Hi, My lab has recently started looking into de novo peptide sequencing methods to identify proteins in our samples that have unknown cleavage patterns and are thus missed during our regular database searches. I noticed TPP v5.1 has some integration with novor. I have tried running novor2xml.pl on my novor results file but I keep getting the error message "Warning: skipping potentially incomplete (10 vs expected 0) search result in" for all peptides, resulting in an empty results file. I presume this is because I don't understand what format the modifications input file should be. Do you know what I'm doing wrong? Could you explain the integration of novor with TPP - primarily can I then run proteinprophet on the novor2xml results file?
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