Walnut

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: https://bitbucket.org/searleb/encyclopedia/wiki/Home

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.

Inputs

• 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
  

Outputs

• 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, ...