SILAC gives you more reliable quantification, as labeling is very easy and  you can mix your samples early during your experiment(sample prparation, while iTRAQ labeling happens rather late , can be incomplete and may give you variations during labeling of your samples. 

SILAC on the other hand does not work with all cells (albeit with most cell lines), as some cells do not grow in the medium with dialized FBS. SILAC might get also more expensive (depends on how much cells you need), although in most cases you can titrate down arginine concentration quite alot.

So, if possible, I would go for SILAC.

Hi,

Those are valid points made by Christian, especially on the timing of label introduction: the easier the better, considering the sample work up that is usually required for cell lysates. 

Some other considerations that could lead (force..) you in either direction: how many states/situations do you want to analyze; A versus B, or multiplexing? The latter is slightly more straightforward using iTRAQ or TMT labeling.

What amino acid(s) is your cell line auxotrophic for (i.e. what amino acids can you use to introduce stable isotopes into your proteins)?

And what type of MS are you envisioning to use to generate the quantitative data? Not all mass spectrometers are equally suited to generate/analyse iTRAQ reporter ions.

Finally, as in all cases: you'll need the right software to enable extraction of quantitative information from your data sets; do you already have this, or are you planning to buy that?

Good luck!

Exspanding on what Christian said, SILAC is basically the equivalent of having an internal standard at the very beginning of your sample preparation.

All your sample prep steps (and their associated errors/variability) will be in the same range for all your experiments. Therefore, you will most likely get the best relative quantification available with current technology.

With post-digestion labelling, you don't really know what sample prep variation you have from experiment to experiment

At the same time, SILAC is expensive, as both Christian and Eef already pointed out.

Hello all,

Thank you very much for your input.

I am working with the same cell and applying the same protocol to all conditions. THerefore, the advantage of having an internal control is not obvious.

To start, I will use both approaches to compare. I understood the iTraq still requires some validation.

Best wishes

Hi Julien,

The following manuscript can be a good reference (Benchmarking stable isotope labeling based quantitative proteomics)

http://www.sciencedirect.com/science/article/pii/S187439191200704X#

There they found an interesting interplay between the identification and quantification rate for iTRAQ compared to SILAC and dimethyl labeling.