Data Formats and Pre-processing

Mass Spectrometry data analysis is plagued by an overabundance of file formats. The good news is that the Mass Spec community, including many instrument vendors have developed a standard file format for raw data, mzML. The bad news is that many of the old formats are still in widespread use, and most instruments don't produce it natively. The reference implementation of the mzML standard is a software suite called ProteoWizard. ProteoWizard includes a very handy tool called msconvert that is capable of converting raw data from most instruments into mzML or into one of many other formats. In addition to format conversion, msconvert can also perform a wide variety of noise filtering and peak-picking functions to prepare data for analysis. A typical pre-processing involves;

  1. Conversion from instrument .raw to mzML
  2. Peak picking on both MS1 and MS2 data using vendor-native peak picking routines (built in to msconvert)
  3. Denoising of MS2 data either by thresholding or by keeping only the largest peaks withing a moving window
  4. Convert spectrum identifiers into a standardized format

To convert files from raw instrument native formats to mzML a windows PC is required. If you need to do this, be sure to download ProteoWizard with vendor reader support . This package comes with MSConvertGUI which allows conversion of raw files using a graphical interface. Once files are in mzML or mgf format they can be converted to various other formats using the msconvert3 tool in Galaxy.