## Usage:

crux xlink-assign-ions [options] <peptide A> <peptide B> <pos A> <pos B> <link mass> <charge state> <scan number> <ms2 file>

## Description:

Given a spectrum and a pair of cross-linked peptides, assign theoretical ion type labels to peaks in the observed spectrum.

## Input:

• peptide A – The sequence of peptide A.
• peptide B – The sequence of peptide B.
• pos A – Position of cross-link on peptide A
• pos B – Position of cross-link on peptide B
• link mass – The mass modification of the linker when attached to a peptide.
• charge state – The charge state of the peptide.
• scan number – Scan number identifying the spectrum.
• ms2 file – The name of one or more files from which to parse the fragmentation spectra, in any of the file formats supported by ProteoWizard.

## Output:

• stdout – tab-delimited text in which each row is a peak in the observed spectrum, and the columns are
1. The m/z value.
2. The observed intensity.
3. The matched intensity.
4. The calculated m/z value of the theoretical peak.
5. The mass associated with the observed peak.
6. The mass difference (in ppm) between the observed and theoretical peaks.
7. The ion type, specified as b or y, followed by the charge state in parentheses.
8. The amino acid sequence of the fragment.

## Options:

• ### Search parameters

• --fragment-mass average|mono – Specify which isotopes to use in calculating fragment ion mass. Default = mono.
• --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.
• --mz-bin-width <float> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = 1.0005079.
• ### Input and output

• --verbosity <integer> – 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.
• --spectrum-parser pwiz|mstoolkit – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed here. The alternative is MSToolkit parser. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = pwiz.
• --precision <integer> – Set the precision for scores written to sqt and text files. Default = 8.