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.
