Fundamentals and Applications of Fourier Transform Mass Spectrometry

Cover......Page 1
FUNDAMENTALS
AND
APPLICATIONS OF
FOURIER
TRANSFORM MASS
SPECTROMETRY
......Page 3
Copyright......Page 4
Contributors......Page 5
Foreword......Page 9
Preface......Page 11
Acknowledgments......Page 14
Section A: Historical chapters
......Page 15
1
Historical developments in Fourier transform ion cyclotron resonance mass spectrometry......Page 16
Introduction......Page 17
1965......Page 18
1967......Page 19
1970......Page 20
1971......Page 21
1973......Page 22
1974......Page 23
1976......Page 24
1980......Page 25
Developments from 1981 to 1990......Page 26
Developments from 1991 to 2000......Page 28
Developments from 2001......Page 30
Conclusion......Page 35
References......Page 36
Section B: Fundamental/technology chapters
......Page 47
2
Fundamentals of Orbitrap analyzer......Page 48
Principles of operation......Page 49
Non-ideal orbital traps and their calibration......Page 54
Fourier transform methods......Page 59
Autocorrelation methods......Page 62
Maximum likelihood parameter estimators......Page 63
Deconvolution method......Page 64
Evolution of the Orbitrap platform and selected applications......Page 65
References......Page 68
3
Fundamentals, strengths, and future directions for Fourier transform ion cyclotron resonance mass spectrometry......Page 73
FT-ICR fundamentals......Page 77
Significant recent developments in FT-ICR......Page 82
References......Page 91
Ion motion in the electromagnetic field......Page 99
Ion motion in traps with quadrupolar type field distribution......Page 101
The detection of induced signal by cylindrical geometry electrodes......Page 102
Harmonics and multiple electrode detection......Page 104
The influence of inharmonicity of electrostatic field and inhomogeneity of the magnetic field on ion motion synchronizatio .........Page 106
Ion traps with dynamic harmonization......Page 110
Coalecsence......Page 113
Conclusion......Page 118
References......Page 119
ICR and Orbitrap FTMS: A preamble......Page 122
Mass spectra processing: From a single to a summed (averaged) mass spectrum......Page 124
Representation of mass spectra in full and reduced profile modes......Page 127
FTMS resolution performance: Orbitrap and ICR......Page 130
Conclusions......Page 137
Acknowledgments......Page 138
References......Page 139
Introduction......Page 142
Noise and de-noising in FTMS......Page 143
Correct assignment of chemically relevant peaks in FTMS......Page 150
Magnitude mode detection in FT-ICR-MS......Page 153
Absorption mode detection in FT-ICR-MS......Page 155
Non-Fourier transform techniques......Page 159
Apodization......Page 166
Calibration......Page 168
The physics behind the need of additional terms in the calibration equation......Page 170
Further developed external calibration equations......Page 171
Beat patterns in time-domain FTMS transients [121]......Page 178
FT artifacts in FTMS and their implications on data processing......Page 180
Batch processing of FTMS mass spectra......Page 181
Automation of FTMS instruments......Page 183
References......Page 186
Introduction......Page 195
Contemporary FT-ICR mass spectrometers and tandem mass spectrometry......Page 197
Mass spectrometry in the second dimension......Page 201
Interpretation of a 2D mass spectrum......Page 205
Noise in 2D-MS......Page 209
Resolving power and mass accuracy......Page 212
Alternative 2D-MS......Page 214
MSn/2D-MS......Page 216
Data acquisition and processing......Page 217
Data analysis......Page 222
Applications of 2D-MS......Page 226
Conclusion......Page 233
Glossary......Page 235
References......Page 236
Introduction......Page 241
Background......Page 242
TIMS analyzer......Page 243
OSA-TIMS......Page 245
G-TIMS (linear, non-linear targeting and nonlinear stepping)......Page 246
2D-TIMS-FT-ICR MS plots and Ko determination......Page 247
TIMS-TOF MS vs. TIMS-FT-ICR MS......Page 250
Conclusions......Page 251
References......Page 253
Introduction......Page 260
Common preservation methods for cancer tissues......Page 263
