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File Handling

General information about peak and feature maps

  If you want some general information about a peak or feature map, use the @b FileInfo tool.
  - It can print RT, m/z and intensity ranges, the overall number of peaks, and the distribution of MS levels
  - It can print a statistical summary of intensities
  - It can print some meta information
  - It can validate XML files against their schema
  - It can check for corrupt data in peak files
  See the 'FileInfo --help' for details.

Problems with input files

  If you are experiencing problems while processing an XML file you can check if the file 
  does validate against the XML schema:
FileInfo -v -in infile.mzML

Validation is available for several file formats including mzML, mzData, mzXML, FeatureXML and IdXML.

Another frequently-occuring problem is currupt data. You can check for corrupt data in peak files with FileInfo as well:

FileInfo -c -in infile.mzML

Converting your files to mzML

  The TOPP tools work only on the HUPO-PSI @a mzML format. If you need to convert @a mzData, @a mzXML or @a ANDI/MS
  data to @a mzML, you can do that using the @b FileConverter, e.g.
FileConverter -in infile.mzXML -out outfile.mzML

If you use the format names as file extension, the tool derives the format from the extension. For other extensions, the file formats of the input and output file can be given explicitly.

Converting between DTA and mzML

  Sequest DTA files can be extracted from a mzML file using the @b DTAExtractor:
DTAExtractor -in infile.mzML -out outfile

The retention time of a scan, the precursor mass-to-charge ratio (for MS/MS scans) and the file extension are appended to the output file name.

To combine several files (e.g. DTA files) to an mzML file use the FileMerger:

FileMerger -in infile_list.txt -out outfile.mzML

The retention times of the scans can be generated, taken from the infile_list.txt or can be extrated from the DTA file names. See the FileMerger documentation for details.

Extracting part of the data from a file

  If you want to extract part of the data from an mzML file, you can use the
  @b FileFilter tool. It allows filtering for RT, m/z and intensity range or for MS level.
  To extract the MS/MS scans between retention time 100 and 1500, you would use the following command:
FileFilter -in infile.mzML -levels 2 -rt 100:1500 -out outfile.mzML

OpenMS / TOPP release 1.9.0 Documentation generated on Sun Oct 27 2013 01:11:37 using doxygen 1.8.4