Let ($\Omega^{\ast}(M), d$) be the de Rham cochain complex for a smooth
compact closed manifolds $M$ of dimension $n$. For an odd-degree closed form
$H$, there are a twisted de Rham cochain complex $(\Omega^{\ast}(M),
d+H_\wedge)$ and its associated twisted de Rham cohomology $H^*(M,H)$. We show
that there exists a spectral sequence $\{E^{p, q}_r, d_r\}$ derived from the
filtration $F_p(\Omega^{\ast}(M))=\bigoplus_{i\geq p}\Omega^i(M)$ of
$\Omega^{\ast}(M)$, which converges to the twisted de Rham cohomology
$H^*(M,H)$.
We study the twisted cohomology groups of $A_\infty$-algebras defined by
twisting elements and their behavior under morphisms and homotopies using the
bar construction. We define higher Massey products on the cohomology groups of
general $A_\infty$-algebras and establish the naturality under morphisms and
their dependency on defining systems. We construct a spectral sequence
converging to the twisted cohomology groups an show that the higher
differentials are given by the $A_\infty$-algebraic Massey products.
For two complex vector bundles admitting a homomorphism with isolated
singularities between them, we establish a Poincar\'e-Hopf type formula for the
difference of the Chern character numbers of these two vector bundles. As a
consequence, we extend the original Poincar\'e-Hopf index formula to the case
of complex vector fields.