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.
Inputs¶
-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
Output¶
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
.