sequence attributed to a "wrong" protein after combining pepxml

[Delphine]

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' 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) 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

[Eric Deutsch]

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

--
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 spctools-discu...@googlegroups.com.
To post to this group, send email to spctools...@googlegroups.com.
Visit this group at http://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.

[delphine wood]

Hi Eric,

Yes it does make sense.

Thanks a lot

Best regards,

Delphine 

--
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 spctools-discu...@googlegroups.com.

[Luis Mendoza]

Hello,

This incorrect mapping bug has been fixed and will be in the next release of TPP.  Thanks for reporting it!

--Luis