Using the MaxQuant algorithm, I am analyzing some data using label-free experiment.
However, I didn't find a good guide about the experimental design. In fact, different web pages say totally opposite things. Even in Max Quant course, they do not explain correctly how to do this.
Assuming that my experiment is: 2 groups (Control and treatment) with 3 biological replicates each.
How would be your experimental design?
I found this examples:
Parameter Group |Experiment | Fraction |
Group 0 | C1 | 1
Group 0 | C2 | 1
Group 0 | C3 | 1
Group 0 | T1 | 11
Group 0 | T2 | 11
Group 0 | T3 | 11
I also found this, but I don't know what Max Quant does when you don't enumerate the biological replicates.
Parameter Group |Experiment | Fraction |
Group 0 | C | 1
Group 0 | C | 1
Group 0 | C | 1
Group 0 | T | 11
Group 0 | T | 11
Group 0 | T | 11
Thank you in advance.
Hello Enrique,
if you don´t numerate the biological replicates MQ will put them together in the output (this is useful if you have technical replicates that you will put together for a better overall comparison). In case of biological replicates I guess you are intending to perform a statistical analysis afterwards, then it is necessary to numerate your samples in MQ. If you dont have a fractionation all C and T samples should have the same number. This is necessary for a good match between run alignment between your samples. Finally you should think about the number of replicates in a LFQ experiment. In most cases 3 replicates are not enough to describe the desired changes. In our hands 6 replicates per group in LFQ experiments works well and enables the usage of i.e. at least 4 out of 6 valid values in Perseus analysis.
Best, Murat
Hello Murat Eravci
which are the differences between biological replicates and technical replicates?
thank you
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