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Welcome to the RawTools wiki! On this page you will find information related to using RawTools, and helpful documents to aid in making sense of the output. If you notice anything missing from this page or you encounter any issues with RawTools, please do not hesitate to make a post on the Issues page.
These guides have been separated by operating system to make them easier to follow. Find your operating system and follow through the guides to start using RawTools!
Please note that, unlike MSFileReader, the new RawFileReader from Thermo Fisher does not require a separate installation.
Minimum/Recommended System Requirements
RawTools requires a 64-bit operating system.
There are no real minimum requirements in terms of processor speed, hard drive space or RAM. However, to increase processing speed, significant portions of the raw file are extracted into memory, so your RAM needs will scale with the size of raw file with which you are working. For very large raw files (>~2GB) the memory usage can become quite high. Even when the memory usage exceeds your physical RAM, there is usually enough virtual memory or swap space to process these large files, but things will get slower. If you deal with very very large files (>5GB) you run a real risk of running out of virtual memory or swap space, so, if you run into problems, increasing these values might help.
Windows
RawTools requires .NET 4.6.2 or greater, and thus the operating system requirements are based on the requirements of this package.
- Download and install .NET 4.6.2 from Microsoft for Windows.
- Download and prepare RawTools for Windows.
- Optional: download a test dataset for processing with RawTools for Windows.
- Optional: download and prepare X! Tandem
- Run RawTools for parsing and quantification for Windows.
- Run RawTools for quality control for Windows.
Linux
For Linux, we will be using a CentOS 7 system. RawTools requires the use of Mono as a .NET package on Linux.
- Download and install Mono for Linux.
- Download and prepare RawTools for Linux.
- Optional: download a test dataset for processing with RawTools for Linux.
- Optional: download and prepare X! Tandem
- Run RawTools for parsing and quantification for Linux.
- Run RawTools for quality control for Linux.
MacOS
For MacOS, we will be using a MacBook Air system ('High Sierra' 10.13.1). RawTools requires Mono as a .NET package on MacOS.
- Download and install Mono for MacOS.
- Download and prepare RawTools for MacOS.
- Optional: download a test dataset for processing with RawTools for MacOS.
- Optional: download and prepare X! Tandem
- Run RawTools for parsing and quantification for MacOS.
- Run RawTools for quality control for MacOS.
Results output annotation and identifiers
If you have already processed your data with RawTools and just need help understanding what is in the output, visit the pages below describing the data.