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:
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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:
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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:
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-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.