Re: [spctools-discuss] Query related to PTMprophet results in TPP

['Luis Mendoza' via spctools-discuss]

Hello Mehar,

Unfortunately PTMProphet does not calculate the protein position of the
modified amino acids; we may add this to a future version of TPP.

In the meantime, you would need to determine it from mapping the peptide
sequence onto its corresponding protein, with the caveat that the peptide
sequence may map to more than one protein (or in rare cases more than once
to the same protein) and thus have different positions.

Cheers,
--Luis



On Fri, Aug 7, 2020 at 12:38 AM Mehar Un Nissa 
wrote:

> Dear Sir/Madam,
>
>
> I have a query related to PTMprophet analysis.
>
>
> I performed comet search for an mzml file and put it for further analysis
> as under:
>
>
>
> -Using TPP tools Analyse peptides Checked for iprophet proteinprophet
> PTMprophet
>
>
> -Mass added for PTMs were:
>
>
> - 79.966 Da for Phosphorylation- STY
>
>
>
> I filtered the data on the basis of error table values.
>
>
> - I exported the excel showing results as under.
>
>
> [image: image.png]
>
>
>   *Query: Everything is fine except that the position of modified amino
> acid is not there, only the mass is there and amino acid is highlighted. *
>
>
>
> *How can I get to know the modified site (I mean exact position of
> modified amino acid?*
>
>
> *Is there a way that I can get these modified sites with respect to
> protein. e.g. S27 or T82 etc. *
>
>
>
> Could you please help me for this.
>
>
> Thanks and regards,
>
> *Mehar Un Nissa*
> Research Scholar,
> Proteomics Lab.
> Department of Biosciences and Bioengineering,
> Indian Institute of Technology, Bombay-400076
>
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> 
> .
>

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[spctools-discuss] Query related to PTMprophet results in TPP

[Mehar Un Nissa]

Dear Sir/Madam,


I have a query related to PTMprophet analysis.


I performed comet search for an mzml file and put it for further analysis
as under:



-Using TPP tools Analyse peptides Checked for iprophet proteinprophet
PTMprophet


-Mass added for PTMs were:


- 79.966 Da for Phosphorylation- STY



I filtered the data on the basis of error table values.


- I exported the excel showing results as under.


[image: image.png]


  *Query: Everything is fine except that the position of modified amino
acid is not there, only the mass is there and amino acid is highlighted. *



*How can I get to know the modified site (I mean exact position of modified
amino acid?*


*Is there a way that I can get these modified sites with respect to
protein. e.g. S27 or T82 etc. *



Could you please help me for this.


Thanks and regards,

*Mehar Un Nissa*
Research Scholar,
Proteomics Lab.
Department of Biosciences and Bioengineering,
Indian Institute of Technology, Bombay-400076

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