MALDI-FT-ICR MSI in metabolomic-based cancer research......Page 266
Data processing in high-resolution MALDI MSI......Page 273
Discovery of diagnostic markers and tissue-based disease classification by mass spectrometry imaging......Page 276
Inter- and intratumoral heterogeneity at metabolite levels......Page 277
Therapy response prediction and prognosis......Page 279
Conclusion......Page 280
References......Page 281
Introduction......Page 287
General concepts of laser-matter interaction......Page 289
Standing of the laser fluence and laser irradiance......Page 293
Simulation of laser-matter interaction and influence of the electrons......Page 294
Principles of matrix-assisted laser desorption/ionization......Page 296
The laser induced acoustic desorption (LIAD) technique......Page 300
Laser gas phase ion dissociation......Page 302
First instruments fitted with internal ion sources......Page 303
Instruments fitted with external ion sources......Page 305
Laser-based ionization techniques at atmospheric pressure......Page 306
Mass spectrometry imaging (MSI or IMS)......Page 308
Some applications of laser ionization coupled to FT-ICR MS......Page 312
Study of inorganic cluster ions......Page 313
Study of gas phase thermochemistry of ions and cluster ions in the FT ICR cell......Page 315
Organic compounds......Page 316
Petroleomics (petroleum and bio-oils)......Page 317
Environmental organic contaminants......Page 318
Conclusions......Page 319
References......Page 320
Further reading......Page 328
Section C: Applications chapters
......Page 329
Introduction......Page 330
Sample preparation......Page 333
Data acquisition......Page 334
Data preprocessing......Page 335
Statistical analyses......Page 336
Metabolite identification......Page 337
The input of Fourier mass spectrometry to metabolite detection and quantification......Page 338
LC/HRMS-based metabolomics......Page 339
High-throughput metabolomics......Page 340
Towards high-throughput LC/HRMS-MS metabolomics......Page 342
Automatic peak detection, alignment and integration of features......Page 343
Correction of analytical drifts and batch to batch variations......Page 344
The input of Fourier transform mass spectrometry to metabolome annotation and metabolite identification......Page 345
Acknowledgment......Page 352
References......Page 353
Introduction to metabolomics......Page 362
Primary analysis: Annotation, identification, knowns and unknowns......Page 366
Secondary analysis: Pathways and fluxes......Page 367
Mass differences in instrumental quality parameters......Page 369
Compositional space......Page 376
Traditional means of UHR-MS data visualization and interpretation......Page 378
Mass difference networks in the visualization and primary analysis of UHR-MS data......Page 383
MDiN's for dereplication......Page 385
MDiN's for third and fourth level identification......Page 387
MDiN strategies for second level identification......Page 389
MDiN strategies for contextualization of 4th level identification......Page 390
Classical pathway mapping......Page 392
Genome scale metabolic models and flux analyzes......Page 393
Mass difference networks and genome scale models......Page 396
Mass difference enrichment analysis (MDEA)......Page 398
Conclusion......Page 401
References......Page 402
General introduction......Page 411
Drinking water and the discovery of new disinfection by-products......Page 412
DOM precursors of DBPs......Page 413
DBPs in drinking water......Page 415
DBPs in hydraulic fracturing fluids......Page 416
The composition of effluent organic matter (EfOM)......Page 417
Hydraulic fracturing organic matter......Page 418
Non-targeted approaches in characterizing pollutants......Page 419
Contaminants in surface and groundwater......Page 421
Conclusions and suggestions for future work......Page 422
References......Page 423
Introduction......Page 428
FTMS basics......Page 429
FTMS for mass fingerprinting of peptides......Page 431
Fourier transform tandem mass spectrometry......Page 434
Collisional activation......Page 436
