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427

INDEX

Abscesses, examined by IMS, 291Absolute chemical structure, in-depth

knowledge of, 246Absolute metabolite quantitation kit, 393Absolute quantitation, from tissue samples,

233–234Absorption assays, 98Absorption, distribution, metabolism, and

excretion (ADME) assays. See also ADME entries; In vitro ADME entries

frequently performed, 97–98mass spectrometry for in vitro, 97–113

Absorption, distribution, metabolism, and excretion (ADME) parameters, therapeutic siRNAs and, 372

Absorption/distribution/metabolism/excretion/toxicity (ADMET) assays, 304

Absorption, metabolism, and excretion (AME) studies, 131

Accelerator mass spectrometry (AMS), 2, 27–28

Acetonitrileeffect of, 69in sample extraction, 133–134, 135

Acetonitrile methanol elution, 63–65Acetonitrile precipitation, 81

Mass Spectrometry for Drug Discovery and Drug Development, First Edition. Edited by Walter A. Korfmacher.© 2013 John Wiley & Sons, Inc. Published 2013 by John Wiley & Sons, Inc.

Acid hydrolysis, MALDI-MS and, 369Acidic matrices, 368Active drug compounds, assessing

homogeneity of, 324–325Active pharmaceutical ingredients (APIs),

249impurities in, 191

Acylglucuronides, 56, 73, 74, 133Adduct ions, 3Adenosine triphosphate (ATP), depletion

of, 318ADME program, for drug registration, 129.

See also Absorption, distribution, metabolism, and excretion (ADME) entries

ADME properties, of siRNAs, 364ADME studies, 117, 129, in animals, 132ADME support, 102Adverse drug reactions (ADRs), 339–340AEE788 vascular endothelial growth factor

receptor inhibitor, 318–320Affinity selection–MS (ALIS) method, 261,

262Agilent, 106Albumin depletion method, 178–179Alkali ion exchange, with ammonium ions,

368

428 INDEx

Alternative fragmentation process, 28Alternative ionization methods, 28Alzheimer’s biomarkers, 42Ambient desorption techniques, 7–11Ambient ionization mass spectrometry, 7Ambient sampling/ionization techniques,

109Ambient surface profiling, LESA for,

221–238Amine adducted ions, in PEGylated protein

analysis, 167Ammonium hydroxide (NH4OH), 412Ammonium ions, alkali ion exchange with,

368AMS system, components of, 28. See also

Accelerator mass spectrometry (AMS)Amyloid peptides, HPLC-MS/MS

quantification of, 413β-Amyloid peptides, 408–410Analog-to-digital converter (ADC), 344Analyte expression, 60Analyte extraction

LESA in, 231–232organic solvents for, 67–68using LLE, 66–67

Analytesanalysis of, 3–4, 8annotation of, 395, 396capturing quantitative information on,

394chromatographically separating from

phospholipids, 65ionization efficiency of, 225post-acquisition extraction of accurate

masses of, 107Analyte stabilization, chemical agents in,

57Analytical approaches, fingerprinting

techniques and, 391–392Analytical data acquisition, in

metabolomics, 390Analytical fingerprints, 391Analytical instrumentation, creation of, 49Analytical/wet chemistry techniques, 142Anatomy, intact protein analysis of,

284–288Animals

ADME studies in, 132metabolic profiles in, 130

Animal studiesAUC pooling method in, 136incurred sample from, 81

Anion exchange, 367Annotation

of analytes, 395, 396in nontargeted metabolomics, 395, 396

Antibacterial compounds, cannibalistic factors as, 291

Antibiotic-resistant bacteria strains, 291Antibody fragmentation, 208Anticoagulants, 57Antidrug antibody purification method,

178–179Antioxidants, 133Antisense oligonucleotide therapeutic

discovery, 372APCI HPLC-MS applications, 6. See also

Atmospheric pressure chemical ionization (APCI); High-performance liquid chromatography–mass spectrometry (HPLC-MS)

