Thermo Raw File Reader

The Thermo Raw File Reader is a .NET DLL for reading Thermo .raw files, as acquired on Thermo mass spectrometers

• The Raw File Reader is a wrapper for the ThermoFisher.CommonCore C# DLLs

Supported C# Versions

• .NET Framework 4.7.2
• .NET Framework 4.8
• .NET Framework 4.8.1
• .NET 6.x
• .NET 7.x
• .NET 8.x
• On Linux, Mono 6.12, or newer

Incompatible C# Versions

The Thermo Raw File Reader does not work with .NET Core 2.x or .NET Core 3.x

Features

The Thermo Raw File Reader DLL provides several methods for parsing the information extracted from Thermo .raw files, 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

Usage Instructions

Download the newest ThermoRawFileReader .zip file from the Releases page

• Extract the DLL files and place in a Lib directory inside your project directory
• In Solution Explorer, right click references and add references to the following DLLs (using Browse to select each DLL file)
  • ThermoRawFileReader.dll
  • ThermoFisher.CommonCore.RawFileReader.dll
  • ThermoFisher.CommonCore.BackgroundSubtraction.dll
  • ThermoFisher.CommonCore.Data.dll
  • ThermoFisher.CommonCore.MassPrecisionEstimator.dll
• A reference to PRISM.dll will get auto-added since the ThermoRawFileReader references the PRISM Library NuGet package
  • See also https://github.com/PNNL-Comp-Mass-Spec/PRISM-Class-Library

Software Example 1

The Test_ThermoRawFileReader directory in the Thermo Raw File Reader source code contains a .NET command-line application that illustrates how to interface with ThermoRawFileReader.dll

Software Example 2

The Thermo Peak Data Exporter application is an example console application that uses ThermoRawFileReader.dll

• Clone the source code from https://github.com/PNNL-Comp-Mass-Spec/Thermo-Peak-Data-Exporter

When running on Linux with Mono, use command line option -LoadMethod:false to disable loading method information

• This is required because the Thermo CommonCore DLLs cannot read method information when using Mono
• Example command line:
  mono ThermoPeakDataExporter.exe DatasetFile.raw -LoadMethod:false

Contacts

Written by Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
Copyright 2019, Battelle Memorial Institute. All Rights Reserved.
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics

License

The Thermo Raw File Reader is licensed under the 2-Clause BSD License; you may not use this program except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause

Copyright 2018 Battelle Memorial Institute

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.