Cells either in response to stimulus or in homeostasis require dynamic signaling through alterations in protein composition. Identification and temporospatial profiling of post translational modifications constitutes one of the most challenging tasks in biology. These challenges comprise both experimental and computational aspects. From the computational point of view identification of post translational modifications by mass spectrometry analysis frequently leads to algorithms with exponential complexity which in practice is approached by algorithms with lower complexity. Regulation of post translational modifications has been implicated in a number of diseases such as cancer, neurodegenerative diseases and metabolic diseases. Furthermore, some post translational modifications are considered as biomarkers and surrogate markers. Consequently, there is a high interest in methodologies that can identify and quantify post translational modifications. We found few papers addressing the issue of which modifications should be considered in a standard database dependent search of MS data for protein analysis. Furthermore, the few papers on the topic are from a time where MS instruments with high precision in both MS and MS/MS were not available. Therefore, based on literature search and extensive analysis we provide recommendations on post translational modifications to be included in mass spectrometry database searches of MS data with high precision in both MS and MS/MS (e.g. <5 ppm).