APCI ionization mechanism, 6APCI-MS, 6. See also Mass spectrometry

entriesAPI sources, introduction of samples into,

108. See also Atmospheric pressure ionization (API)

API techniques, 28AQ4N prodrug, 318Aqueous mobile phase, phase collapse and,

75–76Area under the curve (AUC), 135, 136Artificial deamidation, minimizing, 212Artificial degradation, in peptide mapping,

211–213Asn deamidation/isomerization scheme,

205. See also Asparagine (Asn) residues

Asparagine (Asn) residues, deamidation of, 167, 177, 204

Aspartate (Asp)isoAsp residues from, 206isomerization of, 177

Aspartate products, isoaspartate vs., 177Astemizole, MALDI imaging results for,

316, 317Atmospheric pressure chemical ionization

(APCI), 1, 5–6, 109, 240, 241, 245Atmospheric pressure IEM, 5. See also Ion

evaporation model (IEM)Atmospheric pressure ionization (API), 1

sources of, 39Atmospheric pressure ionization methods/

techniques, 8, 240

INDEx 429

Atmospheric pressure ion source geometries, 2

Atmospheric pressure MALDI (API-MALDI), 13. See also Matrix-assisted laser desorption/ionization (MALDI)

Atmospheric pressure photoionization (APPI), 1, 5, 6–7, 240, 241, 250

Atmospheric pressure solid probe analysis (ASAP), 9

AUC plasma pooling, volume calculation for, 135

AUC pooling method, in animal studies, 136

Automated anion-exchange purification/desalting HPLC system, 367

Automated component detection, 121Automated compound purification systems,

243Automated infusion, 108Automated optimization workflows, 404Automated tryptic digestion, 156Automatic analyte extraction, LESA in,

231–232Automatic gain control (AGC) procedure,

17Automaton™, 100Autoradiography, 221–222. See also Whole

body autoradiography (WBA)MALDI imaging as a complement to,

323Autoradiography imaging, 304, 305. See also

Quantitative whole-body autoradiography entries

Autosampling, fraction-collecting, 367–368Avion TriVersa-NanoMate robotic ion

source, 222, 223Axial ejection, radial ejection vs., 19

Background subtraction (BgS), 48, 47, 48with noise reduction algorithm, 348–350real-time dynamic, 123

Bacteria, antibiotic-resistant strains of, 291Bacterial colonies, study of, 290–291Bacterial infection, IMS applied to, 290–292Best quantification strategy, 408β-amyloid peptides, 408–410β-RAM flow scintillation analyzer (FSA),

136, 137BgS-NoRA, 348–350. See also Background

subtraction (BgS)Bile metabolic profiling, 49Bioactivation, 352

Bioactivation potential, of drug candidates, 340

Bioanalysis, with full scan acquisition, 105–106

Bioanalytical (BA) applications, 240Bioanalytical mass spectrometry (MS),

99–100Bioanalytical methods, 55

for target quantitation, 78Biochemical changes, 41–42Biological drugs

defined, 149MS analysis of, 149–190qualitative/quantitative analysis of, xii

Biological fluids, tracking siRNAs in, 360Biological matrices. See also Biomatrices

analysis of siRNA from, 372–376endogenous components in, 127extracting siRNAs from, 365–366

Biological properties, assessment of, 248–259

Biological sample analysis, HRMS for, 414–415

Biological samplescollection, storage, and preparation of,

56–59drug-derived material in, 133ensuring stability of, 133pooling of, 135–136

Biologic pharmaceuticals, characteristics of, 201. See also Biologics drugs

Biologicscharacterization of, 191chemical degradations in, 210degradation characterization in, 201–211future developments in imaging, 326impurities and degradation products in

small-molecule, 191–220MALDI-MS technique and, 192

Biologics drugs, U.S. market for, 201–202Biomarker concentration measurements, 42Biomarker measurement assays, targeted

metabolomic analyses vs., 393–394Biomarker research, 42Biomarkers, 41–42

in disease assessment, 403interest in, 289

Biomatrices, isolation of siRNAs from, 364. See also Biological matrices

Biomedical field, AMS in, 28Biotransformation analysis, of radioactive

samples, 136, 137

430 INDEx

Biotransformation studies, samples for, 132–133

Blood samples, 118–119Boronphenylalanine (BPA)-mediated boron

neutron capture therapy, 307Bottom-up methods, 192Brain regions, IMS in redefining, 286–287Breast cancer, IMS and, 289Breast cancer tissues, imaging, 290Bromine, in trapping agents, 341n-Butyl chloride, 67, 68

