In tandem mass spectrometry experiments, the spectra relating peak intensity to the mass-to-charge of the ions is used to identify the peptides in a sample. However, multiple factors influence the spectra profile. An all-encompassing model that describes tandem mass spectra intensity and can offer insights into the factors that influence ion intensity was developed and applied to 61,543 mouse peptides. Several factors had a significant association with the intensity of ions formed. Among these factors are: the type of ions formed after the fragmentation of peptides, the residue content of the fragmenting peptide, proton mobility, neutral mass loss and peptide-ion charge combination. The results from our model support the precise prediction and realistic simulation of mass spectra and augment the understanding of the factors influencing ion intensity in mass spectrometry experiments.