Advances in analytical methodology for speciation of manganese in pine nuts are presented in this work. The approach is based on the use of orthogonal chromatographic systems, namely size-exclusion chromatography (SEC) of the extracts and strong anion exchange (IEC) of the fractions collected by the first column. In both columns, manganese elution is first monitored by a quadrupole inductively coupled plasma mass spectrometry (ICP-MS) instrument equipped with an octopole reaction cell and an ultraviolet (UV) detector. SEC is performed by using two columns covering the molecular weight range from <10 to 70 kDa that allows an initial screening of the molecular weight of the Mn species. The higher resolution capability of the low molecular weight range column is the reason to use the latter for further experiments. The fraction from SEC-ICP-MS in which Mn is present at highest concentration is submitted to IEC-ICP-MS allowing Mn-citrate and MnCl(2) identification by retention time matching with standards. The concentration of these species is estimated to be 75 and 125 microg kg(-1) (as Mn), respectively, in the pine nuts samples and the presence of Mn-citrate is confirmed by nanoelectrospray ionization quadrupole time-of-flight mass spectrometry (nESI-QqTOF-MS). In the same fraction, a third Mn-containing peak is detected in the IEC-UV-ICP-MS chromatogram. This peak corresponds to a protein containing Mn that was later submitted to a tryptic digestion and analyzed by nESI-QqTOF. The MS/MS data of a doubly charged peptide are used to obtain the sequence of the protein with the Mascot search engine. The peak turned out to be isocitrate dehydrogenase, a protein commonly associated with Mn.