C16:0 lyso-PC, extraction of, 68Cancer biology, IMS studies of, 288–290. See

also Breast cancer entries; Oncology drugs; Tumor entries

Cancer tissue microarrays, analyzing after in situ digestion, 293. See also Pancreatic cancer tissue microarray

Cancilla, Mark T., ix, 357Cannibalistic factors, as antibacterial

compounds, 291Capillary columns, monolithic, 367Capillary electrophoresis (CE), 391, 394Caprioli, Richard M., ix, 277, 327, 328CaptiveSpray™ ion source, 48–49Carboxylic acid metabolite, 74Cassette analysis, 104Cassette incubation, 104Cassette incubation/HRAM analysis

approach, 106. See also High-resolution accurate mass (HRAM) systems

Cation exchange (CEx), in desalting samples, 365. See also CEx fractionation

Cation exchange chromatography, 155Cations, effects of small, 60Centroid data, 79Centroiding methodology, 419Centroid mode, MEWS applied in, 420Cetrorelix, 410CEx fractionation, 169. See also Cation

exchange (CEx)Chalcone synthetase gene, suppression of,

357“Charge residue,” 5Charge residue model (CRM), 4, 5Charge state reduction methods, in

PEGYLATED protein analysis, 167Charge states, CID behavior of, 369–370,

371Chelating agents, 365

Chemical agents, in analyte stabilization, 57Chemical biomarkers, 42Chemical degradants, detection of, 210Chemical degradation, 204–210Chemical derivatization

applications of, 140–141for structural elucidation, 140–141

Chemical derivatization experiments, 192Chemically modified oligonucleotides

fragmentation of, 370sequencing program for, 378

Chemically reactive metabolites, 339Chemical modifications. See also Chemically

modified oligonucleotidesapplied to siRNAs, 358–360influence on LC-MS response, 362–364

Chemical stability, assessing, 251Chemical structure(s)

in-depth knowledge of, 246growing variety of, 241

Chemical testing, 251–253Chemistry, in drug discovery process, 239Chemometrics, in metabolomics, 390Chen, Guodong, ix, 191Chick heart, visualizing molecular

morphology of, 285–286Chinese hamster ovary (CHO) cells, 207,

208Chip-based infusion nano-ESI system, 9, 10Chip-based nESI emitter array, 222–223.

See also Nanoelectrospray (nESI) entries; nESI chip

Chowdhury, Swapan K., ix, 339Chromatographic elution behavior, of

phospholipids, 62–65Chromatographic retention time, 60Chromatographic separation, 55, 73, 372,

396–397direct MS analysis without, 108–109between drugs and metabolites, 70–71, 72

Chromatographic surface, 13Chromatography

enhancing, 74–77mass spectrometry metabolomics and,

396–397reversed-phase, 62–65

Chromatography-interfaced techniques, 392

CID behavior, of charge states, 369–370, 371. See also Collision-induced dissociation (CID)

CID experiments, 26

INDEx 431

CID fragmentation, 207CID MALDI TOF/TOF, 23. See also

Matrix-assisted laser desorption/ionization (MALDI); Tandem TOF combinations (TOF/TOF); Time-of-flight (TOF) entries

CID MS/MS, 24. See also Tandem mass spectrometry (MS/MS)

