What does the Search Compare message “A problem has been encountered setting a coverage map.” mean?
When saving the results of the database search Protein Prospector stores the start amino acid number of the peptide within the protein. One thing these are used for is to display protein coverage maps. There is a problem with this approach if the database protein sequence has changed between doing the search and looking at the results. This particular error is encountered when the start amino acid number is greater than the protein length. You can generally look at the history of the protein sequences associated with a given accession number on the database web site. One reason that the database entry could be shorter would be if the signal peptide had been removed. If you are worried about these errors it is best to repeat the search. If the signal peptide has been removed from the database sequence you may now detect the protein N-terminus peptide if it previously wouldn’t have been generated by the enzymatic cleavage rules.
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