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Question: How to get protein expression data from MaxQuant
0
gravatar for zero_hsy
4.0 years ago by
zero_hsy • 90
China
zero_hsy • 90 wrote:

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(ulr 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?

 
protein expression data maxquant • 3.2k views
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modified 4.0 years ago by Woa • 2.7k • written 4.0 years ago by zero_hsy • 90
1
gravatar for Woa
4.0 years ago by
Woa • 2.7k
United States
Woa • 2.7k wrote:

Check the files containing  iBAQ intensity data in it, the iBAQ intensity is the measure for  Protein abundance or expression
ADD COMMENT • link written 4.0 years ago by Woa • 2.7k

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 REPLY • link written 4.0 years ago by zero_hsy • 90

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 REPLY • link written 4.0 years ago by Woa • 2.7k
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