Cell Signaling using Mass Spec. Data

Hi,

I am new to research and was recently given a list of mass spec. data: proteins that are present in conditioned media from mouse cancer cells grown in a monolayer or mouse cancer cells grown in a 3D matrix (there are about a 1000 proteins).  I need to start a project to identify if any proteins secreted by mouse cancer cells grown in a 3D matrix inhibit the growth of monolayer mouse cancer cells.  Where do I begin??  

I have thought of using RNAi to knockdown gene expression of cells in the 3D matrix but I would initially need to knockdown gene expression one at a time.  ...and what if inhibition is regulated by a cascade or multiple proteins (which I'm guessing it is), I would have to try all the proteins in a matrix - this seems virtually impossible!!

Is there a different approach that I can try??  A screening process??  Data mining??