Mobi-DIK ======== Overview -------- Mobi-DIK (Ion Mobility DIA Tool-Kit) is a workflow for the analysis of DIA data coupled with ion mobility (**diaPASEF**) [1]_. Mobi-DIK is an extension of the OpenSWATH workflow [2]_ that is optimized for ion mobility analysis as well as diapysef [3]_, a Python package for converting diaPASEF data from vendor format to open mzML format. .. figure:: ../img/diapasef_openswath_extraction.png :alt: diaPASEF OpenSWATH data extraction :target: https://www.nature.com/articles/s41592-020-00998-0/figures/3 :align: center Mobi-DIK workflow for targeted data extraction from diaPASEF data. Image adapted from figure 3 from Meier. et al. (2020) [1]_. Contact and Support ------------------- We provide support for Mobi-DIK on `OpenMS github issue tracker `_, `diapysef github issue tracker `_ and other available `OpenMS discord server `_. Installation ------------ Mobi-DIK is fully integrated within the tools of the OpenSWATH workflow. Please follow the `installation instructions `_ for the latest development branches. Tutorial -------- Conversion ~~~~~~~~~~ Taking the raw tdf files in sqlite format, ``diapysef`` can convert the raw files to standard format mzML. :doc:`dataconversion` shows the functionalities of the data conversion in details. Different comands can be used for data conversion: .. code-block:: bash diapysef converttdftomzml --help diapysef converttdftomzml --in=input.d --out=output.mzML Library Generation ~~~~~~~~~~~~~~~~~~ Library generation can be performed similar to traditional DIA data, see :doc:`../generic` and :doc:`../pqp`. See :doc:`../fragpipe` for a FragPipe-based spectral library generation workflow. For the legacy library generation workflow using MaxQuant output and diapysef, please follow instructions at :doc:`librarygeneration`. Calibration Libraries ---- For retention time and ion mobility calibration, please follow instructions at :doc:`../calibration/generic` and :doc:`../calibration/run_specific`. For calibration libraries used in the original publication [1]_, please find below: - iRT files from HeLa cell lysate can be obtained here: `linear iRT files `_. - iRT files from HeLa cell lysate can be obtained here: `nonlinear iRT file `_. Identification and quantification ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ For targeted data extraction, please follow instructions at :doc:`../openswath` and see the :doc:`openswath_mobidik` section for ion mobility specific parameters. For statistical scoring and FDR estimation, please follow instructions at :doc:`../pyprophet`. Other Functionalities ~~~~~~~~~~~~~~~~~~~~~ The data acquisition window schemes can be acquired with ``get_dia_windows.py`` from the `diapysef repo `_: .. code-block:: bash get_dia_windows.py pasef_data_dir.d/ output_scheme.csv A csv file can be written with the m/z isolation windows, collision energies, and the ion mobility isolation windows etc. Output of the scheme can also be plotted over the MaxQuant outputs in the mz and im dimensions: .. code-block:: bash plot_dia_windows.py output_scheme.csv MQ_output_all_peptides.csv References ---------- .. [1] Florian Meier, Andreas-David Brunner, Max Frank, Annie Ha, Eugenia Voytik, Stephanie Kaspar-Schoenefeld, Markus Lubeck, Oliver Raether, Ruedi Aebersold, Ben C. Collins, Hannes L. Röst, Matthias Mann. diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition. Nature Methods volume 17, pages 1229–1236 (2020). doi: https://www.nature.com/articles/s41592-020-00998-0 .. [2] Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R. OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol. 2014 Mar 10;32(3):219-23. doi: 10.1038/nbt.2841. PMID: 24727770 .. [3] see https://github.com/Roestlab/dia-pasef/