crux-get-ms2-spectrum

Usage:

crux-get-ms2-spectrum [options]  <scan number>  <input filename>

Description:

Using a binary search, extract one or more MS-MS spectra from an MS2 file by scan number. Optionally output some summary statistics for each spectrum.

Input:

• <scan number> – The scan number for the MS-MS spectrum to extract from the MS2 file. This is an integer in the range [1, 100000], and uniquely identifies a particular MS-MS spectrum within an MS2 file. Optionally, this argument may be provided as a range of scan numbers of the form <mix>-<max>. In this case, all scans within the specified range (inclusive) will be output.
• <input filename> – A file containing multiple MS-MS spectra in MS2 format.

Output:

The program prints the requested spectrum to standard output in MS2 format.

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 <name>:<value> (e.g. "TIC:1000.0\n"). 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
  For each possible spectrum charge state, the statistics are as follows:
  • Charge state
  • Neutral mass
  • Charged mass
  • M+H+ mass
• --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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