
use the appropriate redirection operator for your operating system. 
For example invoking the ms Windows version of the program from the 
command line as follows:

emass >testfile

would send the output to a file named "testfile" rather than to the 
screen. 

To quit the program when using it interactively, press ctrl-d (in
Linux systems) or ctrl-z (in ms Windows systems).


Command line options:
---------------------
-i         The name of the isotope data file, default ISOTOPE.DAT
-l         The pruning limit, default 0
-d         Number of significant significant digits  in the output, 
           default 6

In order to avoid possible loss of accuracy we recommend that you 
use the default pruning option, although, for most purposes, a 
pruning limit of 1e-30 gives sufficiently accurate results. These 
options may be used singly or in combination. For example, to run 
emass for the compound C2H6 with a pruning limit of 2e-5 and 4 
significant digits use the following command line:

emass -l 2e-5 -d 4

This would generate an output of

formula: C2H6 charge : 0 limit: 2.000000e-005
30.0469 100.00000
31.0504 2.3288
32.0541 0.0145

The number of significant digits is the number of digits to the 
right of the decimal point for both mass and abundance. Note that 
the number of significant figures for the base peak abundance is 
actually greater than the number specified by the significant 
digits parameter.

