xlink-score-spectrum

Usage:

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

Description:

Given a cross-linked peptide and a spectrum calculate the corresponding XCorr score a number of different ways, depending upon the xlink-score-method parameter:

• composite – compute a combined XCorr score
• modification - score the two peptides separately, treating the second peptide as a variable modification on the first peptide
• concatenated - score as the concatenation of the two peptides. Note that this mode gives four scores, corresponding to the two relative orders of the peptides (AB and BA) and the modification appearing on the first or second peptide.

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 – XCorr score(s) in descending order

Options:

• xlink-score-spectrum options

  • --xlink-score-method composite|modification|concatenated – Score method for xlink {composite, modification, concatenated}. Default = composite.

• Search parameters

  • --use-flanking-peaks T|F – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = false.

• Fragment ion parameters

  • --use-a-ions T|F – Consider a-ions in the search? Note that an a-ion is equivalent to a neutral loss of CO from the b-ion. Peak height is 10 (in arbitrary units). Default = false.
  • --use-b-ions T|F – Consider b-ions in the search? Peak height is 50 (in arbitrary units). Default = true.
  • --use-c-ions T|F – Consider c-ions in the search? Peak height is 50 (in arbitrary units). Default = false.
  • --use-x-ions T|F – Consider x-ions in the search? Peak height is 10 (in arbitrary units). Default = false.
  • --use-y-ions T|F – Consider y-ions in the search? Peak height is 50 (in arbitrary units). Default = true.
  • --use-z-ions T|F – Consider z-ions in the search? Peak height is 50 (in arbitrary units). Default = false.

• 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.