File Handling

General information about peak and feature maps

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.

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-occurring problem is corrupt 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 mzML format. If you need to convert mzData, mzXML or ANDI/MS data to mzML, you can do that using the 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 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 extracted 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 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