Dear specL maintainers,
I think I discovered a bug in specL. In short, I prepared a Mascot search including two N-terminal peptide modifications:
- dimethylation (N-term)
after that I created a spectral library from these search results using the bibliospec implementation in skyline-daily and based on this I created a assay library for Spectronaut using specL. When importing the lib I all of a sudden get asked to "explain" a huge amount of modifications to Spectronaut (see screenshot). To me it looks like the following happend. You use the following to write modified peptide sequences:
X[+|-Int]XX[+|-Int]XXX with X being any amino acid in single letter code. While this might work for internal modifications, it creates confusion for the terminal modifications. A simple example: Mascot ident. the peptide to be N-term. dimethylated, specL expresses this as:
But Spectronaut now needs to know if the peptide was modified on the side chain or on the alpha amine (N-term of peptide) and X[+28]XXXX is not clear in this respect.
Could somebody please look into this?