Circulating human metabolites, characterization of, 132, 136

Clot formation, minimization of, 57Clozapine

distribution of, 323, 324, 325in zebrafish, 324, 325

Clozapine measurement, 309, 310Cluster-assisted desorption, 9Cluster ion sources, 307Coefficients of variation (CVs), 410Collision cells, 15, 16, 22, 23, 24

Orbitrap, 26Collision energy (CE), 16, 404

predicting, 407Collision gases, 17, 18, 27Collision-induced dissociation (CID), 15–16,

19–20, 38. See also CID entries; MS2 trap CID

GSH and, 340, 342, 343of phospholipids, 61–62of siRNA duplexes, 364

Collision-induced fragmentation (CID), 176, 177

in determining PEGylation site, 166Colon cancer biomarkers, 43Column/mobile phase combinations, testing,

83Column mobile phase screening, 74–75Columns, monolithic, 59Column selection, 75Column stationary phase screening, 74–75Column washing, via increasing organic

component, 65Commercial libraries, 395, 396Comparability studies, 150Compensation voltage (CV), 80Complex mixtures, analytical techniques

for, 192Compound-specific analysis, 99Compound-specific in vitro ADME

experiments, 100. See also Absorption, distribution, metabolism, and excretion (ADME) entries; In vitro ADME entries

Concentration–time plasma profiles, 131, 132

Consortium projects, human metabolome, 395

Constant neutral loss scan (CNLS), 341, 342

Continuous beams, 22Controlled gas-phase synthesis, 248Control sample background subtraction

routines, 46Conventional imaging technologies,

304–305Co-solvent method, 250COSY spectrum, 264Covalent binding, 258–259

adverse drug reactions and, 339–340Cross-ring cleavage, 159–160Cryo-sectioning, 313–314Crystallin proteins, 287–288CTC autosampler valve configurations, 100,

101C-terminal lysine variation, 208C-trap, 26, 345Cuyckens, Filip, ix, 405Cyanide, 258–259Cyanide-trapped reactive iminium ions,

350Cyclotron frequency (f), 25Cyclotronic motion, 24–25CYP phenotyping, 130. See also

Cytochrome P450 (CYP) entriesCys disulfide bonds, 207Cysteine (Cys), 208Cysteine connectivities

analysis of, 164characterization of, 160MS for determining, 161

Cysteine residues, degradants/impurities related to, 207

Cytochrome P450 (CYP) enzyme activities, 99

Cytochrome P450 (CYP) isoforms, identifying, 130

Data acquisition/analysis, 315Data analysis, 376–378Data analysis/interpretation, in

metabolomics, 390“Data independent” MS/MS strategy, 156Data interpretation software, 107Data interrogation routines, automating,

46

432 INDEx

Data mining, post-run, 123Data mining tools

for metabolite detection/identification, 256–258

for reactive metabolite screening, 345–351

use of, 256–258Data processing, in metabolomics, 390Data processing software tools, 121DBS-LESA-MS approach, 232. See also

Dried blood spots (DBS) cards; LESA entries; Liquid extraction surface analysis (LESA); Mass spectrometry entries

DC voltages, 15. See also RF/DC potentials“Dead time,” minimizing, 103Dealkylation tool, 256Deamidated peptides, detection of,

204–206Deamidation

of asparagine residues, 167, 177, 204minimizing, 212of therapeutic proteins, 168–170

Deconvoluted ESI mass spectra, 374Deconvoluted ESI-TOF mass spectra, 152,

154. See also Time-of-flight (TOF) entries

Deconvoluted mass spectra, 209Deconvolution software, 406, 419“Decoy” oligodeoxynucleotides, 326, 327Defensins, 289Deglycosylated heavy chain (HC) mAb

fragments, intact mass analysis of, 154. See also mAb entries; Monoclonal antibodies (mAbs)

Degradant molecular weights, 198–199Degradants, cysteine-related, 207Degradant structures, 198, 200Degradation, in peptide mapping, 211–213Degradation pathways, 198, 199–201Degradation products

characterization of, xii, 191in small-molecule pharmaceuticals/

biologics, 191–220Dempster, J. J., 1De novo sequencing, 369Derivatization, 326–327Derivatization techniques, 140–141

for distinguishing oxidation and glucuronidation sites, 141

Desalting, 365Desaturation, 124

DESI imaging, 309–311. See also Desorption electrospray ionization (DESI)

