Select only top matching protein in spectrast

[shubha...@gmail.com]

Hi, 

     I am using RefSeq database which has isoforms. My pipeline includes Mascot, peptide prophet, iProphet and spectraST.

In the spectraST output .sptxt file, for some spectra there are multiple proteins identified. eg. Protein=4/NP_001448.2|gn|FLNB:2317|/NP_001157791.1|gn|FLNB:2317|/NP_001449.3|gn|FLNC:2318|/NP_001447.2|gn|FLNA:2316|

Is there a way to select only top match protein?

Thanks!

Best regards,

Shubham

[David Shteynberg]

Hi Shubham,

Thanks for using the TPP tools and submitting your question here. A peptide may map to more than one protein, when this happens the TPP will usually map each peptide to all proteins where it can occur.  There are some exceptions to this such as I/L substitutions and protein specific context that may change according to the enzyme used which may change the number of enzymatically specific termini on the peptide.  The tool that does the mapping in the TPP is called RefreshParser (it is called automatically.)  By default it should only return protein mappings consistent with your search parameters' enzyme rule.  For example, if you do a fully tryptic search RefreshParser should, in theory, return only fully tryptic mappings.  Hopefully, this makes sense to you and is consistent with your observations, if not please write back.

Cheers,

-David

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[shubha...@gmail.com]

Dear David,

   Thanks for explaining the principle of multiple match. I was asking if there is any flag in spectraST that returns only top match.

eg Protein= 1/NP_001447.2|gn|FLNA:2316|

instead of all four 4/NP_001448.2|gn|FLNB:2317|/NP_001157791.1|gn|FLNB:2317|/NP_001449.3|gn|FLNC:2318|/NP_001447.2|gn|FLNA:2316|

Thanks!