1. Introduction 2. Elemental Composition 3. The Molecular Ion 4. Basic Mechanisms of Ion Fragmentation 5. Postulation of Molecular Structures 6. Auxiliary Techniques 7. Theory of Unimolecular Ion Decompositions 8. Detailed Mechanisms of Ion Fragmentation 9. Mass Spectra of Common Compound Classes 10.Computer Identification of Unknown Mass Spectra 11.Solutions to Unknowns Bibliography Appendix Index

Interpretation of Mass Spectra

An Introduction to ICP Spectrometries for Elemental Analysis. The Art and Science of Microwave Sample Preparations for Trace and Ultratrace Elemental Analysis. Sample Introduction in ICPMS. Plasma Generation in ICPMS. Fundamental Aspects of Sample Introduction in ICP Spectrometry. Instrumentation for Low-- and High--Resolution ICPMS. Analytical Characteristics of ICPMS. Fundamental Considerations in ICPMS. Novel Applications of ICPMS. Mass Spectrometry with Mixed--Gas and Helium ICPs. Mass Spectrometry with Microwave--Induced Plasmas. Index.

Inductively coupled plasma mass spectrometry

Ion mobility-mass spectrometry (IM-MS) is enhancing many areas of (bio)chemical analysis because it can separate ions both by their mass-to-charge ratio and differences in their cross-sectional area. IM-MS can be used for structural characterization, enhanced analysis of complex mixtures or to gain insights into conformational dynamics.
 Mass spectrometry is a vital tool for molecular characterization, and the allied technique of ion mobility is enhancing many areas of (bio)chemical analysis. Strong synergy arises between these two techniques because of their ability to ascertain complementary information about gas-phase ions. Ion mobility separates ions (from small molecules up to megadalton protein complexes) based on their differential mobility through a buffer gas. Ion mobility-mass spectrometry (IM-MS) can thus act as a tool to separate complex mixtures, to resolve ions that may be indistinguishable by mass spectrometry alone, or to determine structural information (for example rotationally averaged cross-sectional area), complementary to more traditional structural approaches. Finally, IM-MS can be used to gain insights into the conformational dynamics of a system, offering a unique means of characterizing flexibility and folding mechanisms. This Review critically describes how IM-MS has been used to enhance various areas of chemical and biophysical analysis.

/pdf/the-power-of-ion-mobility-mass-spectrometry-for-structural-1da43zeaym.pdf

The power of ion mobility-mass spectrometry for structural characterization and the study of conformational dynamics

Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) has become a key technique for monitoring structural and dynamic aspects of proteins in solution. This approach relies on the fact that exposure of a protein to D2O induces rapid amide H → D exchange in disordered regions that lack stable hydrogen-bonding. Tightly folded elements are much more protected from HDX, resulting in slow isotope exchange that is mediated by the structural dynamics (“breathing motions”) of the protein. MS-based peptide mapping is a well established technique for measuring the mass shifts of individual protein segments. This tutorial review briefly discusses basic fundamentals of HDX/MS, before highlighting a number of recent developments and applications. Gas phase fragmentation strategies represent a promising alternative to the traditional proteolysis-based approach, but experimentalists have to be aware of scrambling phenomena that can be encountered under certain conditions. Electron-based dissociation methods provide a solution to this problem. We also discuss recent advances that facilitate the applicability of HDX/MS to membrane proteins, and to the characterization of short-lived protein folding intermediates. It is hoped that this review will provide a starting point for novices, as well as a useful reference for practitioners, who require an overview of some recent trends in HDX/MS.

Hydrogen Exchange Mass Spectrometry for Studying Protein Structure and Dynamics

In this review we examine techniques, software, and statistical analyses used in label-free quantitative proteomics studies for area under the curve and spectral counting approaches. Recent advances in the field are discussed in an order that reflects a logical workflow design. Examples of studies that follow this design are presented to highlight the requirement for statistical assessment and further experiments to validate results from label-free quantitation. Limitations of label-free approaches are considered, label-free approaches are compared with labelling techniques, and forward-looking applications for label-free quantitative data are presented. We conclude that label-free quantitative proteomics is a reliable, versatile, and cost-effective alternative to labelled quantitation.

Less label, more free: approaches in label-free quantitative mass spectrometry.

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and defini- tions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy's Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some addi- tional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, par- ticularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrom- etry terminology that represents the current consensus of the mass spectrometry community.

/pdf/definitions-of-terms-relating-to-mass-spectrometry-iupac-35asdjsrex.pdf

Definitions of terms relating to mass spectrometry (IUPAC Recommendations 2013)

https://link.springer.com/content/pdf/10.1016%2Fj.jasms.2010.04.017.pdf

The mobile proton hypothesis in fragmentation of protonated peptides: a perspective.

