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B American Society for Mass Spectrometry, 2011

J. Am. Soc. Mass Spectrom. (2011) DOI: 10.1007/s13361-011-0086-z

BOOK REVIEW Practical Aspects of Trapped Ion Mass Spectrometry Volumes IV and V Raymond E. March and John F. J. Todd, Editors CRC Press: Taylor & Francis Group Boca Raton, FL, USA Volume IV ISBN: 978-1-4200-8371-2 Volume V ISBN: 978-1-4200-8373-6 2010, Volume IV: 922 pp plus xxviii; Volume V: 534 pp plus xxxi; $179.95 each Reviewed by: O. David Sparkman University of the Pacific, Department of Chemistry, 3601 Pacific Avenue, Stockton, CA 95211, USA e-mail:


ifteen years ago, when the three volumes of Practical Aspects of Ion Trap Mass Spectrometry, edited by March and Todd (a 1268-page, 30-chapter work) were published, the ion trap was clearly understood to mean the quadrupole ion trap (QIT) described by Wolfgang Paul. Although the Penning (magnetic) trap was known through the 1989 Nobel Prize in Physics shared by Paul and Dehmelt, the development of FTICR mass spectrometry by Marshall and Comisarow, and the commercial manufacturers of these devices, there were fewer applications than those of the Paul trap and, as such, FTICR was given short shrift. At this time, Finnigan had just introduced an atmospheric pressure (APCI and electrospray) QIT and an external ionization GC/MS QIT instrument that followed the erstwhile Varian’s introduction of the Saturn 3D in 1994 [the first commercial QIT GC/MS/MS (tandem-in-time) instrument], and Bruker had introduced a QIT LC/MS/MS instrument at the International MS Conference in Budapest. Now, 15 years later, many manufacturers are using trapped ion technology, and the term ion trap is more encompassing than then. This is why these same editors of Volume IV (Theory and Instrumentation) and Volume V (Applications of Ion Trapping Devices), made a change in the title to Practical Aspects of Trapped Ion Mass Spectrometry, as pointed out in their Preface. This two-volume set consists of 1369 pages (862 in Volume IV and 507 in Volume V) and 37 chapters (21 in Volume IV and 16 in Volume V). The two volumes are well indexed and, like the first three volumes in the series, have useful Author Indices. Unlike the first three volumes, all of the literature citations include titles. Chapter 1 of Volume IV, “An Appreciation and Historical Survey of Mass Spectrometry,” serves as a refresher for the evolution of the m/z analyzer going back to Dalton and the evolution of modern atomic theory. This 128page chapter authored by March and Todd has 475 references Correspondence to: O. Sparkman; e-mail:

and is followed by its own Appendix entitled “Theory of Radio Frequency of Quadrupole Devices,” which is 20 pages long with an additional 20 citations. Details are provided on the physics of both the static and dynamic Kingdon trap (SKT and DKT, respectively). This chapter will likely become a seminal reference just as the works of Dawson [1] on quadrupole technology and March and Hughes [2] on the quadrupole ion trap have become seminal references. In the opening of Chapter 1, the Author’s quote from the Elizabeth Browning Poem Sonnet 43, How do I Love Thee? They point out that, “…the author seeks to define the dimensions through which her soul may reach as she examines the ways in which one human being can love another.” They state, “We propose that Browning’s poem is a fitting analogy to our task of introducing the ways in which a bewildering variety of ions can be trapped, initially for the satisfaction of human curiosity and, ultimately, for the benefit of mankind.” These statements show the passion with which these editors have undertaken the task of providing that understanding for ion trappers, young and old, everywhere. To explain further the title change, March and Todd provide a definition of a trapped ion: “an ion is ‘trapped’ when its residence time within a defined spatial region exceeds that had the motion of the ion not been impeded in some way.” As seen from the Table of Contents (below) for these two volumes, they cover most of the new technologies associated with the storage of and interaction with ions for mass spectrometry purposes. Not only is the ion cyclotron resonance mass spectrometer given the credit it now garners, but also the issue of the Fourier transform and its role in the detection of trapped ion mass spectrometry is provided in the three-chapter Part III of Volume IV entitled Fourier Transform Mass Spectrometry. This is in addition to Alexander Makarov’s excellent article on the Orbitrap in Part II, New Trapping Techniques, and the role of the Fourier transform in ion detection in this instrument. In addition to Makarov’s chapter on the “Orbitrap,” Part II contains chapters on the more esoteric digital ion trap (DIT), which uses a rectangular waveform as opposed to the conventional sinusoidal rf potential. It also has a chapter detailing the toroidal and halo ion traps. The toroidal ion trap is the heart of the Guardion-7 GC-MS from Torion Technologies, Inc., American Fork, UT, a popular instrument. Part II also has the chapter on “High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS),” which may at first appear to be out of place because it is a process for improving signal-to-background for ions of interest in a dynamic ion beam at atmospheric pressure; however, after the relationship of FAIMS and ion trapping is put in perspective with the above-cited definition of trapped ions, it becomes overwhelmingly clear as to why such a chapter is

