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! On Tuesday, December 8, 2020 at 4:52:16 PM UTC-5 David Shteynberg wrote: > 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 > > On Tue, Dec 8, 2020 at 1:37 PM [email protected] <[email protected]> > wrote: > >> 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 >> >> -- >> 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/6f597aca-f8a0-49a2-be5d-0770ce4c1050n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/6f597aca-f8a0-49a2-be5d-0770ce4c1050n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/0c9e3243-f077-40b5-ad9c-86497d11b9acn%40googlegroups.com.
