Query related to protein abundances in TPP

[Mehar Un Nissa]

Dear Sir/Madam,

Which tool in TPP is used to get the abundance value or is there any other way to measure the protein expression?

 I look forward to hearing from you. 

Thanks and regards,

Mehar Un Nissa

Research Scholar,

Proteomics Lab.

Department of Biosciences and Bioengineering,

Indian Institute of Technology, Bombay-400076

[Robert Winkler]

Hi,

You could use ProtyQuant, which calculates the 'accumulated peptide
presence' for each hypothetical protein:

https://chemrxiv.org/articles/preprint/ProtyQuant_Comparing_Label-Free_Shotgun_Proteomics_Datasets_Using_Accumulated_Peptide_Probabilities/12404363

The algorithm is similar to spectral counting (e.g. used by the StPeter
plugin of the TFF), but integrating the protein inference calculation
and quantification.

The input files are pepXML of the Trans-Proteomic Pipeline. Results are
plain text files (tables.)

You can find the software at:
https://bitbucket.org/lababi/protyquant/

Feedback and questions are welcome (the manuscript is currently under review).

Best regards, Robert

Excerpts from Mehar Un Nissa's message of 2020-08-25 14:47:34 +0530:

> Dear Sir/Madam,
> Which tool in TPP is used to get the abundance value or is there any other
> way to measure the protein expression?
>
> I look forward to hearing from you.
>
> Thanks and regards,
>

> *Mehar Un Nissa*

[Mehar Un Nissa]

Hi Robert,

Thank you very much for quick response.

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