N-terminal modifications are not clearly distinguished from side chain modifications
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Last seen 4.3 years ago

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)

- Acetylation

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?



specL • 436 views
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I had a look into the .blib files and saw something really sad: The BiblioSpec people already do not handle the N-term. modifications correctly. Here is the head of the Modifications table in the SQLlite dump (.blib file):

> head(my_Modifications)
Source:   query [?? x 4]
Database: sqlite 3.11.1 [joined_Gluc_control.blib]

     id RefSpectraID position     mass
  <int>        <int>    <int>    <dbl>
1     1            2        3 57.02146
2     2            2        6 28.03130
3     3            6        3 28.03130
4     4            6       10 28.03130
5     5            9       13 28.03130
6     6            9       17 28.03130

The modifications is just an integer (Da units). No link to UNIMOD IDs. Really poor, since the Mascot server used the org. UNIMOD definitions. di-methylation is UNIMOD acc 36 and it comes with different specificities:


The Bibliospec people do not catch this information in any way but flatten it to an integer :-(


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