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If you want some general information about a peak or feature map, use the 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.
If you are experiencing problems while processing an XML file you can check if the file does validate against the XML schema using the FileInfo tool.
Validation is available for several file formats including MzData, FeatureXML, IdXML.
The TOPP tools work only on the HUPO-PSI mzData format. If you need to convert mzXML or ANDI/MS data to mzData, you can do that using the FileConverter, e.g. FileConverter -in infile.mzXML -out outfile.mzData
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.
Sequest DTA files can be extracted from a mzData file using the DTAExtractor: DTAExtractor -in infile.mzData -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 mzData file use the FileMerger:
FileMerger -in infile_list.txt -out outfile.mzData
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.
If you want to extract part of the data from an mzData file, you can use the 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.mzData -levels 2 -rt 100:1500 -out outfile.mzData
Generated Tue Apr 1 15:36:40 2008 -- using doxygen 1.5.4 |
OpenMS / TOPP 1.1 |