How can I use Mascot for the interpretation of results as fold-change protein in quantification? it is possible to determine through spectral counting values obtained from the matches?
Hi Miroslav Ferko,
Normalized emPAI can be used for broad comparison of entire proteomes as it offers label-free, relative quantitation of the proteins in a mixture based on protein coverage by the peptide matches in a database search result.
Thanks!
Hallo Mohanty, thank you very much .. I want to ask, is it better to use emPAI values or matches values? Can this result also be written as a fold change?
What is the lower limit - the numerical limitations when using emPAI .. with maches it should be work with numbers higher then 10, right?.. and when using emPAI ??
Thanks a lot!
Hi Miroslav Ferko,
I am attaching one paper which gives in detail how the fold change can be calculated using emPAI. Specifically, Supplementary table S4 ( Combined final emPAI master list 41°C v 37°C xls file.) gives the formula for the calculation.
Thank you.
Thank you very much, you helped me a lot, I will try to apply on my results. Thank you again.
M.
Sorry, i have one small question. The sum of emPAI values is taken as the sum of all the proteins identified in the given spot, or always the sum of the proteins that are included in the comparison, only those that are found in both groups that compare .. Thank you.
Hi!
Sorry for the late response.
As far as I know, it should ideally be always the sum of the proteins that are included in the comparison. But you can refer few articles involving emPAI usage for quantitation. In case of a quantitative study (involving TMT, iTRAQ), we generally consider the the proteins identified in all the groups rather than the entire proteins identified.
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