About ===== This workflow uses a modified version of `TIMSCONVERT `_ to take multiple raw MALDI-qTOF Dried Droplet MS datasets from the Bruker timsTOF fleX from successive AutoXecute runs with different, non-overlapping mass range windows and combines them into a single consensus spectrum with the "full" mass range. Installation ------------ Installing on Windows ^^^^^^^^^^^^^^^^^^^^^ 1. Download and install `Anaconda for Windows `_ if not already installed. Follow the prompts to complete installation. 2. Download and install `Git for Windows `_ if not already installed. 3. Run ``Anaconda Prompt``. 4. Create a conda instance. .. code-block:: conda create -n maldi_polymerization python=3.11 5. Activate conda environment. .. code-block:: conda activate maldi_polymerization 6. Install dependencies. .. code-block:: pip install -r https://raw.githubusercontent.com/gtluu/flex_maldi_dda_automation/gui/maldi_polymerization/requirements.txt 7. Simply clone the `flex_maldi_dda_automation `_ repo or download the standalone script `here `_. 8. See below for usage information and example. Installing on Linux ^^^^^^^^^^^^^^^^^^^ 1. If not already installed, download and install `Anaconda for Linux `_. Anaconda3-2023.07-2 for Linux is used as an example here. * Alternatively, the script can be downloaded in the ``Terminal`` using the following command. .. code-block:: wget https://repo.anaconda.com/archive/Anaconda3-2023.07-2-Linux-x86_64.sh 2. If not already installed, install ``git``. On Ubuntu 23.04.3 LTS, this can be done using the following command. .. code-block:: sudo apt-get install git 3. Install Anaconda for Linux via the bash script that was downloaded. After installation, restart the terminal (or open a new terminal window). .. code-block:: bash [path to]/Anaconda3-2023.07-2-Linux-x86_64.sh 4. In the terminal, create a conda virtual environment. .. code-block:: conda create -n maldi_polymerization python=3.11 5. Activate conda environment. .. code-block:: conda activate maldi_polymerization 6. Install dependencies. .. code-block:: pip install -r https://raw.githubusercontent.com/gtluu/flex_maldi_dda_automation/gui/maldi_polymerization/requirements.txt 7. Simply clone the `flex_maldi_dda_automation `_ repo or download the standalone script `here `_. 8. See below for usage information and example. Usage ----- This workflow is run from the command line. Parameters ^^^^^^^^^^ ``--input``: One or more MALDI-MS .d directories acquired from the timsTOF fleX in successive AutoXecute runs with different, non-overlapping mass range windows. ``--output``: Name of the resulting mzML file. ``--mode``: Choose whether to export to spectra in ``profile``, ``centroid``, or ``raw`` mode. Defaults to centroid. ``--compression``: Choose between ZLIB compression (``zlib``) or no compression (``none``). Defaults to ``zlib``. ``--encoding``: Choose encoding for binary arrays: 32-bit (``32``) or 64-bit (``64``). Defaults to 64-bit. ``--barebones_metadata``: Only use basic mzML metadata. Use if downstream data analysis tools throw errors with descriptive CV terms. Example ^^^^^^^ .. code-block:: python maldi_polymerization/maldi_polymerization.py --input strain1_mr1.d strain1_mr2.d strain1_mr3.d --output test.mzML