Question: Proteomics Data Analysis

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osamashehzad.786 •

**10**wrote:I have come across proteomics data which measures the expression profile of protein X in 6 different sampes

- B1: untreated control cells
- B2: untreated control cells
- B3: untreated control cells
- A1: drug treated cells
- A2: drug treated cells
- A3: drug treated cells

A = treated and B = control; performed in triplicates.

Below is the data I have:

Name: ProteinX

(A1+A2+A2)/(B1+B2+B3): 1.035

(A1+A2+A2)/(B1+B2+B3) Count: 1362

(A1+A2+A2)/(B1+B2+B3) Variability (%): 9.9

B1/(B1+B2+B3): 0.978

B1/(B1+B2+B3) Count: 1346

B1/(B1+B2+B3) Variability (%): 17.5

A1/(B1+B2+B3): 1.032

A1/(B1+B2+B3) Count: 1358

A1/(B1+B2+B3) Variability (%): 24.2

I think that

(A1+A2+A2)/(B1+B2+B3): 1.035

is the fold ratio, but I do not understand what does "count" and "variability percentage" means in terms of given data.

Also, any ideas about what

B1/(B1+B2+B3): 0.978

and

A1/(B1+B2+B3): 1.032

indicate in terms of the data??

Did this data come from a publication? Is there a methods description that includes the experimental design? What was the protein measurement technology? If this is mass spec data, count might refer to number of supporting peptides or spectra...or it might not. Variability percentage might be a coefficient of variation expressed in percentage terms...or it might not. Unless the author of this data set happens to be on Biostars, without more information about the experiment I think it's unlikely you'll get a definitive answer here.

1.9kThis data came from Thermo Fisher Orbitrap Fusion Lumos Mass Spec (TMT-tag based LC-MS/MS Mass spectrometry) where A1, A2, A3 and B1, B2, and B3 are TMT tags which were added in 6 samples. It does not come from publication unfortunately. Does this information alone could shed more light ?

Can you please explain what does coefficient of variation means? and also what would it mean to say B1/(B1+B2+B3) and A1/(B1+B2+B3) ?

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