crux get-ms2-spectrum
Usage:
crux get-ms2-spectrum [options] <input filename>
Description:
Extract one or more MS-MS spectra from an MS2 file by scan
number. Optionally output summary statistics for each spectrum.
Input:
-
<input filename> – A file containing multiple
fragmentation spectra in MS2
format.
Output:
The program prints the requested spectrum or spectra to standard
output in MS2 format.
Options:
-
--scan-number <int>|<int>-<int>
–
The scan number for the MS-MS spectrum to extract from the MS2
file. This is an integer in the range [1, 100000] that uniquely
identifies a particular spectrum within an MS2 file. Optionally, this
argument may be provided as a range of scan numbers of the form
<min>-<max>. In this case, all scans within the specified
range (inclusive) will be output.
-
--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"). 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=F.
-
--spectrum-parser pwiz|mstoolkit
–
Specify the parser to use for reading in MS/MS spectra. The default,
ProteoWizard parser should be able to 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.
-
--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.
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