Hello Timo, Thank you for the excellent question. We have been encoding the modifications this way in the modified peptide string, the pepXML contains the tags encoding the full mass of each modification. In the interest of being able to separate modifications such as phosphorylation from sulfonation, for example, I think in the future we would like to move towards representing the modifications in the bracket notation using the PSI-MS Names. This would be a longer term project.
Cheers, -David On Thu, Aug 4, 2016 at 1:08 AM, Timo Sachsenberg <[email protected]> wrote: > Hi, > I am a member of the OpenMS team. Regarding the pepXML file format, we > would like to improve compatibility with TPP. > We are thinking about how to properly represent modifications in the > "modified_peptide" > attribute of "modification_info". > An example we came across looks like: "n[35]RQLNK[162]LQHK[162]GEAR" and > uses the nominal total mass of the N-terminus or the respective amino acids. > Is this the preferred way to represent the modified_peptide string or do > you suggest a different one? > Best, > Timo > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
