The title of the book, The Angel Experiment, is about as straightforward as they come. It refers to all of the flock members who live with Max, since they are all scientific experiments. The kids are human-avian hybrids and can fly, so they're otherwise known as "angels," even though the scientists treat them more like naughty pets than higher beings.
In addition, angel could refer to the character Angel, who is one of the most fascinating experiments in the study. She's the one who got the extra cool powers, like being able to read minds and influence people's actions, after all. These powers play key parts in the plot, helping the flock along on their quest.
Finally, mentioning the experiment up front sets the reader up for the book's science fiction slant, and the expectation that there will be some sort of scientific shenanigans within. Readers certainly won't be disappointed, either—there are plenty of shady, fascinating studies going on at the mysterious facilities in California and New York City.