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Since single biomarkers are generally of limited accuracy, a group or panel of well\u2010characterized biomarkers appears appropriate, providing a more robust and sensitive <jats:styled-content style=\"fixed-case\">MS<\/jats:styled-content>\u2010based analytical platform. <jats:styled-content style=\"fixed-case\">CE<\/jats:styled-content> coupled to <jats:styled-content style=\"fixed-case\">MS<\/jats:styled-content> has been successfully used in biomarker discovery and application, as it enables the selective detection of peptides and small proteins, combining the high separation capacity of <jats:styled-content style=\"fixed-case\">CE<\/jats:styled-content> with the advanced sensitivity of <jats:styled-content style=\"fixed-case\">MS<\/jats:styled-content>. <jats:styled-content style=\"fixed-case\">CE<\/jats:styled-content>\u2010<jats:styled-content style=\"fixed-case\">MS<\/jats:styled-content> allows the characterization of highly complex samples (such as urine, plasma, and other biofluids) in a consistent and reproducible way. It has a range of applications, many focusing especially in studies on urinary peptide biomarkers in kidney and cardiovascular diseases. Another major field of interest has been malignancy of the genitourinary system. In the first part of this review, we cover technical aspects and performance characteristics of <jats:styled-content style=\"fixed-case\">CE<\/jats:styled-content>\u2010<jats:styled-content style=\"fixed-case\">MS<\/jats:styled-content>, with special focus on the requirements for biomarker discovery and clinical application. In the second part, we review the potential and development of <jats:styled-content style=\"fixed-case\">CE<\/jats:styled-content>\u2010<jats:styled-content style=\"fixed-case\">MS<\/jats:styled-content> in the management of genitourinary cancers, especially bladder cancer. <jats:styled-content style=\"fixed-case\">CE<\/jats:styled-content>\u2010<jats:styled-content style=\"fixed-case\">MS<\/jats:styled-content> has been employed in several studies aimed at discovering biomarkers for bladder cancer that may be useful in diagnosis, monitoring for recurrence, and prediction of the risk for the muscle\u2010invasive stage. 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