get-ms2-spectrum

Usage:

crux get-ms2-spectrum [options] <ms2 file>

Description:

Extract one or more MS-MS spectra from an MS2 file by scan number. Optionally output summary statistics for each spectrum.

Input:

• 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 – the requested spectrum or spectra in MS2 format.

Options:

• get-ms2-spectrum options

  • --stats T|F – Rather than the spectrum, output summary statistics to standard output. Each statistic is placed on a separate line, in the format : (e.g. "TIC:1000.0").
    The following statistics are reported for the entire spectrum:
    • Precursor m/z
    • Total Ion Current
    • Base Peak Intensity
    • Number of peaks
    • Minimum m/z
    • Maximum m/z
    In addition, for each possible spectrum charge state, the following statistics are reported:
    • Charge state
    • Neutral mass
    • Charged mass
    • M+H+ mass
    Default = false.

• Search parameters

  • --scan-number <string> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <empty>.
  • --remove-precursor-tolerance <float> – This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = 1.5.

• 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.
  • --use-z-line T|F – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = true.