Atrial Fibrillation (AF) is the most common cardiac arrhythmia. The incidence and prevalence are expected to increase in the next 30 years by 63% and 66% respectively1. As a multigenic disorder, an understanding of the molecular cascades and the cross-communication between total ion exchange and cellular stress in AF is essential for designing effective AF therapies. Mis-regulation of regulatory proteins in the endocytic pathway, including endo-lysosomes and lysosomes, has been reported in AF2. The discovery of the cardiac lysosome Ca2+ signaling3 has opened a new door to unravel the underlying molecular mechanisms of acidic organelles in AF. Organelle isolation using tissue biopsies facilitates studies investigating the roles of regulatory proteins within these pathways. We developed an endo-lysosome isolation method from tissue biopsies using Percoll and sucrose differential density gradient centrifugation. We present what we believe to be the first comprehensive dataset of C. porcellus endo-lysosomal focused organelle proteomics using label free MS/MS peptide analysis (QExec LumosTM mass spectrometer) on isolated endo-lysosomes from C. porcellus atrial tissue. Experiments performed in accordance with Home Office Guidance on the Animals (Scientific Procedures) Act (1986). Mass spectrometry data from biological replicates (n = 3) were processed and analysed using Max-quant and Perseus software (v1.5.2.4) to identify proteins. Robust criteria was used for filtration and imputation, and significantly upregulated/downregulated proteins in endo-lysosome (EL) and tissue lysate (TL) fractions were identified by volcano plot. The highest abundant EL proteins were separated using cell component filtration in Gene Ontology (GO) analysis, the molecular function was identified using the PANTHER pathway, and functional network interactions were mapped using Cytoscape analysis (v3.7.2). The presence of the EL marker proteins Lysosome associated membrane protein 2 (LAMP2), beta-Galactosidase (GLB), beta-hexosaminidase (HEXB) and the absence of mitochondrial marker Cytochrome oxidase IV (COX IV) and sarcoplasmic reticulum marker Phospholamban were confirmed by Western blot and enzyme assays.  Our EL preparations demonstrate the enrichment of lysosomal markers GLB, HEXB, Ras-related protein Rab-7a and LAMP2, and identify multiple protein hits relevant to diseases that have been linked to dysfunctional lysosomal enzymes and membrane-bound proteins. These include; lysosomal α-glucosidase (GAA), a key lysosomal enzyme involved in the degradation of glycogen in lysosomes4; Cathepsin A, which serves a protective function by regulating stability and activity of beta-galactosidase, neuraminidase enzymes and plays a role in galactosialidosis5; Clusterin, identified as a potential biomarker for mucopolysaccharidosis; and Decorin, a protein that, when dysregulated, contributes to cardiac fibrosis or fibrotic stiffness. Furthermore, we identified glycogen phosphorylase, brain form (PYGB) in the EL fraction, a lysosomal enzyme that regulates glycogen mobilization, and plays a prominent role as the only marker protein elevated in the early-stage of asymptomatic patients with lysosomal storage disease Fabry disease. In addition, we identified a major complement of lysosomal cathepsins in our proteomic data that have been linked with cardiovascular diseases, such as cathepsins B, C, D and Z.  The successful identification of such disease related proteins highlights the potential usage of these techniques in understanding the role of lysosomal proteins in complex cardiac diseases such as AF.