EXpress in SILAC

[sudarshan kumar]

How do we know that the express ratio is calculated from the normalized intensity /peak area of each peptide?

I ask this question because when we mix the light and heavy samples, there may be difference in the initial quantity of protein taken from the two groups.

[Jimmy Eng]

I don't know what "normalized intensity/peak area" of each peptide means in this context but I can say that XPRESS doesn't do any normalization.  It simply reports light area to heavy area ratios.  You'll have to do adjustments after the fact i.e. centering the mean ratio to 1:1 if you expect the bulk of your samples to be 1:1.

[sudarshan kumar]

Oh ! thank you 

Let me explain-

I have mixed two samples light and heavy labelled proteins (at cell level)

But if the cell count was not equal in the two groups, it will result in unequal contribution of proteins to the mixture. In this case the ratio L/H for individual protein will not be correct. 

The solution is normalization (as we do in St. Peter)

so I wanted to know if such normalization is done in Express before calculating the light to heavy ratio.

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The real voyage of discovery consists not in seeking new lands but seeing with new eyes. — Marcel Proust

Dr. Sudarshan Kumar

(Fulbright-Nehru Fellow)
(B.V.Sc.& A.H., M.V.Sc., PhD.)
Sr. Scientist
Animal Biotechnology Center
(Proteomics and Cell Biology Lab.)
National Dairy Research Institute Karnal, 132001
Haryana, India
Contact No 09254912456
URL www.ndri.res.in

Orcid Id: https://orcid.org/0000-0002-9816-4307

[sudarshan kumar]

Hi Jimmy,

Can you please explain my query.

Regards,

Sud

[Jimmy Eng]

I thought I did.  Here's what I wrote regarding XPRESS:  It simply reports light area to heavy area ratios.  You'll have to do adjustments after the fact i.e. centering the mean ratio to 1:1 if you expect the bulk of your samples to be 1:1.

If that doesn't answer your normalization question, please clarify.

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