Algebraic Compact manifold originates from a proper scheme?

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If $M$ is a compact complex manifold, which is the analytification of some scheme $X$ of finite type over $\operatorname{Spec}(\mathbb{C})$, then must $X$ be proper over $\operatorname{Spec}(\mathbb{C})$?

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Yes.

See SGA 1

http://arxiv.org/abs/math/0206203

Exposee XII, Proposition 3.2.(v), page 245 (261 in the pdf).