Smith M, Thickitt C. Rapid Commun Mass Spectrom. 2009 Sep;23(18):3018-22. Ion trap multiple mass spectrometry (IT-MS) coupled with sample pretreatment has been applied to elucidate the structure of a sulphated pentasaccharide impurity seen in fondaparinux. Valuable structural information was generated through sequential MS^10 fragmentation by isolating specific adducts and assessing their fragmentation pathways. After isolation by preparative ion chromatography, the subject impurity was converted into the ammoniated salt to make it more amenable to IT-MS^n. The
freeze-dried product was dissolved in water and introduced via an infusion pump into a Thermo Fisher LTQ-Orbitrap mass spectrometer.