Abstract Citrate complexes of Mn and Fe, and potentially those of Cu and Zn, are considered as important low molecular mass species in human serum and cerebrospinal fluid (CSF). For example, Mn is supposed to enter the brain under excess exposure as Mn‐citrate leading to neurotoxic effects. Mn‐citrate has been characterised in human CSF using chromatography and electrophoresis online with inductively coupled plasma mass spectrometry, but not yet with molecular mass spectrometry. Therefore, this study explores the potential of electrospray ionisation (ESI) with selected reaction monitoring (SRM) for the detection of metal‐citrate complexes, in particular Mn‐citrate. The collision‐induced dissociation of precursor ions with various metal:citrate stoichiometries was studied for Mn‐citrate, Fe‐citrate, Cu‐citrate and Zn‐citrate. High selectivity was achieved for Mn(II)‐citrate even in respect to Fe(III)‐citrate which forms isobaric precursor ions. The limit of detection for Mn‐citrate was estimated to be around 250 µg L −1 (referring to the total Mn content in the standard) using flow injection. The sensitivity was sufficient for the determination of Mn‐citrate in standard solutions and in an extract of an Mn‐citrate‐containing supplement. An improved ESI source design is expected to reduce the limits of detection significantly. The developed ESI‐SRM method has the potential to provide complementary data for the quality control of current separation methods for metal citrates using element‐selective detection, with application to biomedical samples and further matrices. Copyright © 2009 John Wiley & Sons, Ltd.