crux predict-peptide-ions
Usage:Description:crux predict-peptide-ions [options] <peptide sequence> <charge state>
Given a peptide and a charge state, predict the corresponding fragment ions according to the provided options.
Input:
Output:
- <peptide sequence> – The peptide sequence.
- <charge state> – The charge state of the peptide.
The program prints to standard output a series of lines, describing how the ions were predicted.
# PEPTIDE: <peptide sequence> # CHARGE: <peptide charge>The program then prints a one-line header that labels the tab-delimited columns, followed by one line per ion:The columns contain the following values:
m/z mass charge ion-series peptide-bond-index nh3 h2o isotope flank <m/z> is the ion's mass-to-charge <mass> is the ion's (charged) mass <charge> is the ion's charge e.g. 1,2,3 <ion-type> is a string representing the series 'a', 'b', 'c', 'x', 'y', 'z', and 'p' <peptide-bond-index> is in [1...n), where n is peptide length. Consistent with standard mass spec terminology, where a y-1 and b-1 ions result from cleavage of completely different bonds. <NH3> is the number of NH3 modifications (lost neutral molecules) <H2O> is the number of H2O modifications (lost neutral molecules) <ISOTOPE> is the number of adjacent isotopic peaks <FLANK> is number of flanking ionsOptions:
--primary-ions <a|b|y|by|bya>
– Predict the specified primary ion series. 'a' indicates a-ions only, 'b' indicates b-ions only, 'y' indicates y-ions only, 'by' indicates both b and y, 'bya' indicates b, y, and a. Default by.--precursor-ion <T|F>
– Predict the precursor ions, and all associated ions (neutral-losses, multiple charge states) consistent with the other specified options. Default = F.--isotope <0|1|2>
– Predict the given number of isotope peaks. Default = 0.--flanking <T|F>
– Predict flanking peaks for b- and y-ions. Default = F.--max-ion-charge <1|2|3|peptide>
– Predict ions up to this charge-state. The integer options ('1', '2' and '3') specify a fixed maximum charge-state. The 'peptide' option indicates that the ions should range up to the maximum charge-state of the peptide itself minus 1. (thus, a +2 charge state peptide would have ions of +1). One exception: +1 charge state peptide would have ions of +1. Default = peptide.--nh3 <int>
– Include among the predicted peaks b/y ions with up to n losses of nh3. For example, for--nh3 2
, predict a peak for each b- and y-ion with the loss of one nh3 group and predict a second peak for each b- and y-ion with the loss of two nh3 groups. These peaks will have 1 and 2, respectively, in the NH3 column of the output. Default = 0.--h2o <int>
– Include in the predicted peaks, b/y ions with the loss of 1 to n water molecules. See--nh3
for an example. Default = 0.--fragment-mass <average|mono>
Which isotopes to use in calculating the fragment ion masses. Default = mono.--verbosity <0-100>
– Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = 30.