crux print-processed-spectra
Usage:
crux print-processed-spectra <spectra> <output file>
Description:
Pre-process each spectrum in a given file in preparation for computing XCorr. The pre-processing steps are described in detail in this paper:
J. K. Eng, B. Fischer, J. Grossman and M. J. MacCoss. "A fast SEQUEST cross correlation algorithm process the peaks as for computing." Journal of Proteome Research. 7(10):4598-4602, 2008.The output of this program is equivalent to the spectrum shown in Figure 1D of the above paper.
Input:
- <spectra> – The name of the file containing spectra to process
Output:
- <output file> – The name of the file in which the processed spectra will be printed in MS2 format.
Options:
--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.--parameter-file <filename>
– A file containing command-line or additional parameters. See the parameter documentation page for details. Default = no parameter file.--overwrite <T|F>
– Replace existing files if true (T) or fail when trying to overwrite a file if false (F). Default = F.