Diapysef enables generating a DIA library. For more information: http://openswath.org/en/latest/docs/librarygeneration.html

For most data-independent acquisition (DIA) analysis, a well-represented spectral library is required for precursors, peptide, and protein identifications. Currently, we support library generation with the diapysef package directly from a MaxQuant analysis of several DDA runs.

Inputs

• msms.txt and evidence.txt (output files from MaxQuant)

• peptides used for retention time alignment e.g. iRTs or ciRTs

  • Tabular file with at least three columns for precursor charge, normalized retention time and modified peptide sequence

  • The headers of the columns must be named "PrecursorCharge" "NormalizedRetentionTime" "ModifiedPeptideSequence"

    PrecursorCharge     NormalizedRetentionTime    ModifiedPeptideSequence
           2                       53.2                 ADVTPADFSEWSK
           3                       52.9                 ADVTPADFSEWSK
           2                       43.6                 DGLDAASYYAPVR
          ...
          ...
    

Potential next Steps

After generating the spectral library with diapysef, the tabular file can be imported into OpenSwathAssayGenerator and OpenSwathDecoyGenerator to refine the library.