Spectrum Index Generation

Version: 0.6

Description:

This is a script to read spectrum peak files and output the nativeID, MS-level, and MS2+ index (defined as the 0-based index for all spectra of MS-level 2 and higher) for each spectrum. Supported input types are mzML, mzML.gz, mzXML, and mgf.

A note on the nativeID column. For mzML and mzML.gz the nativeID is read directly, for mzXML it is constructed as a scan=, and for mgf it is constructed as scan= IF there is a SCANS= field in the MGF, otherwise it is constructed as index= and is the 0-based index of all spectra in the file.