Employing ProteoWizard to Convert Raw Mass Spectrometry Data

Curr Protoc Bioinformatics. 2014 Jun 17:46:13.24.1-13.24.9. doi: 10.1002/0471250953.bi1324s46.


After raw data have been captured by mass spectrometers in biological LC-MS/MS experiments, they must be converted from vendor-specific binary files to open-format files for manipulation by most software. This protocol details the use of ProteoWizard software for this conversion, taking format features, coding options, and vendor particularities into account. This protocol will aid researchers in preparing their data for analysis by database search engines and other bioinformatics tools.

Keywords: LC-MS/MS; database search; mzML; proteomics; raw files.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein*
  • Software*
  • Tandem Mass Spectrometry*
  • User-Computer Interface