Run-Specific Calibration Transition Lists ======================== Overview -------- Run-specific transition lists can be generated from search results of pseudo-DDA data (e.g. from DIA-Umpire or diaTracer) derived from the same DIA raw files. This approach can be used to improve the calibration of retention time, mass-to-charge and ion mobility values for each individual run. OpenSWATH supports generic calibration transition lists in tab- or comma-separated value (TSV/CSV) and sqlite-based (PQP) formats. ``OpenSwathAssayGenerator`` is part of `OpenMS `_ and is available for Windows, macOS and Linux. Contact and Support ------------------- FragPipe is supported by a very active community via their `github issues tracker `_. EasyPQP is supported by a very active community via their `github issues tracker `_. For ``OpenSwathAssayGenerator``, we provide support via the `OpenMS `_ support channels. Tutorial -------- The easiest way to generate run-specific transition lists is to use the FragPipe platform. The FragPipe team provides extensive documentation and `tutorials `_ on their website. Please follow their instructions to generate spectral libraries. The resulting ``*_run_peaks.tsv`` files will be in a tab delimited format that can be directly processed with the `OpenSwathAssayGenerator` tool in OpenMS ( follow the remaining steps in the :doc:`../generic` section). OpenSwathWorkflow allows for an optional additional nonlinear calibration step (performed after linear alignment). You can reduce the ``*_run_peaks.tsv`` to a smaller set of peptides to be used for the linear calibration step by using EasyPQP. .. code-block:: bash run1_diau_run_peaks_file=sample_1_run_peaks.tsv OpenSwathAssayGenerator -in $run1_diau_run_peaks_file -out sample_1_run_peaks_irt_nonlinear.pqp easypqp reduce --in sample_1_run_peaks_irt_nonlinear.pqp --out sample_1_run_peaks_irt_linear.pqp --bins 10 --peptides 5