Preface. Acknowledgements. 1 Measurement, Dimensions and Units. 1.1 Introduction. 1.2 The International System of Units (SI). 1.3 'Mass-to-Charge Ratio' in Mass Spectrometry. 1.4 Achievable Precision in Measurement of SI Base Quantities. 1.5 Molecular Mass Limit for Trace Quantitation by Mass Spectrometry. 1.6 Summary of Key Concepts. 2 Tools of the Trade I. The Classical Tools. 2.1 Introduction. 2.2 Analytical and Internal Standards: Reference Materials. 2.3 The Analytical Balance. 2.4 Measurement and Dispensing of Volume. 2.5 Preparation of Solutions for Calibration. 2.6 Introduction to Calibration Methods for Quantitative Analysis. 2.7 Summary of Key Concepts. 3 Tools of the Trade II. Theory of Chromatography. 3.1 Introduction. 3.2 General Principles of Chemical Separations. 3.3 Summary of Important Concepts. 3.4 Plate Theory of Chromatography. 3.5 Nonequilibrium Effects in Chromatography: the van Deemter Equation. 3.6 Gradient Elution. 3.7 Capillary Electrophoresis and Capillary Electrochromatography. Appendix 3.1 Derivation of the Plate Theory Equation for Chromatographic Elution. Appendix 3.2 Transformation of the Plate Theory Elution Equation from Poisson to Gaussian Form. Appendix 3.3 A Brief Introduction to Snyder's Theory of Gradient Elution. List of Symbols Used in Chapter 3. 4 Tools of the Trade III. Separation Practicalities. 4.1 Introduction. 4.2 The Analyte and the Matrix. 4.3 Extraction and Clean-Up: Sample Preparation Methods. 4.4 Chromatographic Practicalities. 4.5 Summary of Key Concepts. Appendix 4.1 Responses of Chromatographic Detectors: Concentration vs Mass-Flux Dependence. 5 Tools of the Trade IV. Interfaces and Ion Sources for Chromatography-Mass Spectrometry. 5.1 Introduction. 5.2 Ion Sources that can Require a Discrete Interface Between Chromatograph and Source. 5.3 Ion Sources not Requiring a Discrete Interface. 5.4 Source-Analyzer Interfaces Based on Ion Mobility. 5.5 Summary of Key Concepts. 5.1 Appendix 5.1: Methods of Sample Preparation for Analysis by MALDI. 6 Tools of the Trade V. Mass Analyzers for Quantitation: Separation of Ions by m / z Values. 6.1 Introduction. 6.2 Mass Analyzer Operation Modes and Tandem Mass Spectrometry. 6.3 Motion of Ions in Electric and Magnetic Fields. 6.4 Mass Analyzers. 6.5 Activation and Dissociation of Ions. 6.6 Vacuum Systems. 6.7 Summary of Key Concepts. Appendix 6.1 Interaction of Electric and Magnetic Fields with Charged Particles. Appendix 6.2 Leak Detection. Appendix 6.3 List of Symbols Used in Chapter 6. 7 Tools of the Trade VI. Ion Detection and Data Processing. 7.1 Introduction. 7.2 Faraday Cup Detectors. 7.3 Electron Multipliers. 7.4 Post-Detector Electronics. 7.5 Summary of Key Concepts. 8 Tools of the Trade VII: Statistics of Calibration, Measurement and Sampling. 8.1 Introduction. 8.2 Univariate Data: Tools and Tests for Determining Accuracy and Precision. 8.3 Bivariate Data: Tools and Tests for Regression and Correlation. 8.4 Limits of Detection and Quantitation. 8.5 Calibration and Measurement: Systematic and Random Errors. 8.6 Statistics of Sampling of Heterogeneous Matrices. 8.7 Summary of Key Concepts. Appendix 8.1 A Brief Statistics Glossary. Appendix 8.2 Symbols Used in Discussion of Calibration Methods. 9 Method Development and Fitness for Purpose. 9.1 Introduction. 9.2 Fitness for Purpose and Managing Uncertainty. 9.3 Issues Between Analyst and Client: Examining What's at Stake. 9.4 Formulating a Strategy. 9.5 Method Development. 9.6 Matrix Effects. 9.7 Contamination and Carryover. 9.8 Establishing the Final Method. 10 Method Validation and Sample Analysis in a Controlled Laboratory Environment. 10.1 Introduction. 10.2 Method Validation. 10.3 Conduct of the Validaton. 10.4 Examples of Methods and Validations Fit for Purpose. 10.5 Validated Sample Analysis. 10.6 Documentation. 10.7 Traceability. 11 Examples from the Literature. 11.1 Introduction. 11.2 Food Contaminants. 11.3 Anthropogenic Pollutants in Water. 11.4 GC-MS Analyses of Persistent Environmental Pollutants. 11.5 Bioanalytical Applications. 11.6 Quantitative Proteomics. 11.7 Analysis of Endogenous Analytes. Epilog. References. Index.

