Good mass spectrometry and its place in good science Mark W. Duncan a,b,c * The mass spectrometry community has expanded as instruments became more powerful, user-friendly, affordable and readily available. This opens up opportunities for novice users to perform high impact research, using highly advanced instrumentation. This introductory tutorial is targeted at the novice user working in a research setting. It aims to offer the benefit of other people’ s experiences and to help newcomers avoid known pitfalls and problematic issues. It discusses some of the essential features of sound analytical chemistry and highlights the need to use validated analytical methods that provide high quality results along with a measure of their uncertainty. Examples are used to illustrate potential pitfalls and their consequences. Copyright © 2012 John Wiley & Sons, Ltd. Keywords: proteomics; quantification; precision; accuracy; certainty; fitness-for-purpose GENERAL INTRODUCTION The sphere of influence of the mass spectrometrist is enormous. Mass spectrometry is central to environmental testing (e.g. to detect, identify and quantify the nature and source of pollutants in our environment), forensics (e.g. to aid in enforcing the law through detection and identification of drugs, toxicological testing and crime scene analysis), drug development (e.g. to provide data at all stages of the drug development process relating to issues such as mechanism of action, uptake, metabolism and dose), clinical chemistry (e.g. the analysis of bodily fluids to aid in the diagno- sis and/or management of patients), workplace testing (e.g. detection of drugs of abuse), drug testing in sports (e.g. detection of performance-enhancing agents including steroids, erythropoietin, growth hormone, stimulants and novel synthetics), monitoring and ensuring fair gambling (e.g. detection and quantification of performance-affecting substances in horse and dog racing) and in many other facets of both basic and applied research. It is true that the cost of carrying out these measurements properly is high, but the stakes are even higher because decisions made on the basis of these results have far-reaching conse- quences. For example, tests confirming the presence of an illicit drug may result in fines, jail terms or even execution in some countries; similarly, identification of environmental contaminants can initiate costly remediation and give rise to hefty fines. In many circumstances, there are powerful financial incentives to perform mass spectrometry to the highest standards and to generate validated data – after all, so much rides on the outcome. Although it is not always appreciated, the stakes are no less significant in a research environment, regardless of the discipline, because the mass spectrometric data will steer the future course of research by providing evidence to either support or falsify a current hypothesis, model or theory. WHY DOES POOR ANALYTICAL SCIENCE OCCUR AS FREQUENTLY AS IT DOES? Although mass spectrometers are becoming increasingly easy to operate with each new generation, the task of performing sound analytical science with them is no less complicated than it has always been. Experienced analytical scientists appreciate the need to use validated methods and to generate good quality data, but poor quality work is sometimes performed, makes its way into the literature, and all too frequently, it changes the course of scientific research. This unfortunate outcome is increasingly common for two reasons. First, there is an increasing tendency for individuals unskilled in the practice of analytical chemistry to purchase their own instru- ment, perform their own studies and generate their own data. Manufacturers have introduced devices to the market that are easy to use, but operating an instrument proficiently is only the first step in performing sound analytical science. The second reason for poor analytical science is less obvious, but no less significant. Top end mass spectrometers remain expensive and difficult to acquire and operate. They are therefore frequently located in central resources where the expertise to maintain and operate them is concentrated. In this setting, the resource and its staff have an obligation to provide results that are fit for the intended purpose of the ‘client’, but this can only happen if there is the intellectual ‘buy-in’ of the core personnel. Both parties must discuss and agree on issues such as the scien- tific problem and the specific objectives of the analytical work, any existing methods and their characteristics, and any relevant data reported in the literature. With these issues in mind, both analyst and client need to cooperatively develop an optimal * Correspondence to: Mark W. Duncan, Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Denver-School of Medicine, MS 8106, 12801 E. 17th Ave, RC 1 South Aurora, Colorado 80045, USA. E-mail: mark.duncan@ucdenver.edu a Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, University of Colorado Denver-School of Medicine, MS 8106, 12801 E. 17th Ave, RC 1 South, Aurora, Colorado 80045, USA b Biodesix Inc., Boulder, Colorado, USA c Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh, 11461, Saudi Arabia J. Mass. Spectrom. 2012, 47, 795–809 Copyright © 2012 John Wiley & Sons, Ltd. Special Feature: Tutorial Received: 14 February 2012 Revised: 10 May 2012 Accepted: 18 May 2012 Published online in Wiley Online Library (wileyonlinelibrary.com) DOI 10.1002/jms.3038 795