We developed a survey to probe student understanding of quantum mechanics concepts at the beginning of graduate instruction. The survey was administered to 202 graduate students in physics enrolled in first-year quantum mechanics courses from seven different universities at the beginning of the first semester. We also conducted one-on-one interviews with fifteen graduate students or advanced undergraduate students who had just finished a course in which all the content on the survey was covered. We find that students share universal difficulties about fundamental quantum mechanics concepts. The difficulties are often due to over-generalization of concepts learned in one context to other contexts where they are not directly applicable and difficulty in making sense of the abstract quantitative formalism of quantum mechanics. Instructional strategies that focus on improving student understanding of these concepts should take into account these difficulties. The results from this study can sensitize instructors of first-year graduate quantum physics to the conceptual difficulties students are likely to face.