Obtaining Intensity Information from an IDA-EPI MS/MS Spectra

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

Answer

To obtain the intensity information from an IDA-EPI MS/MS spectra, the ProteoWizard data conversion tool, MSConvert, can convert SCIEX data files (.wiff and .wiff.scan) to several other formats, including mzML. The format mzML is compatible with many 3rd party software; however, the spectra are compressed using base64 and cannot be easily read. To obtain a file format is needed that is more readable, convert the .wiff data to other formats using MSConvert besides mzML, such as MGF or txt formats. These non-mzML formats create larger files but provide the spectral data in simple mass/intensity text.