Try to use FASP method for solubilisation and digestion of your samples (especially tissues). In the last steps of protocol before enzyme digestion you should wash the membrane of the filter three to four times with ammonium bicarbonate. Precipitation of proteins with acetone is a bad idea as it is very hard to solubilise the protein and get an efficient digestion with trypsin.

If there is no specific reason, you should not precipitate the proteins for iTRAQ kind of studies. There may not be uniform precipitation in all the samples you may use.  

Question to Dr. Atrih:

TEAB buffer seems is the recommended one for iTRAQ.  However your suggested FASP condition for Prashant Khare for his solubilization issue seems interesting.  I am eager to know the FASO method (or buffer) if you could mention.  Have you or someone used this condition for iTRAQ? Thanks

You might be better off avoiding precipitation entirely, if you can. See the discussion linked below.

https://www.researchgate.net/post/Is_acetone_precipitation_necessary_for_iTRAQ_TMT?_tpcectx=qa_overview_asked&_trid=5410bc24d685cc6d108b465c_

After FASP solubilisation of tissues/cell using FASP method, proteins are generally well denatured and therefore easy to digest with trypsin. In the last step of the protocol wash the membranes with TEAB (3 to 4 times), and not with Ammonum bicarbonate as I mentioned earlier,  then do the digestion. We tried this method in our LAB and it works much better than the precipitation of proteins with acetone.

The original FASP protocol and an enhanced FASP protocol are linked below. The original FASP protocol is associated with significant sample loss (in my hands and others). I haven't tried the eFASP protocol, but it appears to be better.

http://www.biochem.mpg.de/226356/FASP

http://www.ncbi.nlm.nih.gov/pubmed/24552128