Hi Eric, We use these elements to detect which modifications that are fixed and which that are variable. I don't see how we could extract this information without the aminoacid_modification elements? As this information is not part of the mod_aminoacid_mass elements? Or is there something I'm missing?
Best regards, Harald On Wednesday, August 10, 2016 at 9:44:09 PM UTC+2, Eric Deutsch wrote: > Hi everyone, I have a question about use of some pepXML tags. It’s a bit > technical and mostly for other developers who use the pepXML format. > > > > The issue involves the amino_acid tags at the top of a pepXML file under > search_summary, like this: > > <search_summary"> > > <aminoacid_modification aminoacid="M" massdiff="15.994915" > mass="147.035400" variable="Y" symbol="*"/> > > <aminoacid_modification aminoacid="S" massdiff="79.966331" > mass="166.998359" variable="Y" symbol="#"/> > > > > Comet and some other search engines write out these entries for the > specified search mass mod parameters. > > > > But SpectraST at least does not put these there, in part because it > doesn’t really know what mods will appear in later in the file, because it > depends on the library. And we now have another case where it is awkward to > put them at the top of the file because they’re not an input parameter, but > a result of the reference. > > > > So the question to all is: does anyone use these data elements at the top > for something important? Would it cause any troubles if for some search > results they are not there or are incomplete? As currently for SpectraST? > > > > What do you think? > > > > Thanks, > > Eric > > > > > > > > > -- 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.
