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.

  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

[Luis Mendoza]

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

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