MS/MS applications in biological problems Donata Favretto and Pietro Traldi zyxwvu CNR, Area della Ricerca di Padova, Corso Stati Uniti zyxwvu 4, 1-35020 Padova, Italy In m y room, the world is beyond m y understanding; But when zyxwvutsr 1 walk I see that it consists of three or four Hills and a cloud. zyxwvuts Wallace Stevens I. INTRODUCTION When the preparation of the present review was proposed to us, our first feeling was one of embarrassment. Although the proposal seemed to us a challenging and stimulating task, the availability of recent books (1-8) and reviews (9-18) on the subject or the wide use of MS/MS in the biomedical field (reflected by the correspondingly large amount of published papers) made us quite skeptical of the possibility of producing a valuable, new, and complete report on this topic. However, we decided to try, and this review represents the result of our work, certainly being neither exhaustive nor complete (for which we apologize, in particular for the possible omission of some references), but we hope it will be easy to read and will lead to some meditation. As described by Hill (15), the sensitivity of an analytical technique can be easily defined in terms of the relationship between the variations in measured signal (As) and analyte concentration (Ac). Such a relationship, called response, would in principle consist of a straight line and the sensitivity can be defined in terms of its slope. As an example, let us consider three different analytical methods leading to three different straight lines, as those given in Fig. 1: method 1 should show the highest sensitivity, but in principle all three methods would have the same detection limit, corresponding to a zero concentration of the analyte. Moving from the theoretical to the real world, it must be considered that the signal corresponding to the analyte overlaps with a nonspecific signal, called "noise," that strongly influences the detection limit. Because of the presence of noise, it has become common practice to define the detection limit for a minimal signal-to-noise (SIN) ratio, for which the value of 3 is often considered to be appropriate. From the above considerations, the signal-to-noise ratio of a specific measurement is a highly relevant number in any analytical determi- nation. Mass Spectrometry Reviews, 1993, 12, 313-395 zyxwv 0 1994 by John Wiley zyxwvutsr & Sons, Inc. CCC 0277-7037/ 94 /05 / 60313-83