Book Review: Practical Aspects of Trapped Ion

included. Other areas of ion mobility and the use of traveling wave technology for ion mobility and trapping ions are well covered. One feature of these publications is cross referencing. A good example is found in Chapter 16 of Volume IV “Unraveling the Structure Details of the Glycoproteome by Ion Trap Mass Spectrometry” in an area where ion mobility and its role are being discussed. There are references to the FAIMS chapter in Part IV and to Chapter 8 “Applications of Traveling Wave Ion Mobility-Mass Spectrometry” in Volume V in this chapter. For many years, R. Graham Cooks and his research group have done research on variations of the quadrupole ion trap. In his chapter in Volume IV, he includes a figure entitled in part Geometric evolution of ion traps for use in miniature and multiplexed mass spectrometer… taken from an article published in Ann. Rev. Anal. Chem., 2009. This figure shows the 3D-quadrupole ion trap with its hyperbolic electrodes evolving into the 3D-cylindrical ion trap (CIT), the so-called 2D-linear ion trap (LIT), which evolved into the rectilinear ion trap (RIT); and the toroidal trap, which evolved into the halo trap. These variations are well described in this chapter and in other chapters covering the 3D QIT and Quadrupole Rod Sets.1 Ray March once made the statement that George Stafford’s development of the mass instability scan function was as significant to making the QIT into a mass spectrometer as Paul’s development of the physics resulting in the device that resulted in his 1989 Nobel Prize. Although, maybe not quite as spectacular as the mass instability scan, the triple resonance scan function developed by Varian is another significant contribution to the 3D QIT and may even be important to the radial scan mode of the LIT. It will be interesting to see what Agilent does with this technology now that they own it. The description of this scan function, which was born out of the necessity to circumvent the Finnigan IP on the resonance instability scan function so that Varian could expand into the area of QIT LC/MS, is well described in Chapter 14 “Electrically Induced Nonlinear Ion Traps” of Volume IV and Chapter 15 “Technology Progress and Applications in GC/MS and GC/ MS/MS” in Volume V. Two MS/MS techniques that use magnetic ion traps and quadrupole ion traps, electron capture dissociation (ECD), and electron transfer dissociation (ETD), are well treated in various chapters in both Volumes IV and V. These techniques, along with electron detachment dissociation (EDD), are especially well discussed in Chapter 15 “Fragmentation Techniques for Protein Ions Using Various Types of Ion Trap [sic]”. The only thing that appears to be missing is a discussion of the new technology from Thermo Fisher involving the dual pressure linear ion trap. There is an article in the seven-chapter Part V of Volume IV 3D-Quadrupole Ion Trap Mass Spectrometry by Dodge Baluya and Rick Yost entitled “Pressure Tailoring’ for Improved Ion Trap Performances,” Chapter 18, which does discuss the performance based on


Euphemism used in the Table of Contents Part IV of Volume IV for the linear ion trap (LIT).

pressure in the 3D-quadrupole ion trap that parallels what Thermo is saying today about its new instrument called the Velos LTQ. Sometimes it appears that the lines between Instrumentation and Applications become blurred. Some articles that may have been better suited for the Instrumentation volume appear in the Applications volume and vice versa. This is just one of the reasons that both volumes should be purchased as a set. These topic confusions may well be the explanation behind the fact that Volume V was introduced in late 2009 and Volume IV came out about 6 months later in 2010; both volumes have copyright dates of 2010. Another chapter that could have been in either volume is Chapter 19 “A Quadrupole Ion Trap/Time-of-Flight Mass Spectrometer Combined with a Vacuum Matrix-Assisted Laser Desorption Ionization Source” authored by the ShimadzuBiotech/Kratos Analytical/Shimadzu group. The role of ion traps and especially quadrupole ion traps as tandem-in-space instrument is well known. This chapter gives detailed information about the role of a 3D QIT as a component in a tandem-inspace instrument. The description of dynamic pressure measurement in the QIT portion of the instrument may help other developments of the 3D QIT. The chapter contains an applications section that discusses glycobiologic and lipidomics uses as well as other areas involving such an instrument using a MALDI ion source. Volume IV ends with a two-chapter Part VI entitled Photochemistry of Trapped Ions. This area has another tandem-in-space QIT (transmission quadrupole coupled with a QIT) example and shows how exposing ions to photons can be an alternate form of ion excitation resulting in fragmentation. One style issue that is particularly useful is that most important acronyms in a chapter are introduced as a level one header so that if you happen to be in the middle of a chapter where a lot of acronyms are being used, it is easy to page back for a definition refresher. There are a few minor issues; in the chapter where ambient ionization [sic–open air ionization] is discussed, there is no reference to DART (direct analysis in real time) and no citation for a screenshot of the results of a mass spectral database search showing a sample peptide spectrum, a database spectrum, and the graphical difference between the two. A small slipup is the use of the term electron impact (EI) ionization in one of the chapters. The editors then use the same term in the Preface to Volume V. Underscoring this “slipup” is that John Todd is cited as the person who prepared for publication the 1991 IUPAC “Recommendations for Nomenclature and Symbolism for Mass Spectroscopy” publication (Pure and Appl. Chem., Vol. 63, No. 10, pp 1541–1566, 1991), which clearly states that the correct term is electron ionization. Ray March and John Todd have been doing research on the quadrupole ion trap longer than anyone. Few have a better understanding of the physics of trapped ions and how this contributes to mass spectrometry, as is reflected in this twovolume set. This is a true tour-de-force and is an outstanding work. Anyone working with trapped ions and any library supporting MS research would be well advised to have these two volumes.

