These notes record, in a slightly expanded way, the lectures given by the first two authors at the College on Moduli Spaces of Vector Bundles that took place at CIMAT in Guanajuato, Mexico, from November 27th to December 8th, 2006. The college, together with the ensuing conference on the same topic, was held in occasion of Peter Newstead's 65th anniversary. It has been a great pleasure and a privilege to contribute to celebrate Peter's outstanding achievements in algebraic geometry and his lifelong dedication to the progress of mathematical knowledge. We warmly thank the organizers of the college and conference for inviting us, thus allowing us to participate in Peter's celebration. The main emphasis in these notes is on the Fourier-Mukai t...