Quantitative analyses in secondary ion mass spectrometry (SIMS) become possible only if ionization processes are controlled. The Storing Matter technique has been developed to circumvent this so-called matrix effect, primarily for inorganic samples, but has also been extended to organic samples. For the latter, it has been applied to polystyrene in order to investigate the extent of damage in the polymer, its fragmentation during the sputter deposition process and the effect of the deposition process on the spectra taken by Time-of-Flight SIMS (ToF-SIMS). In this work, a multi-technique approach, which employs the Storing Matter technique for deposition and ToF-SIMS and X-ray photoelectron spectroscopy for characterization, is used to enhance the control of the deposition process, including the thickness of the deposit, the alteration of the source film and the influence of polymer composition on the Storing Matter process. Poly (methyl methacrylate) (PMMA) is used for this work. More detailed information about the sticking of polymer fragments on the metal collector is obtained by density functional theory calculations. This work allows for the conclusion that a part of the fragments deposited on the collector surface diffuses on the latter, reacts and recombines to form larger fragments. The behaviour observed for PMMA is similar to polystyrene, showing that oxygen has no major influence on the processes occurring during the sputter deposition process. Additionally, we have developed a new methodology using 2D ToFSIMS images of the deposit tomonitor the deposit thickness and to identify surface contaminations. The latter are not only located at the position of the deposit but all over the collector surface.