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.