MALDI imaging vs., 311DESI technology, in many research areas,

308–309Desorption electrospray ionization (DESI),

7, 8, 109, 306, 307–311, 329, 391. See also Electrospray ionization (ESI)

application to tissue distribution studies, 309

direct tissue analysis by, 309in drug imaging studies, 309image resolution of, 311ionization efficiency of, 311

Desorption/ionization on porous silicon (DIOS), 11–12

Deuterium exchange information, 171Development, intact protein analysis of,

284–288Diclofenac glucuronide detection, 229, 230Differential ion mobility (DMS), 27Differential mass spectrometry (DMS), 42Digested peptides, 292–294Dillen, Lieve, ix, 403“Dilute-and-shoot” technique, 58Diluted solutions, electrospray analysis of,

4–5Dimethyl sulfoxide (DMSO), in sample

extraction, 134, 135Direct analysis in real time (DART), 7, 8–9,

109LESA vs., 229–231

Direct ESI technologies, 260. See also Electrospray ionization (ESI)

Direct injection/infusion (DI), 396Direct MS analysis, without

chromatographic separation, 108–109. See also Mass spectrometry entries

Direct online solid phase extraction (SPE), 103–104

Direct tissue analysis, 314Discovery metabolite identification, 116DiscoveryQuant™ Optimize software,

100–102Discriminant analysis. See Principal

component analysis (PCA) followed by discriminant analysis (DA) (PCA-DA)

Diseaseprotein aggregation and, 210RNAi and, 357

Disease assessment, peptide biomarkers in, 403

INDEx 433

Disulfide bondsformation of, 160mapping of, 207

Disulfide-containing peptides, identification of, 160

Disulfide-linked hinge dipeptide, mass spectra of, 163

Disulfide-linked peptide ions, 207Disulfide-linked structures, 161Disulfide mapping, 160–164Disulfides, of IgG2, 161–162Dithiothreitol (DTT), 211–212Dopant radical cations, 7Dose administration, in in vivo AME study,

131“Dosed” samples, 119Dried blood spots (DBS) cards, 231–232Droplet pick-up mechanism, 8Drug analysis, matrices for, 314Drug candidate metabolites, rapid

characterization of, 46Drug candidates

bioactivation potential of, 340concentrations of, 42incubation of, 130optimal pharmaceutical formulation of,

249safety of, 116therapeutic protein, 179

Drug compoundsfirst-pass metabolism of, 321, 322metabolic stability of, 253

Drug concentration(s), 56understanding, 60

Drug-derived material(s)in biological samples, 133maximum recovery of, 134profiling of, 137, 138

Drug detection, from tissue surfaces, 312Drug development. See also Drug

discovery/developmentdiscovery stage of, 244mass spectrometers in, 1–35metabolite identification in, 115–147therapeutic mAbs in, 177

Drug development programs, immunological assays and, 403–404

Drug development studies, 117Drug discovery, xi, 191, 244. See also Drug

metabolism discovery assaysADME assays in, 97mass spectrometers in, 1–35

metabolomics in, 388–390MSI technologies for, 305–312pace of, 258

Drug discovery/developmentLESA applications in, 224–229QWBA and, 221–222role of drug distribution studies in, 304

