Background: The advent of tandem mass spectrometry (MS/MS) had an essential role in the expansion of newborn screening (NBS) for different inborn errors of metabolism (IEMs). Nowadays, almost 50 IEMs are screened in Italy. The use of second-tier tests (2-TTs) in NBS minimizes the false positive rate; nevertheless, the metabolic profile is influenced not only by the genome but also by environmental factors and clinical variables. We reviewed the MS/MS NBS data from over 37,000 newborns (of which 8% required 2-TTs) screened in the Italian Abruzzo region to evaluate the impact of neonatal and maternal variables on propionate-related primary biomarker levels. Methods: Expanded NBS and 2-TT analyses were performed using MS/MS and liquid chromatography–MS/MS methods. We set up layered cut-offs dividing all 37,000 newborns into categories. Statistical analysis was used to create alarm thresholds for NBS-positive samples. Statistically significant differences were found in both neonatal and maternal conditions based on the 2-TTs carried out. According to the stratified cut-offs, only 1.47% of the newborns would have required a 2-TT while still retaining the ability to recognize the true-positive case of methylmalonic acidemia with homocystinuria, which has been identified by NBS. To further support the clinical applicability, we performed an external evaluation considering nine positive cases from an extra-regional neonatal population, confirming the potential of our model. Interestingly, the setting of alarm thresholds and their application would allow for establishing the degree of priority/urgency for 2-TTs. Conclusions: Tailoring NBS by customized cut-offs may enhance the application of precision medicine, focusing on true-positive cases and also reducing analysis costs and times.

Lysosomal Storage Diseases (LSDs) include roughly 70 inherited metabolic disorders, most of which are expressed in an autosomal recessive pattern. These conditions arise from mutations in genes encoding lysosomal enzymes, leading to intracellular buildup of substrates and subsequent lysosomal dysfunction. LSDs can be broadly classified based on the nature of the stored substrate, encompassing Sphingolipidoses, Mucopolysaccharidoses, Lysosomal Glycogen Storage Disease, Oligosaccharidoses, Mucolipidoses, and Lysosomal Proteinoses. Although individually rare, LSDs collectively affect approximately 1 in 5000 live births. They usually manifest in childhood, but adult-onset types are also detected. Clinical manifestations are heterogeneous and may involve the central nervous system, skeletal system, skin, heart, muscles, kidneys, and other organs. Several therapeutic strategies are available for LSDs, including Enzyme Replacement Therapy to restore deficient enzymes, Hematopoietic Stem Cell Transplantation to provide functional donor-derived cells, Substrate Reduction Therapy and pharmacological chaperones to modulate substrate turnover or enhance enzyme stability, alongside symptomatic and supportive treatments. Ongoing research is also exploring gene therapy-based strategies. Current diagnostic criteria remain insufficient for reliable presymptomatic diagnosis, highlighting the need for more sensitive and specific approaches. In this context, untargeted metabolomics is a powerful strategy to investigate pathogenic pathways, identify novel diagnostic and prognostic biomarkers, and uncover potential therapeutic targets. Accordingly, this review provides an overview of LSDs, focusing on untargeted metabolomics studies and their contribution to the discovery of novel biomarkers and previously unrecognised pathogenic mechanisms relevant to diagnostic and therapeutic innovation.