How to use IPC?
ipc understands two types of input: chemical sum formulas and
peptide sequences given in one letter notation.
-c <chemical formula>
passes a chemical formula to the parser. The parser is a very basic one so no
brackets are understood.
example: ipc -c CCl4
This results in the isotopic distribution of Tetra. Atoms given with -c are taken
additional to those given with -a or -p (see below). Until now the parser doesn't
understand all element symbols. But adding new ones is simple, see
ADDING ELEMENTS for this.
-a <peptide sequence>
As I´m working on oligopeptides ipc accepts also peptides and peptide sequences
given in one letter notation. Peptides given this way are additional to atoms
given via -c
example: ipc -a GW
would give the distribution for the dipeptide Glycine-Tryptophane.
As -a and -c are cumulative,
ipc -a GW -c H
would give the distribution for the protonated dipeptide Gly-Trp.
The -f option is a bit special. Normally ipc calculates the exact
distribution. As the possible permutations grow exponential with
the amount of atoms this is very time and memory consuming.
The -f (fast) option is the only one which leads to an approximation
during the calculation of the peak masses.
-f tries to calculate only the first <int> permutations resulting from
each element. If <int> was choosen too small some rel. Int. might be
wrong or some of the more intensive peaks might be missing.
If <int> was choosen properly computation time is reduced dramatically
and the shown peaks are exact.
example for comparison : ipc -a WWW, ipc -a WWW -f 10, ipc -a WWW -f 100,
ipc -a WWW -f 1000
I propose to start with small <int> and increase the value until no
change is observed in the result.
When using -f the overall number of peaks is no longer shown, as it
would be <int>. Instead the sum of the probabilities of the computed
peaks is given in %.
This tells ipc to prepare GNUPlot output. ipc will create two
files: <name> and <name>.gnu in your pwd. The file <name>
contains data which can be plotted as standard x,y-graph. <name>.gnu
contains some commands for GNUPlot for displaying the data in the file
<name>. Per default ipc then calls gnuplot <name>.gnu to display
the calculated pattern.
If there are problems when trying to invoke GNUPlot automaticly
read INSTALL on details how to turn this off.
ipc calculates the masses of the peaks to the 5th place after the
decimal point and displays them with all decimal places.
With -d the result is rounded to the <int>th position after the decimal
point. Peaks which end up with the same mass are combined. This has no
influence on the calculation and changes only the way of displaying
example for comparison: ipc -a GW, ipc -a GW -d 1
This tells ipc to calculate a mass/charge (m/z) ratio which is used
in mass spectrometry. Thus you can give with -z the <int> charges on your
example: ipc -c SO4 -z 2
would show the m/z pattern of the double negativly charged molecule ion of
ipc reads the peptide sequence given in the file <name>.
The file must only contain the peptide sequence and there must
be a terminating new line at the end of each line.
-p is cumumlative with -a and -c.
before printig the isotopic pattern print the sum formula. When
giving peptide sequences to ipc it might be informative what
sum formula is hidden behind it.
example: ipc -a GW -c H -s
would print the isotopic distribution of the protonated dipeptide
GW and the sum formula of the dipeptide.
prevents the calculation of the isotopic distribution. Useful when you
just want the sum formula of a large peptide.
example:ipc -a GW -c H -s -x
This would print only the sum formula of the protonated dipeptide GW
shows a small help text