What Parameters in ProteoWizard Are Needed when Converting .wiff2 Files to mzXML Files?

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For research use only. Not for use in diagnostic procedures.



The parameter settings used when converting a wiff2 file into mzXML format. are listed below. Similar settings apply for mzML file conversion.

  • peakPicking: vendor msLevel=1-
User-added image

The reason why this level of filtering is used is to keep the file size small and the peak lists identical to those in PeakView™ software. It is important to include the “peakPicking” filter as the very first filter in the MS Convert filters list.

In this example, only the Peak Picking filter has been added. The MS level has been selected as 1. The second level is blank so that all higher MS/MS levels are considered. Note it is not added as a filter. In addition, remember that the centroided peak list has units of (cps/Da), which can often have values much smaller than 1.0. Therefore keep in mind that any third-party software is not filtering out intensities below a threshold that removes all your peaks.

In addition, third party data files, such as raw data files, can be converted to mzML ,mzXML or mgf  (Mascot generic data files) files. These files are converted so they can be used in ProteinPilot™ software. 

Please see the recommended settings below.  

raw to mgf