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Vertex paid its outgoing chief executive Matthew Emmens $13.3 million last year

Cambridge biotechnology company Vertex Pharmaceuticals Inc. paid its departing chief executive, Matthew W. Emmens, total compensation of $13.3 million last year, down from the $14.9 million pay package he collected in 2010, according to a regulatory filing Tuesday.

The filing said Emmens’ compensation in 2011 included a salary of $1.1 million, an incentive plan payment of $3 million, and stock and option grants totaling $9.1 million. He stepped down on Feb. 1, turning over the top job at Vertex to Jeffrey Leiden, an industry veteran.

Leiden, who sat on the Vertex board before being named the chief executive designee in December, received stock and option awards valued at $10.7 million last year, according to the filing.

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Vertex posted net income of $29.6 million in 2011 compared with a net loss of $754.6 million in 2010. During the past year, the company has won Food and Drug Administration approval for drugs to treat hepatitis C and cystic fibrosis.

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