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Walnut (version 1.12.34+galaxy0)
mzML conversion from RAW requires special options: msconvert --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw
provides the necessary peptide-to-protein links not specified in the spectrum library
Optional - Only analyze this subset of the background fasta proteome
Rather than full proteins
Parameter Settings
Parameter Settings 0


EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. See:

Walnut is a FASTA database search engine for Data-Independent Acquisition (DIA) MS/MS data. Walnut uses PeCAn-style scoring to extract peptide fragmentation chromatograms from MZML files, assign peaks, and calculate various peak features. These features are interpreted by Percolator to identify peptides.


  • A spectrum file in mzML format

  • A protein data base in fasta format

    The MSConvert command can be used to convert and deconvolute DIA raw files to mzML format. You need to use these options:

    msconvert  --zlib --64 --mzML --simAsSpectra --filter "peakPicking true 1-" --filter "demultiplex optimization=overlap_only" *.raw


  • A log file
  • A Chromatogram Library (.elib)
  • The identified features in tabular format Feature values of scans that are used by percolator to determine matches.
  • The identified Peptide Spectral Match results in tabular format Columns: PSMId, score, q-value, posterior_error_prob, peptide, proteinIds
  • The identified peptides in tabular format Per peptide: the normalized intensity for each scan file. Columns: Peptide, Protein, numFragments, intensity_in_file1, intensity_in_file2, ...
  • The identified proteins in tabular format Per protein: the normalized intensity for each scan file. Columns: Protein, NumPeptides, PeptideSequences, intensity_in_file1, intensity_in_file2, ...