Trace Quantitative Analysis by Mass Spectrometry

The Distinguished Contribution Award of the American Society for Mass Spectrometry “—recognizes a focused, singular achievement in or contribution to fundamental or applied mass spectrometry, in contrast to awards that recognize lifetime achievement—a contribution that has had a significant impact on the fundamental understanding and/or practice of mass spectrometry.” The hypothesis that has come to be known as themobile proton model clearly satisfies both the fundamental and practical criteria. It is a pleasure to have been asked to contribute a brief introductory article to this special issue that honors Vicki Wysocki and Simon Gaskell, the principal originators and proponents of the model and the 2009 recipients of this prestigious award. Two excellent reviews cover the relevant literature up to about 2005 [1, 2]. The purpose of this short article is to attempt to view the mobile proton model relative to a wider perspective. Application of mass spectrometry to determination of molecular structure relies on interpretation of fragment ion spectra, however obtained, using a set of rules that are the result of years of experience in extending concepts of classical physical-organic chemistry. Most of the fragmentation rules were derived from experience with positive ion mass spectra obtained using electron ionization. Probably the best-known guide to these interpretative rules is the book authored by McLafferty and Turecek [3]. The underlying theme of these “classical” rules is that the electron rearrangements involved in decomposition of an activated ion into two or more fragments are triggered by localization of charge (and/or unpaired electron spin in the case of radical ions) on specific sites within the molecular structure of the decomposing ion. It is true that these rules are almost entirely empirical, but their continuing practical success indicates that they must correspond to real phenomena in some sense. The introduction of chemical ionization, and later the powerful fast atom bombardment (FAB) [4], electrospray (ESI) [5], and MALDI [6] ionization techniques led to extension of the rules for fragmentations of molecular radical cations to even-electron molecular species formed by adduction of simple ions, protons in the great majority of cases. Indeed, the mobile proton model can be regarded as an extension of these classical rules that permits their appropriate application to protonated peptides or other organic molecules. The main exceptions to interpretations based on triggering by localized charge sites are the charge-remote fragmentations [7] investigated by Gross and his colleagues starting in the late 1980s. These “pseudo-thermal” reactions are known [8, 9] to contribute to fragmentation of protonated peptides at high levels of internal activation, where they compete with the mechanisms subsumed by the mobile proton theory, particularly for singly-protonated peptides containing an Arg residue. As emphasized previously [2], the mobile proton model is not a complete theory that can predict a fragment ion spectrum for any given protonated peptide, but rather a qualitative framework that permits appropriate application of interpretative rules based on charge-site localization. Essentially, the model assumes that for protonated peptides formed by soft ionization methods such as electrospray (ESI), the protons are initially localized on the most basic sites in the molecule. These sites are the N-terminus and the side chains of basic amino acid residues, particularly Arg, Lys, and His. After ion activation the ionizing proton(s) can be transferred from the less-basic of these initially occupied sites to the various peptide linkages, thus triggering charge-site-initiated mechanisms of various kinds that provide the desired sequence ions. In other words, the mobile proton model also implies that heterogeneous populations of protonated forms can be generated upon ion activation and some of these forms are “fragmenting” structures, while others remain intact during the time frame of the mass spectrometer. This framework has now been extensively reviewed and its practical usefulness amply demonstrated [1, 2]. Of course all useful new ideas appear to be simple and obvious once someone else has described them. To illustrate that the mobile proton model was not always regarded as “obvious” and was “linked” only later to the idea of ion populations generated by an “activated”, i.e., “transferable” proton, one can cite some early work published in 1992 by one of the recipients of the Distinguished Contributions Award [10]. This paper was mainly concerned with demonstrating intraionic interactions in peptides containing cysteic acid plus Address reprint requests to Dr. R. K. Boyd, National Research Council, Bldg. M12, 1200 Montreal Road, Ottawa K1A0R6, Canada. E-mail: robert. boyd@nrc.ca

/pdf/focus-m-obile-proton-model-short-communication-the-mobile-4kg1r2fwid.pdf

FOCUS :M OBILE PROTON MODEL SHORT COMMUNICATION The Mobile Proton Hypothesis in Fragmentation of Protonated Peptides: A Perspective

https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/pdf/10.1002/rcm.1300

John Herbert Beynon

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