We analyze a practical algorithm for sparse PCA on incomplete and noisy data under a general non-random sampling scheme. The algorithm is based on a semidefinite relaxation of the $\ell_1$-regularized PCA problem. We provide theoretical justification that under certain conditions, we can recover the support of the sparse leading eigenvector with high probability by obtaining a unique solution. The conditions involve the spectral gap between the largest and second-largest eigenvalues of the true data matrix, the magnitude of the noise, and the structural properties of the observed entries. The concepts of algebraic connectivity and irregularity are used to describe the structural properties of the observed entries. We empirically justify our theorem with synthetic and real data analysis. We also show that our algorithm outperforms several other sparse PCA approaches especially when the observed entries have good structural properties. As a by-product of our analysis, we provide two theorems to handle a deterministic sampling scheme, which can be applied to other matrix-related problems.