Chapter 6 Data Conversion

6.1 Introduction

Each vendor typically encodes their data in a vendor-specific, proprietary, closed format, with access restricted to a particular operating system. Therefore, raw data must be converted from vendor-specific binary files to open-format files for manipulation by most software.

6.1.1 Thermo RAW files

MSConvert parameters for thermo RAW data

Figure 6.1: MSConvert parameters for thermo RAW data

The parameter setting here is very important. I found this setting can (1) centroid the RAW file, and (2) keep the correct mass accuracy.

Such conversion will convert both MS1 and MS2 data.

6.1.2 Extracting only MS/MS data

Source for this part: Fiehn Lab

  • centroid the MS/MS spectra [Peak Picking option, set MS Levels 2-2]

  • limit the product ion number to the 100 most intense MS/MS peaks [Threshold Peak Filter]

  • Preserve metadata such as sample name, retention time and charge state and precursor abundance

  • Select activation mode such as CID or HCD [Subset: activation]

  • Only export MS2 levels for MS/MS search [Subset: MS Level 2-2]

MSConvert parameters for extracting MS2 level file

Figure 6.2: MSConvert parameters for extracting MS2 level file

6.2 Waters MSE Raw Data

6.3 How to verify your conversion

Open the raw data, and open the converted data (you can used MZmine2 software). Then compare the m/z values and intensities of randomly selected peaks. The values should be the same for the same peaks from the same scan. Do the same for MS2 level file.

6.4 Other file conversion method

  • Many vendor software also the feature to export the raw file as mzML and/or mzXML format

  • AbfConverter can be used to convert raw files for MSDIAL software.

The conversion is simple:

  1. start “AnalysisBaseFileConverter.exe”

  2. Drag & drop MS vendor files into this program

  3. Click “Convert”

  4. The ABF files are generated in the same directory as the raw data files.

Abf converter

Figure 6.3: Abf converter