How to get protein expression data from MaxQuant

Question

[zero_hsy]

Hello:

I am processing the NCI 60 data. And I have known that the paper called "Global Proteome Analysis of the NCI-60 Cell Line Panel" gives the oroteome analysis. And I downloaded the data mentioned in the paper(URL is http://129.187.44.58:7070/NCI60/).

What I exactly want is the protein expression data. The format is like the gene expression data. In detail, it is like this.

             1_cell_line  2_cell_line
protein_1    ******       ***
protein_1    ***          *****

However, when I go to the download page (http://129.187.44.58:7070/NCI60/main/download), the processed data is called "MaxQuant Output Files". When I download it, there are a lot of txt with different names.But it does not include the above data format.

Could anyone using the MaxQuant software tell me how to find the above data format? If there are not such data, what is the purpose of MaxQuant?

Answer 1

[Woa]

Check the files containing iBAQ intensity data in it, the iBAQ intensity is the measure for Protein abundance or expression

[zero_hsy]

Thanks! I have found the file, but there are two methods,with one is called iBAQ and the other LFQ. Could you tell me what is the difference between them?

[Woa]

Check the original paper. I think its iBAQ intensity they used because its Absolute Quantification unlike LFQ (label free quantification), which is relative quantification.