BLANKA2 is a command line tool used to remove noise and blank background signals from mass spectrometry data. It takes mzML files as input and returns modified mzML files without MS/MS files that were found in the specified blanks. Blank detection is performed using MS/MS clustering through falcon. Importantly, full scan MS data is not affected.
This repo contains the current development version of BLANKA actively being worked on. For the publication version, please see here.
If you use BLANKA2, please cite us:
Jessica L. Cleary, Gordon T. Luu, Emily C. Pierce, Rachel J. Dutton, Laura M. Sanchez. (2019). BLANKA: an Algorithm for Blank Subtraction in Mass Spectrometry of Complex Biological Samples. *Journal of The American Society for Mass Spectrometry*; 30, 1426-1434. doi: 10.1007/s13361-019-02185-8.
BLANKA2 is available for use in Linux. Due to the falcon's (and therefore BLANKA2's) use of the Faiss library, which lacks a Windows implementation, BLANKA2 is not available for native Windows use. However, users may run BLANKA2 and other Linux based software in the Windows Subsystem for Linux environment.
- Download and install Anaconda for Linux. Follow the prompts to complete installation. Anaconda3-2021.11 for Linux is used as an example here.
wget https://repo.anaconda.com/archive/Anaconda3-2021.11-Linux-x86_64.sh
bash /path/to/Anaconda3-2021.11-Linux-x86_64.sh
- Add
anaconda3/binto PATH.
export PATH=$PATH:/path/to/anaconda3/bin
- Create a conda instance. You must be using Python 3.8.
conda create -n blanka python=3.8
- Activate conda environment.
conda activate blanka
- Download BLANKA2 by cloning the Github repo (you will need to have Git and
ensure that the option to enable symbolic links was checked during installation). It may be necessary to explicitly
allow for the use of symbolic links by adding the
-c core.symlinks=trueparameter on Windows.
git clone https://www.github.com/gtluu/blanka2
or
git clone -c core.symlinks=true https://www.github.com/gtluu/blanka2
- Install dependencies.
# BLANKA2 dependencies
pip install -r /path/to/blanka2/requirements.txt
To use BLANKA2, run it via the command line. An basic example can be found below:
python /path/to/blanka2/blanka.py --sample_input /path/to/sample/mzML/files --blank_input /path/to/blank/mzML/files
Parameters to optimize clustering using falcon can also be passed through BLANKA2. To see a full list of parameters, run:
python /path/to/blanka2/blanka.py --help