ms2preproc is a software tool to preprocess MS/MS spectra as described in our PROTEOMICS publication:

 Renard BY, Kirchner M, Monigatti F, Invanov AR, Rappsilber J, Winter D, Steen JAJ, Hamprecht FA, Steen H.
 When Less Can Yield More - Computational Preprocessing of MS/MS Spectra for Peptide Identification, Proteomics (2009).

Command line executables for linux and windows are provided at http://hci.iwr.uni-heidelberg.de/mip/proteomics/ .

### Installation
# Windows: click on the .exe file in the zip-folder and follow the instructions to setup ms2preproc in a folder of your choice.
# Linux:   precompiled versions 32- and 64-bit versions are contained in the zip-folder.

### Running ms2preproc
# Windows: open a command window (go for 'start', then 'run' and type 'cmd' to open the Command Window )
           and change to the directory where ms2preproc is installed (eg type 'cd C:\programs/ms2preproc/'), then type ms2preproc.
# Linux:   change into the according directory and choose ./ms2preproc-x86_32 or ./ms2preproc-x86_64 respectively.

You need to at least specify the input file, output file, file type and preprocessing type as options.

### Example:
ms2preproc -i input.mgf -o output.mgf -f mgf -X 200
for preprocessing the input.mgf with a 'Top 200' preprocessing and saving the resulting mgf file as output.mgf

### Mascot:
We obtained best results using -X 200

### Sequest:
We obtained best results using -X 6 -Z 30

### ProteinPilot:
We obtained best results using -X 6 -Z 30

### All Options:

   -i <string>,  --infile <string>
     (required)  name of the MGF/DTA input file

   -o <string>,  --outfile <string>
     (required)  name of the MGF output file

   -f <mgf|dta>,  --informat <mgf|dta>
     (required)  input format

   -X <unsigned integer>,  --top <unsigned integer>
     (required)  number of highest intensity ions to keep

   -Y <unsigned integer>,  --nregions <unsigned integer>
     number of equal-sized regions the MS/MS spectrum is split into

   -Z <double>,  --zwinsize <double>
     m/z window (+/-Z) around high-intensity peaks in which the top X are selected

   -p <unsigned integer>,  --precision <unsigned integer>
     precision of output

   -v,  --verbose
     toggle verbose output

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.