The metal salts ubiquitously present in biological samples cause serious ion suppression, capillary clogging and signal fluctuation in ESI/nESI. Herein, a current-limited high voltage polarity reversing approach was applied for the online separation of intrinsic metal ions in biological samples, resulting in the generation of protonated analytes at the nESI tip for mass analysis without interference from salt cations. Stable and durable signals (∼30-60 s) were observed for protonated proteins, peptides and metabolites in complex biological samples, including liquids, solids and viscous samples, even with very high salt concentration (100 mM NaCl), allowing comprehensive tandem MS analysis with on average ca. 5-times higher analyte signal intensities compared to the conventional nESI analysis. Therefore this approach offers improved performance of nESI/ESI for the sensitive molecular analysis of untreated biological samples, opening new possibilities in various disciplines, including biology, medicine, chemistry, life sciences, etc. Current-limited high voltage polarity reversing nanoelectrospray ionization allows online separation of intrinsic metal ions in complex biological samples, resulting in the generation of protonated analytes without interference from salt cations.