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Example Novel Peptide Filter Workflow

Galaxy Workflow ' Example Novel Peptide Filter'

Step	Annotation
Step 1: Input dataset Ensembl pep.all (Reference Protein FASTA file) select at runtime
Step 2: Input dataset cRAP database of MS contaminants select at runtime
Step 3: Input dataset MS Search Peptide ID results select at runtime	Any MS search software may be used to generate this table-formatted (e.g. excel) list of peptide identifications as long as peptide IDs are listed under one column.
Step 4: Concatenate datasets Concatenate Dataset Output dataset 'output' from step 1 Datasets Dataset 1 Select Output dataset 'output' from step 2	Concatenates the reference proteome (Ensembl pep.all) and the contaminants database (cRAP).
Step 5: FASTA-to-Tabular Convert these sequences Output dataset 'out_file1' from step 4 How many columns to divide title string into? 1 How many title characters to keep? 0	Convert Reference+cRAP fasta into tabular format. Column 1: Accession Column 2: aa sequence
Step 6: find in reference Input file to be filtered Output dataset 'output' from step 3 reference file to search Output dataset 'output' from step 5 select columns to compare Choose the column of input and reference to compare column in input (defaults to last column) 2 (value not yet validated) column in reference (defaults to last column) 2 (value not yet validated) Ignore case when comparing True Choose outputs lines with no match in reference Annotate found input entries with columns from reference No	Input is the list of peptides identified from MS search software. Peptides should be in table format and listed within a column.
Step 7: find in reference Input file to be filtered Output dataset 'novel' from step 6 reference file to search select at runtime select columns to compare Choose the column of input and reference to compare column in input (defaults to last column) 2 (value not yet validated) column in reference (defaults to last column) 2 (value not yet validated) Ignore case when comparing True Choose outputs lines with match in reference Annotate found input entries with columns from reference Yes columns from reference to append to found input lines 1 (value not yet validated) separator to place between annotations from different reference lines ; separator to place between annotation columns from the same reference line ,	Input are list of novel peptides (not present in the reference database) and this step finds to which variations each novel peptide corresponds.