The basic sum-of-squares proof system, introduced under the name of Positivstellensatz refutations by Grigoriev and Vorobjov, is a “static” proof system for showing that a set of polynomial equations and inequations
$$S=\{f_1=0,\dots,f_k=0,h_1\ge0,\dots,h_m\ge0\},$$
where $f_1,\dots,f_k,h_1,\dots,h_m\in\mathbb R[x_1,\dots,x_n]$, has no common solution in $\mathbb R^n$: a refutation of $S$ is given by polynomials $g_i$ and $e_{I,j}$ such that
$$\tag{$*$}-1=\sum_{i=1}^kg_if_i+\sum_{I\subseteq\{1,\dots,m\}}\sum_je_{I,j}^2\prod_{i\in I}h_i.$$
(One could work with any real-closed field in place of $\mathbb R$.) Stengle’s Positivstellensatz guarantees that $S$ has a refutation if and only if it has no solution. The main complexity measure here is the degree of the refutation, which is the maximum of total degrees of the polynomials that appear under the sum signs in $(*)$, that is, $g_if_i$ and $e_{I,j}^2\prod_{i\in I}h_i$.
As usual with algebraic proof systems, one can also consider it as a refutation system for unsatisfiable Boolean formulas $\phi$ by including in $S$ the axioms $x_i^2-x_i$ for each variable $x_i$, and a translation of $\phi$ by polynomial inequalities.
More on the history and development of SOS systems can be found in http://arxiv.org/abs/1211.1958 .