Waters - MassLynx pkl or dta export and conversion to MGF or Mascot, Proteinlynx Thermo - use extractMSn and MSFilereader plus dependency librariesīruker - use Compass MGF export or Skyline MGF export Depending on the complexity they also allow different export settings such as abundance or peak or charge filters.ĪBI Sciex Analyst - Use the Mascot Export Plugin, can be installed as additional option if not preconfigured.Īgilent - MassHunter QUAL, use MGF export and define charge state 1 to 2 and 100 most abundant peaks
Most MS vendor software has an inbuilt MGF file export. Be aware that many software tools do not export the charge state (negative mode) correctly. Except the minimum definition there are no globally accepted format rules, hence every MGF is different and software needs to be tested if its compatible with multiple formats.
There are many flavours of MGF files with different headers and definitions. The minimum field definitions of an MGF file are the precursor mass, charge and m/z - abundance pairs. Format files are the standard format for MS/MS searches in proteomics and are now commonly used for small molecule MS/MS search.
