# predict-peptide-ions

## Usage:

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

## Description:

Given a peptide and a charge state, predict the corresponding fragment ions according to the provided options.

## Input:

- `peptide sequence` – The peptide sequence.
- `charge state` – The charge state of the peptide.

## Output:

- `stdout` – 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:

  > m/z mass charge ion-series peptide-bond-index nh3 h2o isotope flank

  The columns contain the following values:

  - <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, b-1 corresponds to a prefix ion of a single amino acid, and y-1 corresponds to a suffix ion of a single amino acid.
  - <nh3> is the number of NH3 modifications
  - <h2o> is the number of H2O Modifications
  - <isotope> is the number of adjacent isotopic peaks
  - <flank> is the number of flanking ions

## Options:

- ### predict-peptide-ions options

  - `--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-ions T|F` – Predict the precursor ions, and all associated ions (neutral losses, multiple charge states) consistent with the other specified options. Default = `false`.
  - `--isotope <integer>` – Predict the given number of isotope peaks (0|1|2). Default = `0`.
  - `--flanking T|F` – Predict flanking peaks for b- and y ions. Default = `false`.
  - `--nh3 <integer>` – 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 <integer>` – Include in the predicted peaks, b/y ions with the loss of 1 to n water molecules. See --nh3 for an example. Default = `0`.

- ### Search parameters

  - `--max-ion-charge <string>` – Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the charge state of the peptide ("peptide"). If the max-ion-charge is greater than the charge state of the peptide, then the maximum is the peptide charge. Default = `peptide`.
  - `--fragment-mass average|mono` – Specify which isotopes to use in calculating fragment ion mass. Default = `mono`.