Hello, This incorrect mapping bug has been fixed and will be in the next release of TPP. Thanks for reporting it! --Luis
On Mon, Mar 16, 2015 at 3:52 AM, delphine wood <[email protected]> wrote: > Hi Eric, > > Yes it does make sense. > > Thanks a lot > > Best regards, > > Delphine > > 2015-03-13 17:34 GMT+01:00 Eric Deutsch <[email protected]>: > >> Hi Delphine, while MYL6 has: >> >> VFDKEGNGTVMGAEIR >> >> MYL1 and others have >> >> VFDKEGNGTVMGAELR >> >> (note I/L substitution) >> >> Mass spectrometry cannot distinguish I from L, so that peptide >> effectively maps to all of them. >> >> >> >> Does that make sense? You probably shouldn’t be getting the “Unmatched >> pep” error, but everything else is working as designed. >> >> >> >> Regards, >> >> eRic >> >> >> >> >> >> >> >> *From:* [email protected] [mailto: >> [email protected]] *On Behalf Of *Delphine >> *Sent:* Friday, March 13, 2015 4:11 AM >> *To:* [email protected] >> *Subject:* [spctools-discuss] sequence attributed to a "wrong" protein >> after combining pepxml >> >> >> >> Hello, >> >> >> >> As I used xtandempipeline to import the pepxml created through TPP, I got >> an error about a sequence attributed to a protein that doesn't contain this >> sequence in the database. In this example the sequence is VFDKEGNGTVMGAEIR >> and the protein it is wrongly attributed to is the MYL1. I checked the >> database and the sequence is found in the MYL6 protein and not in the MYL1. >> I checked the pepxml files created with different identification methods >> (mascot, comet, xtandem and spectrast). The sequence does not appear in the >> xtandem result file, in spectrast it is attributed to an obsolete protein >> (D3ZCQ5) and it is attributed to MYL6 in the comet and the mascot results. >> After running peptideprophet on each file, the sequence remains attributed >> to MYL6 but in the protein column a +3 appears 'sp|Q64119|MYL6_RAT +3 >> <http://10.143.10.19/tpp/cgi-bin/comet-fastadb.cgi?Db=/opt/tpp/data/fasta/RAT_DECOY.fasta&Pep=VFDKEGNGTVMGAEIR&MassType=1&sample_enzyme=trypsin&min_ntt=2>' >> and when I mouve the mouse above the +3, the MYL1, MYL1-2(isoform) and MYL3 >> appears. After peptide prophe,t I use interprophet to combine all the >> identification results, and the resulting file contains attribution of the >> sequence to the MYL1 protein (sp|P02600|MYL1_RAT +3 >> <http://10.143.10.19/tpp/cgi-bin/comet-fastadb.cgi?Db=/opt/tpp/data/fasta/RAT_DECOY.fasta&Pep=VFDKEGNGTVMGAEIR&MassType=1&sample_enzyme=trypsin&min_ntt=0>) >> with the MYL1-2, MYL3 and MYL6 in the '+3'. When I click on the protein >> name to see the position of the peptide in the protein the comet page >> says "Unmatched pep: VFDKEGNGTVMGAEIR" >> >> >> How could explain this phenomena? And do you see a solution so that it >> doesn't append anymore? >> >> >> >> Thanks for your help. >> >> >> >> Delphine >> >> -- >> 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 a topic in the >> Google Groups "spctools-discuss" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/spctools-discuss/zOpIN8Hg-CE/unsubscribe >> . >> To unsubscribe from this group and all its topics, 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. > -- 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.