Drug discovery process(es), 239aspects of, 248–249improving, 240

Drug distributionLESA and whole-body, 225–227whole-body images of, 309–311

Drug distribution studies, role in drug discovery/development, 304

Drug–drug interaction (DDI) assays, 98Drug–drug interactions (DDIs), 130

reducing, 39Drug extraction, LLE for, 66–69Drug imaging, sample preparation for,

313–315Drug measurement, accuracy and recision

of, 80Drug metabolism, 27

qualitative/quantitative workflows in, 38–41

Drug metabolism and pharmacokinetic (DMPK) processes, 239

Drug metabolism discovery assays, 40Drug metabolism studies, 14

mass spectrometric approaches/instruments in, 126

techniques in, 1Drug metabolite identification, using mass

defect filters, 45–48Drug/metabolite imaging applications,

imaging mass spectrometry for, 315–326

Drug metabolitesdetection/identification of, 120–121extraction of, 348–349

Drug physicochemical/biological properties, assessment of, 248–259

Drug potency, 40Drug product degradation profiles, 191Drug products/substances, purity of, 243Drug purity, 243

upgrading, 245Drug quantitation, 28, 74

interference with, 69–70Drug retention, MALDI imaging and,

323

434 INDEx

Drugs. See also Pharmaceutical entries; Therapeutic entries

bringing to market, 37chromatographic separation of, 81–82generated from metabolites, 82imaging in whole-body sections,

321–322imaging mass spectrometry for, 303–337instability of, 56, 133ionization efficiencies of, 127PEGylated, 164poor penetration of, 291qualitative analysis of, 414quantitative performance measures for,

40radiolabeled, 116sample denaturing for dissociating, 178

Drug safety, 191Drugs/metabolites

application of MS to tissue distributions of, 329

extraction of, 224–225Drug SRM channel, 82. See also Selected

reaction monitoring (SRM) entriesDrug stability, evaluating, 133Drug targets, 259

characterization of, 259Du, Yi, ix, 149Dual-column system, 59Dual ion sources, 250Dual spray source, 22Dummy transitions, 410Duplex intensities, measured by

MALDI-MS, 368Duplex siRNA, 361–362. See also Small

interfering RNAs (siRNAs)collision-induced dissociation of, 364,

369–370Duplex siRNA metabolites, characterizing,

373–375Duty cycles, 420–421

enhanced, 421Dwell times, 17, 410, 411Dynamic protein affinity selection mass

spectrometry, 261

ECD experiments, 206. See also Electron capture dissociation (ECD)

EC oxidation, 5Eicosanoid metabolites, 393Eikel, Daniel, ix, 221Electrochemical (EC) oxidation reaction, 5

Electron capture dissociation (ECD), 48, 176–177, 180, 206

Electron capture ionization, 6Electron ionization dissociation (EID), 206Electron transfer dissociation (ETD), 48,

176–177, 180, 206. See also ETD fragmentation

on an ion trap, 177Electron volts (eVs), 16Electrophile-associated idiosyncratic drug

reactions, 46Electrophiles, 340

reacting GSH with, 340–343Electrospray (ESI) selected reaction

monitoring (SRM), 61–62Electrospray analysis, 4

of diluted solutions, 4–5Electrospray-assisted laser desorption/

ionization (ELDI), 10Electrospray HPLC-MS, MALDI-MS vs.,

12–13. See also High-performance liquid chromatography–mass spectrometry (HPLC-MS)

Electrospray ionization (ESI), 1, 2–5, 240, 245. See also Desorption electrospray ionization (DESI); ESI entries

introduction of, 277MALDI vs., 13matrix effects in, 59–60in positive and negative ion modes,

406–407siRNA chemistries and, 361

Electrospray ionization (ESI)-quadrupole (Q) mass spectrometry (MS), 151

Electrospray process, 3Electrosprays

flow rates for, 4pneumatically assisted, 2

Electrospray spectrum, for Enfuvirtide, 406Electrostatically trapped ions, 38Electrostatic mirror, 21Elemental compositions, 246Elements

masses of, 347quantitation of, 13–14

ELISA hybridization technique, 367. See also Enzyme-linked immunosorbent assay (ELISA)

ELISA methods, 177Elution, isocratic, 65Elution behavior, of phospholipids, 62–65Emary, William Bart, ix, 37

INDEx 435

Embryo implantation, protein changes during, 284–285

Endogenous biomarker measurement assays, targeted metabolomic analyses vs., 393–394

