Thanks, Luis! This will be good to keep in mind if I notice any other 'mismatched' peptides.
On Wednesday, July 15, 2015 at 5:42:35 PM UTC-7, Luis wrote: > > Hello, > > It looks like a case of a double I->L substitution. The peptide ALAELLR > is found within Q8NFR. Since it is virtually impossible to distinguish I/L > via standard MS/MS, TPP maps all possible I/L versions of a peptide to the > corresponding proteins. Perhaps this should be noted in the SWATHAtlas > data, however. > > Cheers, > --Luis > > > On Wed, Jul 15, 2015 at 5:31 PM, Daniel Hyduke <[email protected] > <javascript:>> wrote: > >> So, I've been interested in using the 10,000 human protein assay library >> from swath atlas >> <https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetDIALibs>. One >> thing that I noticed is that for some assays the peptide sequence is not >> present in one, or more, of the proteins associated with the assay. For >> example, from the peakview file (phl004_canonical_sall_pv.csv): >> '393.247620674 601.366787076 19.8 2/Q8NFR9/Q8WUD4 light 10000.0 >> AIAELIR AIAELIR 2 y 1 5 19.8 2/Q8NFR9/Q8WUD4 >> FALSE 3310 1 TRUE'. AIAELIR is in the Q8WUD4 sequence but not >> in Q8NFR9. >> >> So, I decided to reprocess the data with tpp to see if that would provide >> any insight. >> >> I downloaded the mzXML files from PRIDE >> <http://www.ebi.ac.uk/pride/archive/projects/PXD000953> and searched >> with comet. The peptide (AIAELIR) shows up as a hit in >> the YANLIU_K140110_002.mzXML file and is associated with Q8WUD4 as the >> number 1 hit (Q8NFR9 is not in the hit list for the spectrum_query). >> However, once I run xinteract on the comet search results (xinteract -OARPd >> -dREVERSE_ -Ninteract.comet.pep.xml YANLIU_K140110_002.comet.pep.xml) >> Q8NFR9 now shows up as an alternative_protein for the spectrum_query >> (<alternative_protein protein="sp|Q8NFR9|I17RE_HUMAN" >> protein_descr="Interleukin-17 receptor E OS=Homo sapiens GN=IL17RE PE=1 >> SV=1" num_tol_term="1" peptide_prev_aa="G" peptide_next_aa="A"/>) >> >> I'm wondering why this happens? >> >> I've used comet and xinteract from tpp 4.8.0 and the sashimi-code svn >> repository on CENTOS Linux 7. >> >> -- >> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at http://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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
