Determination of the deposition order of different writing tools is very important for the forensic investigation of questioned documents. Here we present a novel application of two Ion Beam Analysis (IBA) techniques: Secondary Ion Mass Spectrometry using MeV ions (MeV-SIMS) and Particle Induced X-ray Emission (PIXE) to determine the deposition order of intersecting lines made of ballpoint pen ink, inkjet printer ink and laser printer toners. MeV-SIMS is an emerging mass spectrometry technique where incident heavy MeV ions are used to desorb secondary molecular ions from the uppermost layers of an organic sample. In contrast, PIXE provides information about sample elemental composition through characteristic X-ray spectra coming from greater depth. In the case of PIXE, the information depth depends on incident ion energy, sample matrix and self-absorption of X-rays on the way out from the sample to the X-ray detector. The measurements were carried out using heavy ion microprobe at the Ruđer Bošković Institute. Principal Component Analysis (PCA) was employed for image processing of the data. We will demonstrate that MeV-SIMS alone was successful to determine the deposition order of all intersections not involving inkjet printer ink. The fact that PIXE yields information from deeper layers was crucial to resolve cases where inkjet printer ink was included due to its adherence and penetration properties. This is the first time the different information depths of PIXE and MeV-SIMS have been exploited for a practical application. The use of both techniques, MeV-SIMS and PIXE allowed the correct determination of deposition order for four out of six pairs of samples.