# print-processed-spectra

## Usage:

`crux print-processed-spectra [options] <ms2 file> <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." 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:

- `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 file` – File where spectrum will be written.

## Output:

The program writes files to the folder `crux-output` by default. The name of the output folder can be set by the user using the `--output-dir` option. The following files will be created:

- `output file` – The name of the file in which the processed spectra will be printed in MS2 format.

## Options:

- ### print-processed-spectra options

  - `--stop-after remove-precursor|square-root|remove-grass|ten-bin|xcorr` – Stop after the specified pre-processing step. Default = `xcorr`.
  - `--output-units mz|bin` – Specify the output units for processed spectra. Default = `bin`.

- ### Input and output

  - `--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`.
  - `--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`.
  - `--parameter-file <string>` – A file containing parameters. See the parameter documentation page for details. Default = `<empty>`.
  - `--overwrite T|F` – Replace existing files if true or fail when trying to overwrite a file if false. Default = `false`.