You can \smash the whole of the first line and then open up with e.g. \\[1ex] at the end. In this case it is only the depth of the expression that you want to hide so probably it is most appropriate to use \smash[b]. This leaves the height intact, so spacing to the previous text is unaffected. If you want to reduce that space too then use \smash instead of \smash[b].

\documentclass{article}
\usepackage{amsmath}
\usepackage{mathtools} % for \smashoperator[lr]{...}
\usepackage[retainorgcmds]{IEEEtrantools} % for \begin{IEEEeqnarray*}{rl}...
\begin{document}
\begin{IEEEeqnarray*}{rl}
\IEEEeqnarraymulticol{2}{l}{
\smash[b]{\frac12\;
\smashoperator{\sum_{\substack{k+l=p \\ \sigma\equiv(p,q)\text{-shuffles}}}}
\;\pm\left[
U_k(\gamma_{\sigma(1)},\dots,\gamma_{\sigma(k)}),
U_l(\gamma_{\sigma(k+1)},\dots,\gamma_{\sigma(k+l)})
\right]
}}
\\[1ex]
&\qquad\qquad\qquad
+\sum_{i<j}U_{p-1}
\left(
[\gamma_i,\gamma_j],\gamma_1,\dots,\widehat{\gamma_i},\dots,
\widehat{\gamma_j},\dots,\gamma_p]
\right)
\\
&\qquad\qquad = [d,U_p] \left( \gamma_1,\dots,\gamma_p \right)
\end{IEEEeqnarray*}
\end{document}
Note on my machine the package is IEEEtrantools, not trantools.
As Mico points out the spacing after the \pm is too big. This is a strange bug with spacing around \left...\right discussed in Spacing around \left and \right . One solution is to use the mleftright package as follows:

\documentclass{article}
\usepackage{amsmath}
\usepackage{mathtools} % for \smashoperator[lr]{...}
\usepackage[retainorgcmds]{IEEEtrantools} % for \begin{IEEEeqnarray*}{rl}...
\usepackage{mleftright}
\begin{document}
\begin{IEEEeqnarray*}{rl}
\IEEEeqnarraymulticol{2}{l}{
\smash[b]{\frac12\;
\smashoperator{\sum_{\substack{k+l=p \\ \sigma\equiv(p,q)\text{-shuffles}}}}
\;\pm\mleft[
U_k(\gamma_{\sigma(1)},\dots,\gamma_{\sigma(k)}),
U_l(\gamma_{\sigma(k+1)},\dots,\gamma_{\sigma(k+l)})
\mright]
}}
\\[1ex]
&\qquad\qquad\qquad
+\sum_{i<j}U_{p-1}
\left(
[\gamma_i,\gamma_j],\gamma_1,\dots,\widehat{\gamma_i},\dots,
\widehat{\gamma_j},\dots,\gamma_p]
\right)
\\
&\qquad\qquad = [d,U_p] \left( \gamma_1,\dots,\gamma_p \right)
\end{IEEEeqnarray*}
\end{document}
\\[-1ex]? – Olivier Bégassat Oct 25 '14 at 20:53\\[1ex]- without it the lines are too close together. You may well prefer a smaller value, but with\\[-1ex]they overlap. – Andrew Swann Oct 26 '14 at 07:52\smash[b]to begin with and tell in the final note that in other cases\smash[t]or\smashcould be beneficial. – egreg Oct 26 '14 at 11:25\leftand\rightmay not be right even if the size of the brackets happens to be correct: the extra space inserted to the left of\left[makes the\pmsymbol like it's a binary operator. Using\bigl[does not insert extra space, and it would be clearer that\pmis a unary operator. – Mico Oct 26 '14 at 19:59\mleftand\mrightmacros (from Heiko'smleftrightpackage) the best. – Mico Oct 26 '14 at 21:06