In the forensic investigation of questioned documents, it is often very important to know the deposition order of ink traces from two different writing tools at their intersection on a paper. In the present work, intersections of inks from several writing tools were studied using optical techniques that are standardly applied for questioned documents examination in a forensic laboratory, and an accelerator-based Ion Beam Analysis (IBA) technique called Secondary Ion Mass Spectrometry using MeV ions (MeV SIMS) that is applied in an accelerator facility. MeV SIMS provides molecular information about the studied inks from writing tools, which is an added value and can be also applied for determination of deposition order but was so far relatively rarely used in forensic studies. Aim of this paper is to compare performance of optical techniques and MeV SIMS for several combinations of intersecting lines. Cases were divided into those in which optical techniques can distinguish used inks and those which are optically completely indistinguishable. In the latter cases, we show that although mass spectra of used inks (from blue ballpoint pens) had extremely small differences, these in combination with advanced and most importantly objective multivariate algorithms could be very beneficial in resolving the deposition order at the intersection of optically indistinguishable inks. In general, MeV SIMS proved to be more efficient for oil-based inks while difficulties were encountered with water-based ones, similar to optical methods.