Re: [spctools-discuss] Select only top matching protein in spectrast

[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!
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 shubha...@gmail.com  
> 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 spctools-discu...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/6f597aca-f8a0-49a2-be5d-0770ce4c1050n%40googlegroups.com
>>  
>> 
>> .
>>
>

-- 
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-discuss+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/spctools-discuss/0c9e3243-f077-40b5-ad9c-86497d11b9acn%40googlegroups.com.

Re: [spctools-discuss] Select only top matching protein in spectrast

['David Shteynberg' via spctools-discuss]

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 shubha...@gmail.com 
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 spctools-discuss+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/6f597aca-f8a0-49a2-be5d-0770ce4c1050n%40googlegroups.com
> 
> .
>

-- 
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-discuss+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-%3DNt-jmj0531mdT89Yn%2BgjhXLt1bdLTR-u-E_XEX4wow%40mail.gmail.com.

[spctools-discuss] 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

-- 
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-discuss+unsubscr...@googlegroups.com.
To view this discussion on the web visit 
https://groups.google.com/d/msgid/spctools-discuss/6f597aca-f8a0-49a2-be5d-0770ce4c1050n%40googlegroups.com.