I've read the article[1] and what they do is compare the proton flux as measured in Geneva with the neutrino signal measured in Gran Sasso. The proton signal is timeshifted a small amount until the curves overlap maximally.

Where the leading and trailing edge are is irrelevant here, as the complete shape of the pulses are compared.

1: http://static.arxiv.org/pdf/1109.4897.pdf