SWATHXtend workflow

SWATHXtend  workflow  takes  a  seed  library,  which  is  usually  a  locally generated spectra library, and one or more add-on libraries which are subjected to an optional cleaning process to remove low confidence and low intensity peptide ion spectra. The cleaned libraries undergo a quality  checking  to  ensure  that  the  add-on  library  and  the  seed  library  have  good  matching  quality  in terms   of   retention   time   and   relative   ion   intensity.   All   quality   libraries   undertake   ion   intensity normalisation  and  supervised  learning  based  retention  time  alignment.  For  peptides  of  conflicting  or overlapping  spectra  between  seed  and  add-on  libraries,  only  seed  library  spectra  are  kept.  Protein accessions  are  consolidated  by  merging  duplicated  protein  accessions  in  heterogeneous  formats.  The extended libraries can be output in PeakView or OpenSwath compatible format.