The Expanding Role of Mass Spectrometry in Biotechnology Second Edition The Expanding Role of Mass Spectrometry in Biotechnology Second Edition Gary Siuzdak The Scripps Research Institute MCC Press San Diego Copyright © 2006 by MCC Press All rights reserved The cover art is derived from a painting by Marianne Wendeborn "All you have to decide is what to do with the time that is given to you." - anonymous, from a 14th century manuscript "Clouds of Consciousness" as translated by Monika Hasserodt Preface My first book "Mass Spectrometry for Biotechnology" introduced the capabilities of mass spectrometry and improvements during the period between 1985 and 1994. These developments continued and were largely covered in the 2003 first edition of The Expanding Role of Mass Spectrometry in Biotechnology. This 2nd edition includes further improvements to the graphics and descriptions as well as covering new advances in mass spectrometry technology. Acknowledgments I express my sincere gratitude to my friends and colleagues (following page) who helped review and edit this manuscript, especially Liz Want and Michael Greig for their contributions to chapters 8 and 9. The editing imprint of Jennifer Bardi can be found on almost every page of the first three chapters and I also thank Darlene Custodio for her extraordinary effort in putting this book together from cover to cover. I am also grateful to Richard Lerner who has created an environment at Scripps that fosters interdisciplinary research, in which the development and application of mass spectrometry thrive. vi vii Table of Contents PREFACE .................................................................................................. vi ACKNOWLEDGMENTS......................................................................... vi TABLE OF CONTENTS ........................................................................viii A MASS SPECTROMETRY HISTORY ..............................................xiii EARLY MASS SPECTROMETRY – THE PHYSICAL ROOTS..........................xiii IMPROVING THE MASS ANALYZER: BRANCHING INTO CHEMICAL AND BIOLOGICAL APPLICATIONS ..................................................................... xv IMPROVEMENTS IN IONIZATION: BLOSSOMING INTO BIOLOGY...............xvii SMALL MOLECULE ANALYSIS AND PROTEIN CHARACTERIZATION: MATURATION.......................................................................................... xix THE LIMITS OF BIOLOGICAL MASS SPECTROMETRY: TOWARD WHOLE ORGANISM ANALYSIS ............................................................................. xxi HISTORICAL DEVELOPMENTS IN MASS SPECTROMETRY ........................xxii USEFUL REFERENCES ............................................................................xxiii CHAPTER 1: IONIZATION AND THE MASS SPECTROMETER .. 1 PERSPECTIVE.............................................................................................. 1 WHAT IS MASS SPECTROMETRY?............................................................... 2 Some Basics............................................................................................ 3 Sample Introduction Techniques ............................................................ 3 IONIZATION ................................................................................................ 6 Protonation............................................................................................. 6 Deprotonation ........................................................................................ 6 Cationization .......................................................................................... 7 Transfer of a charged molecule to the gas phase................................... 7 Electron ejection..................................................................................... 8 Electron capture..................................................................................... 8 IONIZATION SOURCES............................................................................... 10 Electrospray Ionization ........................................................................ 11 Electrospray Solvents........................................................................... 15 Configuration of the Electrospray Ion Source...................................... 16 Nanoelectrospray Ionization (NanoESI) .............................................. 17 Atmospheric Pressure Chemical Ionization ......................................... 19 Atmospheric Pressure Photoionization ................................................ 20 Matrix-Assisted Laser Desorption/Ionization (MALDI)....................... 21 Desorption/Ionization on Silicon (DIOS)............................................. 26 Fast Atom/Ion Bombardment ............................................................... 27 Electron Ionization............................................................................... 29 Chemical Ionization ............................................................................. 31 SUMMARY ................................................................................................ 36 QUESTIONS............................................................................................... 36 viii USEFUL REFERENCES ............................................................................... 37 CHAPTER 2: MASS ANALYZERS...................................................... 39 PERSPECTIVE............................................................................................ 39 MASS ANALYSIS ...................................................................................... 39 Performance Characteristics ............................................................... 41 Accuracy............................................................................................... 41 Resolution (Resolving Power).............................................................. 42 Mass Range .......................................................................................... 43 n Tandem Mass Analysis (MS/MS or MS ).............................................. 43 Scan Speed ........................................................................................... 44 MASS ANALYZERS ................................................................................... 45 Quadrupoles......................................................................................... 45 Quadrupole Ion Trap ........................................................................... 47 Linear Ion Trap.................................................................................... 49 Ion Trap’s Limitations: Precursor ion scanning, “1/3 rule” & Dynamic range .................................................................................................... 50 Double-Focusing Magnetic Sector....................................................... 50 Quadrupole Time-of-Flight Tandem MS.............................................. 51 The MALDI with Time-of-Flight Analysis............................................ 54 Quadrupole Time-of-Flight MS............................................................ 55 Fourier Transform Mass Spectrometry (FTMS) .................................. 56 Ion Detectors........................................................................................ 63 Electron Multiplier............................................................................... 64 Faraday Cup ........................................................................................ 65 Photomultiplier Conversion Dynode.................................................... 65 Array Detector ..................................................................................... 66 Charge (or Inductive) Detector............................................................ 66 VACUUM IN THE MASS SPECTROMETER ................................................... 68 OVERVIEW ............................................................................................... 69 QUESTIONS............................................................................................... 70 USEFUL REFERENCES ............................................................................... 70 CHAPTER 3: PRACTICAL ASPECTS OF BIOMOLECULAR ANALYSIS................................................................................................ 73 PERSPECTIVE............................................................................................ 73 QUANTITATION ........................................................................................ 74 CALCULATING MOLECULAR WEIGHT ...................................................... 76 ISOTOPE PATTERNS .................................................................................. 78 SOLUBILITY.............................................................................................. 80 TIMING..................................................................................................... 81 CALIBRATION/ACCURACY ....................................................................... 81 SAMPLE PURITY AND CLEAN CONTAINERS .............................................. 84 SENSITIVITY / SATURATION...................................................................... 87 IONIZATION CHARACTERISTICS................................................................ 88 MATRIX SELECTION/PREPARATION.......................................................... 89 ix OVERVIEW ..............................................................................................