The central dogma of biology dictates that sequence information encoded in DNA is transferred via transcription to RNA and through translation encodes a protein. While this provides one level of control, the majority of DNA, RNA and proteins are fine-tuned through chemical modifications that modulate their structure and function. Proteomics by liquid chromatography/mass spectrometry (LC-MS/MS) is an unbiased view into the world of these modifications by providing a tool to uncover their regulation and function. Specifically, the study of RNA modifications has exploded due to the parallel advancement of next generation sequencing and LC-MS/MS, but these technologies are incomplete due to the inability to capture the full depth of RNA modifications in robust manner. In this work, we designed new methods for the study of RNA modifications by creating a platform focused solely on improving the RNA MS. Separately, we have applied new methods in LC-MS/MS to virus biology to uncover how post-translational modifications (PTMs) of proteins govern RNA-protein interactions (RPIs). To this end, we investigated how PTMs are globally affected by adenovirus infection and uncovered key PTMs required for viral protein function. We identified a striking loss of arginine methylation due to the shuttling of protein arginine methyl transferase 1 (PRMT1) into the cytoplasm, away from nuclear RBPs. Overall, both works provide advances in mass spectrometry methods and illustrate their application, providing the tools to ask deeper questions about RNA and protein modifications and viral biology.