Isotopic Pattern Calculator

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 Im 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.

OPTIONS
-f <int>

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 %.

-g <name>

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.

-d <int>

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 the results.

example for comparison: ipc -a GW, ipc -a GW -d 1

-z <int>

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 ion.

example: ipc -c SO4 -z 2

would show the m/z pattern of the double negativly charged molecule ion of sulfate

-p <name>

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.

-s

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.

-x

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

-h shows a small help text