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]> 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]. > 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. > -- 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.
