Quantitative phosphoproteomics using iTRAQ

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Bo1001
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Quantitative phosphoproteomics using iTRAQ

Postby Bo1001 » Mon Mar 02, 2015 6:01 am

Hi all,

I have some iTRAQ-labeling based phosphoproteomic data. Does anyone know which software can be used to do the quantification for this kind of data?

And usually, how to handle the replicate design when do the quantification?

Best regards!
Bo

Infinity
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Postby Infinity » Mon Mar 02, 2015 7:46 am

You can use MaxQuant

Bo1001
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Postby Bo1001 » Tue Mar 03, 2015 6:32 am

Infinity wrote:You can use MaxQuant


Thanks. I have tried MaxQuant (version 1.5.2.8). But I don't find that it can do iTRAQ quantification.
Best regards!
Bo

Infinity
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Postby Infinity » Wed Mar 11, 2015 9:30 am

Sorry for the late response. You have to get familiar with MaxQuant, particularly if you open the second tab "Group Specific Parameters"-->"General" and choose "Type" option to "reporter ion" you will be able to do iTRAQ. In fact in MaxQuant you can do almost any type of quantification.


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