Raw Beans is a quality control tool for assessment of data coming off mass spectrometry DDA (Data-Dependent Acquisition) experiments. It is an identification-free tool that can process either Thermo RAW or mzML formats. The results is a HTML report the provides some key data for a quick impression of the quality of the data itself and detect some obvious issues.
This tool is available for linux and windows:
Git repository is located here: https://bitbucket.org/incpm/prot-qc/src/master/README.md
A tutorial for running RawBeans:
There are 3 input types that this tool can handle:
The order of the input types is has follows - raw file → mzML file → json file
You can put any of the file types in your input folder, and for each sample, the tool will the take the most advanced file type so it will not redo anything that already been done.
Thermo - Raw files can be read directly instead of converting them to mzML first, in order to accomplish that all you need to is:
For windows, there is an executable that opens this view:
ProteoWizard msconvert.exe - The location of the msconvert.exe file in the ProteoWizard installation folder (this value needs to be inserted only ones, after that, the software will remember the last location you inserted), for example: C:\Program Files\ProteoWizard\ProteoWizard 3.0.10738\msconvert.exe
Input Directory - The input folder which your input files (as explained above) are located in.
Output Directory - The output folder which the html report will be written to.
Mass List - A list of masses (one per line) to track during file processing for the mass deviation section.
Batch - If True - a web report will be created for each sample (file), if False - one web report will be created for all of the samples (files).
Num Cores - The number of cores you want to use for parallel processing, this number shouldn't be bigger then the number of cores (logical cores) you have on your computer.