Electron-based dissociation......Page 442
Photoactivation......Page 449
Combining different activation methods......Page 450
Conclusion......Page 461
References......Page 462
Introduction......Page 472
Illicit abused drugs......Page 474
Marijuana......Page 476
Cocaine......Page 479
Hallucinogens......Page 482
New psychoactive substances......Page 484
Foods and beverages falsification......Page 489
Evidence analysis......Page 497
Conclusions......Page 504
References......Page 505
Introduction......Page 512
Ionization methods......Page 513
Electrospray ionization......Page 514
Atmospheric pressure chemical ionization (APCI)......Page 515
Atmospheric pressure photoionization (APPI)......Page 516
Matrix-assisted laser desorption/ionization (MALDI)......Page 517
High-resolution mass analyzers applied to petroleomics......Page 518
FT-ICR......Page 519
Orbitrap......Page 524
Conclusion......Page 527
References......Page 528
Introduction: the importance of proteins in a multi-omics context......Page 532
Analytical strategies: from top-down to bottom-up and vice versa......Page 534
Sequencing and activation methods......Page 537
Bioinformatics......Page 543
Separative techniques......Page 544
LC-MS hyphenation......Page 545
Scan modes, targeted analysis and data independent analysis......Page 546
Quantification......Page 549
Top-down proteomics......Page 552
Purification and separation of proteins......Page 553
Specificity of MS analysis......Page 555
Epilogue......Page 557
References......Page 558
Further reading......Page 570
Introduction......Page 571
Hydrogen and rare gases......Page 572
Carbon, silicon, and germanium......Page 574
Nitrogen, phosphorus, and arsenic......Page 576
Oxygen, sulfur, selenium, and tellurium......Page 584
Fluorine and chlorine......Page 586
References......Page 587
Introduction......Page 594
Pressure dependent peak broadening......Page 595
Black body induced radiative dissociation (BIRD)......Page 596
In chemistry......Page 600
In nuclear physics......Page 605
Cryo spectroscopy by X-rays: magnetic moments......Page 607
Cryo kinetics of trapped ions......Page 609
Cryo spectroscopy in the IR: molecular vibrations......Page 612
The future-a short outlook......Page 613
Conclusions......Page 617
References......Page 618
Further reading......Page 622
An introduction to glycan biology......Page 623
Introduction......Page 627
Ionization......Page 628
Structural characterization......Page 629
Electron activation......Page 634
Liquid chromatography (LC)......Page 638
Capillary electrophoresis (CE)......Page 639
Ion mobility (IM)......Page 640
Challenges in automation......Page 641
Automated software suites......Page 643
Conclusion......Page 644
References......Page 645
Further reading......Page 649
Introduction......Page 650
High-resolution mass spectrometry in foodomics......Page 651
Data management in FT-ICR-MS......Page 654
New insights in food processing-the Maillard reaction......Page 655
Wine......Page 658
Spirits......Page 664
Aspects of nutritive quality of foods: vitamins......Page 666
Conclusions......Page 670
References......Page 671
Introduction......Page 677
Pyrolysis bio-oil......Page 680
Liquefaction bio-oil......Page 682
Upgrading treatments......Page 683
Sample preparation......Page 684
Targeted analytical methods......Page 685
Introduction......Page 686
Analyses of bio-oils by ESI-FTMS......Page 687
Influence of dopants added to the bio-oil solution......Page 694
ESI-FTMS analysis of bio-oils from various feedstock......Page 696
Water-soluble and water-insoluble fractions......Page 699
Other fractionation processes......Page 701
ESI FT-MS analysis for optimizing the production and upgrading processes of bio-oils......Page 702
Comments on the ESI FT-MS analysis of bio-oil......Page 705
Analyses of bio-oils by APPI, APCI, and LDI-FTMS-Additional insights to ESI-FTMS analyses......Page 706
Concluding remarks on the characterization of bio-oil by FT-MS......Page 717
References......Page 719
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Back Cover......Page 752