The PReMiS™ software is able to analyze Thermo (.raw), AB Sciex (.wiff and associated), and .mzML format files. MS FileReader is needed to analyze Thermo .raw files and will need to be available on the user's computer. The Wiff Reader Library is needed to analyze AB Sciex (.wiff and associated) files. This library is installed with the PReMiS™ software and the user should not need anything further. Data can be converted to mzML in a variety of ways.

MS FileReader

MS FileReader is typically present on computers associated with a Thermo mass spec instrument, but you may need to install it for other machines. To obtain MS FileReader, please see the Thermo Scientific MS FileReader document or contact Thermo Scientific.

Wiff Reader Library

The Wiff Reader Library is included with the PReMiS™ installer. Please contact AB Sciex for additional information.

mzML conversion

Data in formats that are not supported by the PReMiS™ Software will need to be converted to mzML format. It is not recommended to convert directly analyzable data to mzML as conversion can be time consuming, analysis is slower, and some data is lost during conversion.

There are a number of tools for converting mass spec data to mzML format. We recommend the use of MSConvert which is part of the ProteoWizard Library. ProteoWizard is available for download.

MSConvert has been tested with the following settings:

• Output format: mzML
• Extension: mzML
• Binary precision: 64-bit
• Write index: checked
• TPP compatibility: checked
• Use zlib compression: checked
• Package in gzip: unchecked

View the documentation for MSConvert.
More information on the mzML format can be found at the HUPO-PSI page.