Several spectroscopic techniques are utilized complementarily for structure elucidation. The most important are mass spectrometry (MS), nuclear magnetic resconance (NMR) and infrared spectroscopy (IR). Mass spectrometry offers the possibility to determine molecular weight and fragmentation patterns. High-resolution mass spectrometry with determination of accurate mass, can be used to calculate the elemental composition of an unknown molecule. Tandem mass spectrometry (QTOF (MS/MS) or IonTrap (MS)n) can be utilized to perform isolation and fragmentation which is helpful to explore the structure of an unknown compound.

NMR is an extremely powerful tool for structure elucidation, especially in combination with MS. Proton and carbon NMR with computer assisted structure elucidation (CASE), gives searchable libraries and efficient recognition of chemical structures. One drawback with NMR is, however, the need for pure samples in milligram amounts. For this reason, purification of biological extracts is mandatory prior to NMR analysis.

Preparative liquid chromatography (HPLC) is used for purification of compounds from biological extracts after fermenting. The HPLC systems operate with chromatographic separation columns with mobile phase flow up to 100 mL per minute and a loading capacity of several milligrams of compound on column. However, in some cases the preparation of one mg of pure compound may require several days of chromatographic work. In addition to preparative HPLC, solid phase (SPE) and liquid-liquid extraction methodology is used to purify extracts.

Determination of chemical structure is an important activity within several research areas of the department. Examples are bioprospecting, production of biopharmaceuticals and identification of degradation products in process chemistry.