Valid word is a difficult thing to quantify. As I've said before, a word exists as long as people use it.
You say in your question that you have read it in literature, so therefore we must conclude that it does exist, and, given the context of its use, is a synonym for quantify.
The meaning according to OED1 is a synonym for quantify, chiefly used in biological or medical contexts, so I feel quite sure that its use is typical.
As can be seen in the above ngram, quantify is more popular than quantitate, but quantitate's use is not insignificant in proportion.
The main difference between the two words is that quantitate is (i.e. can be) used to mean "to perform quantitative analysis upon", which is not really synonymous with quantify. Also, I think it's fair to say, outside of scientific literature, you are unlikely to encounter quantitate.
(1): "quantitate, v.". OED Online. March 2013. Oxford University Press. 20 May 2013 http://www.oed.com/view/Entry/155922?redirectedFrom=quantitate.