Question: How to get protein expression data from MaxQuant
gravatar for zero_hsy
5.8 years ago by
zero_hsy100 wrote:


    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(ulr is

   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(, 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?


ADD COMMENTlink modified 5.8 years ago by Woa2.8k • written 5.8 years ago by zero_hsy100
gravatar for Woa
5.8 years ago by
United States
Woa2.8k wrote:

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

ADD COMMENTlink written 5.8 years ago by Woa2.8k

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?

ADD REPLYlink written 5.8 years ago by zero_hsy100

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

ADD REPLYlink written 5.8 years ago by Woa2.8k
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