U.S. Department of Energy

Pacific Northwest National Laboratory

Thermo Raw File Reader

The Thermo Raw File Reader is a .NET DLL that demonstrates how to read Thermo-Finnigan .Raw files using Thermo's MS File Reader.

Area of Research: 

The Thermo Raw File Reader DLL provides several methods for parsing the information returned by MSFileReader, including:

  • Determining the parent ion m/z and fragmentation mode in a given scan filter
  • Determining the Ionization mode from a given scan filter
  • Extracting MRM masses listed in a given scan filter
  • Reporting the number of spectra in the .Raw file
  • Returning details on a specific spectrum
  • Obtaining the raw m/z and intensity values for a given spectrum

Also available for download is a .NET command-line application that illustrates how to interface with ThermoRawFileReaderDLL.dll

Prior to using ThermoRawFileReaderDLL.dll you must download and install the MSFileReader by creating an account at https://thermo.flexnetoperations.com/control/thmo/login, then logging in and choosing "Utility Software". Alternatively, use batch file registerFiles.bat in the lib folder to register MSFileReader.XRawfile2.dll

Package icon Thermo Raw File Reader Source Code2.66 MB


All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, as shown in the Readme file for the given application or on the website that more fully describes the application.



These programs are primarily designed to run on Windows machines. Please use them at your own risk. This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.

We would like your feedback about the usefulness of the tools and information provided by the Resource. Your suggestions on how to increase their value to you will be appreciated. Please e-mail any comments to proteomics@pnl.gov

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