This chapter presents our practical experience in method development for the determination of trace amounts of DNA adducts by gas chromatography-electron capture-mass spectrometry (GC-EC-MS). We have detected femtomole amounts of such analytes by optimizing sample preparation (involving extraction, chemical reaction, and purification steps starting with a biological sample) and low-attomole amounts of pure, derivatized standards by GC-EC-MS. Although such methodology is already useful, the concepts and techniques described should extend sample preparation to the attomole level. In this chapter our work on chemical transformation is emphasized as part of sample preparation. This is a means to broaden the range of compounds that can be detected by GC-EC-MS. Also, our experience in operating a GC-EC-MS to achieve attomole detection limits routinely (for standards) is presented. New ionization techniques for MS, such as electrospray and matrix-assisted laser desorption, are increasing the ability of MS to analyze "nonvolatile" substances present even in aqueous samples. Less new but of continuing importance as a desorption/ionization technique in this respect is fast atom bombardment. In contrast, we are focusing on procedures in which significant chemical treatment of the sample precedes the "old technique" of GC to deliver the analyte into the MS. The desorption approaches are attractive because they can minimize sample preparation. They are also unique in their ability to achieve the direct detection of medium to high molecular weight biopolymers by MS. For trace organic analysis, however, the use of chemical steps to aid in the characterization and purification (including recovery) of smaller analytes by changing their physicochemical properties, coupled with the additional purification provided by GC (including the high purity of GC carrier gases), may be important.