Book Review: Practical Aspects of Trapped Ion

Table of Contents: Volume IV: PART I Chapter 1 Chapter 2 PART II Chapter 3 Chapter 4 Chapter 5 Chapter 6 PART III Chapter 7 Chapter 8 Chapter 9 PART IV Chapter 10 Chapter 11 Chapter 12 PART V Chapter 13 Chapter 14 Chapter 15 Chapter 16 Chapter 17 Chapter 18 Chapter 19 PART VI Chapter 20 Chapter 21

Fundamentals An Appreciation and Historical Survey of Mass Spectrometry Raymond E. March (Trent University) and John F. J. Todd (University of Kent) Ion Traps for Miniature, Multiplexed, and Soft-Landing Technologies Scott A. Smith, Christopher C. Mulligan, Qingyu Song, Robert J. Noll, R. Graham Cooks, and Zheng Ouyang, (Purdue University) New Ion Trapping Techniques Theory and Practice of the Orbitrap Mass Analyzer Alexander Makarov (Thermo Fisher Scientific) Rectangular Waveform Driven Digital Ion Trap (DIT) Mass Spectrometer: Theory and Applications Francesco L. Brancia and Li Ding (Shimadzu Research Laboratory) High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS), Randall W. Purves (Merch Frost Canada Ltd, currently National Research Council) Ion Traps with Circular Geometries Daniel E. Austin (Brigham Young University) and Stephen A. Lammert (Torion Technologies, Inc.) Fourier Transform Mass Spectrometry Ion Accumulation Approaches for Increasing Sensitivity and Dynamic Range in the Analysis of Complex Samples Mikhail E. Belov, Yehia M. Ibrahim, and Richard D. Smith (Bio. Sci. Div. Pacific Northwest National Laboratory) Radio Frequency-Only-Mode Event and Trap Compensation in Penning Fourier Transform Mass Spectrometry Adam M. Brustkern, Don L. Rempel, and Michael L. Gross (Washington University) A Fourier Transform Operating Mode Applied to a Three-Dimensional Quadrupole Ion Trap Y. Zerega, J. Andre, M. Carette, A, Janulyte, and C. Reynard (Université de Provence – CNRS Laboratoire Chimie Provence) Quadrupole Rod Sets Trapping and Processing Ions in Radio Frequency Ion Guides Bruce A. Thomson, Igor V. Chernushevich, and Alexandre V. Loboda (MDS Analytical Technologies) Linear Ion Trap Mass Spectrometry with Mass-Selective James W. Hager (MDS Analytical Technologies) Axially Resonant Excitation Linear Ion Trap (AREX LIT) Yuichiro Hashimoto (Central Research lab Hitachi, Ltd.) 3D-Quadrupole Ion Trap Mass Spectrometry An Examination of the High-Capacity Trap (HCT) Desmond A. Kaplan, Ralf Hartmer, Andreas Brekenfeld, Jochen Franzen, and Michael Schubert (Bruker Daltonics) Electrically Induced Nonlinear Ion Traps Gregory J. Wells and August A. Specht (Varian, Inc.) Fragmentation Techniques for Protein Ions Using Various Types of Ion Trap Jochen Franzen (Bruker Daltonics)and Kari Peter Wanczek (Univ. Bremen) Unraveling the Structural Details of the Glycoproteome by Ion Trap Mass Spectrometry Vernon Reinhold, David J. Ashline, and Hailong Zhang (Univ. New Hampshire) Collisional Cooling in the Quadrupole Ion Trap Mass Spectrometer (QITMS) Philip M. Remes and Gary L. Glish (Univ. North Carolina) ‘Pressure Tailoring’ for Improved Ion Trap Performance Dodge L. Baluya and Richard A. Yost (Univ. Florida) A Quadrupole Ion Trap/Time-of-Flight Mass Spectrometer Combined with a Vacuum Matrix-Assisted Laser Desorption Ionization Source Dimitris Papanastasiou, Omar Belgacem, Helen Montgomery, Mikhail Sudakov, and Emmanuel Raptakis (Shimadzu Biotech) Photochemistry of Trapped Ions Photodissociation in Ion Traps Jennifer Brodbelt (Univ. Texas) Photochemical Studies of Metal Dication Complexes in an Ion Trap Guohua Wu, Hamish Stewart, and Anthony J. Stace (Univ. of Nottingham)

