Sebastian Gibb

Based on this flow chart water loss happens just on *internal* S:  In my interpretation an *internal* S means `XSX` (that's why I used the regular expression `.S.`). So...

I am afraid that the `unimod` package won't be released in the near future (it is not my highest priority). So please add both to `MSnbase`'s internal amino acids dataframe.

Maybe I don't completely understand your request but at least your second suggestion is already possible: ``` r library("MSnbase") calculateFragments("ACE", modifications=c(C=57.02146)) # Modifications used: C=57.02146 # mz ion type pos...

Ok, thanks for the clarification. Great idea. I like your second solution more than the first. For the first you have to know the length of the peptide sequence before...

@lgatto we changed the way the `modification` argument was handled in `MSnbase => 1.17.6`. Currently the `modification` is added to the amino acid (before the modification _replaced_ the amino acid)....

Sry, we have to rethink the handling of modification once again. We changed to _add_ instead of _replace_ because we allow modifications to `Cterm` and `Nterm`: https://github.com/lgatto/MSnbase/issues/47#issuecomment-113902500 - for `Nterm`/`Cterm`...

Adding a new class would be surely the cleanest solution and even support unimod would be great but is that what the user really wants? The mzIdentMl code is very...

Sorry for being so slow and quiet regarding this topic. I think the best way would be to provide a `Modification` class (with unimod support). That's why I started (the...

@yafeng Unfortunately I had no time to implement it yet. I have to fix a few issues in `MSnbase` before. Next I would focus on [unimod](https://github.com/ComputationalProteomicsUnit/unimod) to provide a unique...

Unfortunately I have much to do with my real job. We started to implement the unimod modifications in the [unimod](https://github.com/ComputationalProteomicsUnit/unimod) package. Currently it can download and parse the data from...