Hi there, I'm looking to search orbitrap data against a strain specific protein database to annotate the peptides and build a SpectraST library. I would like to widen the search for possible PTMs as we currently have no data regarding the use of PTMs for regulation.
I'm a little confused as to the format of the tandem.params.xml file for including possible phosphorylation modifications to peptides. I get that the modification mass element will look something like this for M oxidation and STY phosphorylation <note type="input" label="residue, potential modification mass">15.994915@M,79.66633@S,79.66633@T,79.66633@Y</note> But I'm not sure whether I should be setting the value of <note type="input" label="residue, potential modification motif"></note> as well. Should I be using this to set the -80 and -98 values for neutral loss? Does anyone have a good example of what a tandem.params.xml file looks like when including common modifications in the search? Many thanks, Ben -- 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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
