crux get-ms2-spectrum [options] <ms2 file>
Extract one or more MS-MS spectra from an MS2 file by scan number. Optionally output summary statistics for each 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.
stdout– the requested spectrum or spectra in MS2 format.
--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
- Charge state
- Neutral mass
- Charged mass
- M+H+ mass
--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 =
--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 =
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 =
--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 =
--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 =