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Quantification and Identification

Using the assay library and the mzML files, identification and quantification of peptides can be performed with OpenSwathWorkflow and PyProphet. For detailed description and documentation of the downstream analysis, please refer to their documentation website. The newest OpenMS version 2.4.0 includes functionalities in handling ion mobility informations. Here are some of the input parameters that are additional to the regular parameters.


  • -ion_mobility_window: Ion mobility extraction window of precursor
  • -im_extraction_window_ms1: Use ion mobility on MS1 level
  • -irt_im_extraction_window: iRT extraction of the ion mobility correction values
  • -use_ms1_ion_mobility: Performs extraction on MS1 level ion mobility level
  • -Calibration:ms1_im_calibration: Use MS1 for ion mobility calibration
  • -Calibration:im_correction_function: Choose im correction function
  • -Calibration:debug_im_file: Record the ion mobility correction data
  • -Scoring:Scores:use_ion_mobility_scores: Add ion mobility for scoring


OpenSwathWorkflow can generate .tsv, .osw for identification and scoring output. It is also capable of generating the chromatogram files with extension .sqmass. The quantified output .tsv and .osw can be statistically validated with PyProphet.

Statistical Validation

PyProphet can take the scores generated from OpenSwathWorkflow and statistically validate the precursor identifications. For detailed documentation, please refer to :doc:`pyprophet`.