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251 273 309 373 401 433 469

525 545 573 593 619 671 707 739 769 793 827 874

Book Review: Practical Aspects of Trapped Ion

Table of Contents Volume V PART I Chapter 1 Chapter 2 Chapter 3 PART II Chapter 4 Chapter 5 Chapter 6 Chapter 7 Chapter 8 Part III Chapter 9 Chapter 10 Chapter 11 PART IV Chapter 12 Chapter 13 Chapter 14 Chapter 15 Chapter 16

Ion Reactions Ion/Ion Reactions in Electrodynamic Ion Traps Jian Liu and Scott A. McLuckey (Purdue Univ.) Gas-Phase Hydrogen/Deuterium Exchange in Quadrupole-Ion Traps Joseph E. Chipuk and Jennifer S. Brodbelt (Univ. Texas) Methods for Multi-Stage Ion Processing Involving Ion/Ion Chemistry in a Quadrupole Linear Ion Trap Graeme C. McAlister and Joshua J. Coon (Univ. Wisconsin) Ion Conformation and Structure Chemical Derivatization and Multistage Tandem Mass Spectrometry for Protein Structural Characterization Jennifer M. Froelich, Yali Lu, and Gavin E. Reid (Michigan State University) Fourier Transform Ion Cyclotron Resonance Mass Spectrometry in the Analysis of Peptides and Proteins Helen J. Cooper (Univ. Birmingham) MS/MS Analysis of Peptide–Polyphenols Supramolecular Assemblies: Wine Astringency Approached by ESI-IT-MS Benoît Plet and Jean-Marie Schmitter (Univ. Bordeaux) Structure and Dynamics of Trapped Ions Joel H. Parks (The Rowland Institute at Harvard) Applications of Traveling Wave Ion Mobility-Mass Spectrometry Konstantinos Thalassinos and James H. Scrivens (Univ. Warwick) Ion Spectroscopy The Spectroscopy of Ions Stored in Trapping Mass Spectrometers Matthew W. Forbes, Francis O. Talbot, and Rebecca A. Jockusch (Univ. Toronto) Sympathetically-Cooled Single Ion Mass Spectrometry Peter Frøhlich Staanum, Klaus Højbjerre, and Michael Drewsen (Univ. Aarhus) Ion Trap: A Versatile Tool for the Atomic Clocks of the Future Fernande Vedel (Physique des interactions ioniques et moléculaires (PIIM) Université Provence) Practical Applications Boundary-Activated Dissociations (BAD) in a Digital Ion Trap (DIT) Francesco L. Brancia, Luca Raveane, Alberto Berton, and Pietro Traldi (CNR-ISTM Corso Stati Uniti 4) The Study of Ion/Molecule Reactions at Ambient Pressure With Ion Mobility Spectrometry and Ion Mobility/Mass Spectrometry Gary A. Eiceman (New Mexico State Univ.) and John A. Stone (Queens University) The Role of Trapped Ion Mass Spectrometry for Imaging Timothy J. Garrett and Richard A. Yost (Univ. Florida) Technology Progress and Application in GC/MS and GC/MS/MS Mingda Wang and John E. George III (Varian, Inc.) Remote Monitoring of Volatile Organic Compounds in Water by Membrane Inlet Mass Spectrometry Romina Pozzi, Paola Bocchini, Francesca Pinelli, and Guido C. Galletti (Univ. Bologna)

References 1. Dawson, P.H. (ed.): Quadrupole mass spectrometry and its applications. Elsevier, Amsterdam (1976) 2. March, R.E., Hughes, R.J.: Quadrupole storage mass spectrometry. Wiley Interscience, New York (1989)

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Book Review: Practical Aspects of Trapped Ion Mass Spectrometry, Volumes IV & V  

Book review of Practical Aspects of Trapped Ion Mass Spectrometry, Volume IV: Theory and Instrumentation and Practical Aspects of Trapped Io...

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