Mass spectrometry (MS) is increasingly used in clinical laboratories due to its specificity, sensitivity, and speed. However, ion suppression, caused by nonvolatile compounds, can interfere with ionization efficiency and affect detection. Ion suppression is influenced by factors such as sample matrix, coeluting compounds, and ion-pairing agents. Common suppressors include salts, ion-pairing agents, endogenous compounds, drugs, and proteins. Ion suppression can be evaluated through experimental protocols, including signal recovery studies and postcolumn infusion of analytes. Strategies to minimize ion suppression include enhanced sample cleanup, chromatographic changes, reagent modifications, and internal standardization. Ion suppression can also occur in other MS techniques like Fourier transform mass spectrometry (FTMS), matrix-assisted laser desorption/ionization (MALDI), and surface-enhanced laser desorption/ionization (SELDI). To counter ion suppression, alternatives to trifluoroacetic acid (TFA) in mobile phases, such as acetic or formic acid, can be used. Additionally, modifying chromatographic conditions or using internal standards can help mitigate ion suppression effects. Ion suppression studies should be performed when developing MS assays to ensure accurate and reliable results.Mass spectrometry (MS) is increasingly used in clinical laboratories due to its specificity, sensitivity, and speed. However, ion suppression, caused by nonvolatile compounds, can interfere with ionization efficiency and affect detection. Ion suppression is influenced by factors such as sample matrix, coeluting compounds, and ion-pairing agents. Common suppressors include salts, ion-pairing agents, endogenous compounds, drugs, and proteins. Ion suppression can be evaluated through experimental protocols, including signal recovery studies and postcolumn infusion of analytes. Strategies to minimize ion suppression include enhanced sample cleanup, chromatographic changes, reagent modifications, and internal standardization. Ion suppression can also occur in other MS techniques like Fourier transform mass spectrometry (FTMS), matrix-assisted laser desorption/ionization (MALDI), and surface-enhanced laser desorption/ionization (SELDI). To counter ion suppression, alternatives to trifluoroacetic acid (TFA) in mobile phases, such as acetic or formic acid, can be used. Additionally, modifying chromatographic conditions or using internal standards can help mitigate ion suppression effects. Ion suppression studies should be performed when developing MS assays to ensure accurate and reliable results.