<p>Translational research utilizing mass spectrometry to identify and validate biomarkers requires high-quality samples to maintain the integrity of research results. Key steps, including study design and sample/data quality control, are often overlooked or undervalued, which can compromise the consistency, accuracy, and verifiability of scientific and clinical outcomes. This is a prospective, longitudinal, multicenter cohort clinical trial that is recruiting participants who are victims of snakebite in Brazil and healthy individuals. Previously published studies on clinical trials and clinical-epidemiological research related to snakebites have identified universal measures and their categories, which were used to develop the study design and prepare the Case Report Forms. The biorepository presents a collection of clinical and epidemiological data, images of clinical manifestations, results of laboratory tests, and biological samples (serum and plasma in the presence of EDTA and sodium citrate). This article presents recommendations for essential steps in designing and implementing a mass spectrometry-based biomarker and mechanistic study focused on snakebite envenomation. We outline critical reporting models for conducting each phase of clinical data acquisition, such as collecting biological materials (serum and blood plasma) and processing samples to minimize the study’s pre-analytical variables. The guidelines provided, covering everything from study design to implementation and data interpretation, serve as a reference to increasing the rigor and reproducibility of clinical proteomics studies. The results of this study can transcend basic research, connecting technological development to real clinical application, optimizing diagnosis and monitoring, but also contributing to reducing the economic burden, morbidity and mortality associated with these accidents.</p>