crux predict-peptide-ions

Usage:

crux-predict-peptide-ions [options] <peptide sequence> <charge state>

Description:

Given a peptide and a charge state, predict the ions according to the provided options. These are the ions used in crux-search-for-matches.

Input:

• <peptide sequence> – The literal peptide sequence (e.g. EAMAPK) that is used to predict the ions.
• <charge state> – The charge state of the peptide used to predict the ions.

Output:

The program prints to standard output a series of header lines, describing how the ions were predicted.

  # PEPTIDE: <peptide sequence>
  # CHARGE: <peptide charge>

And then the predicted ions, in the following format:

  <m/z> <mass> <charge> <ion-series> <bond-index> <NH3> <H2O> <ISOTOPE> <FLANK>

where

  <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 an integer representing the series where 0=a, 1=b, 2=c, 3=x, 4=y, 5=z, 6=p
  <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 SEQEUST-style flanking ions

Options:

• --primary-ions <b|y|by> – Predict the specified primary ion series. 'b' indicates b-ions only, 'y' indicates y-ions only, 'by' indicates both. 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.
• --neutral-losses <none|h2o|nh3|all> – Predict the the specified neutral loss peaks. 'none' indicates no neutral losses, 'h2o' indicates water loss only, 'nh3' indicates ammonia losses only, 'all' indicates all three kinds of losses. Default = all.
• --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 (thus, a +2 charge state peptide would have ions of +1 and +2). Default = peptide.
• --nh3 <int> – Predict peaks with the following max nh3 modification. Default = 1.
• --h2o <int> – Predict peaks with the following max h2o modification. 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.
• --version T – Print the version number and quit. Please note that you must include the 'T' after --version.

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