On this topic, I've looked through the additional information at the protein sequence level and for an identified peptide there is a table "observed peptides" below the protein sequence which has the sequence position information for the entire peptide (see attached). This shows the positions of the amino acids...is this information available in the pep.xml file? The only thing that I can think of at this time is to develop an approach using the Biostrings package (http://bioconductor.org/packages/release/bioc/html/Biostrings.html) to extract the information and output the amino acid position corresponding to the modified site using the fasta file that was searched.
Best, Adam On Friday, May 18, 2018 at 1:38:11 PM UTC-5, Emma Whittington wrote: > > I have used PTMprophet in the past but wondered if there's a way of > outputting the position of the modification in the protein? I have found in > the pep.xml output a line giving the position in the peptide but what I > really want to know is where the modification is in the associated protein. > Is this something more easily seen using the petunia GUI than command line? > or is it something that can't be done? > > Thanks! > > All the best, > Emma > -- 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.
