Background: Recently, next-generation genomic sequencing has shown potential as an accurate predictor of phenotype and for understanding genes conferring antibiotic resistance (AMR) in bacterial communities. In the clinic, antibiotic disc assays can provide a visual indication of the type and strength of AMR in an isolate, but do not observe the phenotype on a molecular level. Aim & Objectives: Our research aims to understand the AMR capabilities of an isolate on a molecular level through examination of its genome and proteome, with and without antibiotic challenge. This research seeks to connect AMR genes to gene end-products on the proteoform-level (peptides, proteins, post-translational modifications), which has yet to be experimentally shown. Methods: Long- and short-read genomic sequencing and assembly was conducted in-house on multi-drug resistant E. coli isolates to ascertain the presence of AMR-related genes and antibiotic disc assays were performed to visualise phenotypic effectiveness for related-AMR. To correlate phenotype with genotype on a molecular level, a shotgun proteomics pipeline using LC-MS/MS was used to generate data on proteome changes with and without antibiotic challenge. PEAKS Studio was used to analyse this data, and UniProt and STRING databases were used to assess the significance of reported protein and protein interactions implicated in AMR. Results: Several interesting proteins related to AMR were upregulated, despite no antibiotic challenge, including proteins previously annotated as hypothetical and multi-drug resistance proteins. Conclusion: This research establishes that proteomic techniques validate the potential for genomic sequencing to replace current clinical tests and provide more specificity in selecting the right antibiotic in the clinic. Our research findings are significant for being the first to experimentally link an AMR-related gene to the AMR-related protein using a systems biology approach.