To address Harald's point, we should simple add something like "static" and "variable" attributes to the "mod_aminoacid_mass" elements as below. I think it makes a lot of sense to do something like this especially if we're going to be adding other (optional?) attributes such as "source".
<mod_aminoacid_mass position="6" mass="181.014010" variable="79.966331" source="peff"/> <mod_aminoacid_mass position="10" mass="166.109380" static="57.021494" /> <mod_aminoacid_mass position="14" mass="176.109380" static="57.021494" variable="10.00000" source="param" /> The only issue I see with something like this that n-terminal and c-terminal static and variable modifications are handled differently and there's no good way to denote the static and variable modifications on them. Back in January on the spctools-dev group, I brought up this issue with respect to terminal mods. They're really no different than amino acid modifications but there just needs to be a way to denote the terminal positions. There was objection to change where the proposed change was removing the "mod_nterm_mass" attribute from the "modification_info" element and encoding the terminal mods the way we do amino acid mods: <mod_aminoacid_mass position="n" mass="230.170757" static="229.162932" /> Is there an adequate, backwards compatible work-around where terminal static and variable modifications can be encapsulated? To keep things as backwards compatible as possible, we can leave the existing "mod_nterm_mass" and "mod_cterm_mass" where they are and simply allow terminal mods to be represented as above? If a non-integer "position" value is an issue then use "0" to represent the n-term and whatever the integer value of peptidelength+1 to represent the c-term? On Thu, Aug 11, 2016 at 12:16 PM, Harald Barsnes <harald.bars...@gmail.com> wrote: > > 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
