RAW to mzML

Description

Convert Thermo Finnigan RAW files to the open mzML format. This script only runs on computers that have the Thermo Finnigan XDK installed.

Input files

• at least 1 RAW data file (.raw)

Output files

This is a converter script which produces a mzML files file for every input RAW data file.

Context

No context information available.

Common problems

If the file conversion does not work, you probably need to install the MS File Converter from Thermo: http://sjsupport.thermofinnigan.com/public/detail.asp?id=703.

In addition, the following packages are required:

• MSVC 2008 SP1 Redistributable Package (x86)
• .NET Framework 3.5 SP1

Parameters

m/z precision

Choices: 32 bits (default), 64 bits

Intensity precision

Choices: 32 bits (default), 64 bits

Write index

Choices: yes (default), no

Compress spectra

Choices: yes, no (default)

Compress result file

Choices: no compression, gzip (default), bzip2

Strip MS1 scans

Choices: no (default), yes

Source code

raw-to-mzml.rb, raw-to-mzml.yaml (GitHub)