LC-MS-Based Metabolomics and Proteomics Sample Preparation of Urine: Methods and Multi-Omics Integration

Urine is an ideal biological fluid due to the highly metabolomic and proteomic information it provides and its easy collection in large amounts. Urinary biomarkers reported for different types of diseases included the urological tract and systemic diseases. Although the most common approach in omics is single-omics studies, combining multi-omics biomarkers such as metabolomics, proteomics, transcriptomics, and genomics can improve diagnostic accuracy and provide deeper insights into disease mechanisms than single biomarkers. The gold standard technique for bioanalysis is liquid chromatography coupled to mass spectrometry (LC-MS/MS) due to its high sensitivity, specificity, and selectivity for the analysis of metabolites and proteins in complex biological samples. One of the most important aspects in metabolomics and proteomics is sample extraction and preparation before the analysis. Different types of metabolites and protein extraction methods can be used effectively for urine samples, including protein precipitation, liquid-liquid extraction, and solid-phase extraction. However, in the multi-omics approach integrating metabolomics and proteomics, sample preparation could be either individual for each or simultaneous for both from a single sample. In this chapter, we discuss aspects of LC-MS-based metabolomics and proteomics sample preparation, as well as their integration for a multi-omics approach. In clinical practice, the reported sample preparation methods for bladder cancer metabolomics and proteomics were also discussed.