Endogenous components, 133effects of, 60

Endogenous peptides, intact, 294–296Endonuclease degradation, 374–375Enfuvirtide, 406, 412–413, 415–416, 417Enhanced duty cycle, 421Enhanced product ion (EPI) scans, 20Enzymatic digestion, 169, 412Enzyme-linked immunosorbent assay

(ELISA), 42, 43. See also ELISA entries

siRNAs and, 360Epidermal growth factor receptor (EGFR),

318Epimerization, 57, 73ESCi sources, 245ESI analysis, siRNAs and, 362. See also

Electrospray ionization (ESI) entriesESI efficiency

effect on mobile phase, 75siRNA hydrophobicity and, 364

ESI-ion trap, 151ESI-ISF-CID method, in determining

PEGylation site, 166–167. See also Collision-induced dissociation (CID); In-source fragmentation (ISF)

ESI mass spectra, deconvoluted, 374ESI-MS, 210, 211. See also Mass

spectrometry entriesin PEGylated protein analysis, 167

ESI-MS isotopic distribution, 169ESI-Orbitrap™ mass spectrometry (MS),

151ESI-QTOF-MS, 151. See also Fast scanning

Q-TOF MS/MS systems; Q-TOF MS; Quadrupole time-of-flight (Q-TOF); Time-of-flight (TOF) entries

ESI response derivatization, 407ESI-TOF, 179. See also Time-of-flight (TOF)

entriescoupling with HPLC separation, 151RP-HPLC combined with, 153

ESI-TOF mass spectra, 168ESI-TOF MS, 151, 152Ester groups, metabolites containing, 74ETD fragmentation, 207. See also Electron

transfer dissociation (ETD)

Ethyl acetate, 67, 68E to Z isomerization, 73Exonuclease degradation, 374–375Experiments, resolving power of, 396Extracted ion chromatograms (EICs), 40,

45, 79, 107, 122, 405obtained with MEWs, 418

Extracted ion chromatogram (EIC) search, 160

Extraction columns, 58, 59Extraction methodologies, 134Extraction of dissolved ions under

atmospheric pressure (EDIAP), 2Extraction solvent, optimizing, 224Ex vivo imaging technologies, 304

Fab region, 208. See also Fragment-antibody binding (Fab) mAb fragments

FAIMS devices, 80, 174. See also Field asymmetric waveform ion mobility entries

False positives, eliminating, 346Fast-atom bombardment (FAB), 11Fast-atom bombardment (FAB)-MS, 164Fast flow injection analysis (FIA), 241. See

also Flow injection analysis (FIA)Fast-flow online extraction technique, 58Fast Fourier transform (FT), 345Fast scanning Q-TOF MS/MS systems, 253.

See also Q-TOF MS; Time-of-flight (TOF) entries

Fast-scanning triple quadrupole instruments, 410

FDA MIST guidance, 116. See also Food and Drug Administration (FDA)

Fenn, John, 2Fexofenadine, 225–227, 321–322FIA-based method development

approaches, 100Fibrinogen clots, 57FIEHNLIB library, 395Field asymmetric waveform ion mobility

(FAIMS), 27. See also FAIMS devices; High-field asymmetric waveform ion mobility spectrometry (FAIMS); Ion mobility spectrometry (IMS)

Field asymmetric waveform ion mobility mass spectrometry (FAIMS), 404

Fingerprinting profiling, 390, 391–392Fingerprinting techniques, analytical

approaches and, 391–392

436 INDEx

First-in-human (FIH) studies, 81, 116, 120use of samples from, 117–119

First-pass metabolism, of drug compounds, 321, 322

Fixatives, alternative, 280Fixed mode, 16Fixed tissue samples, 279–280Flanagan, W. Michael, ix, 357Flight time, of ions, 343Flow injection analysis (FIA), 100, 102, 396.

See also Fast flow injection analysis (FIA)

Flow-injection RP-HPLC-MS technique, 170. See also Reversed-phase entries

Flow scintillation analyzer (FSA), 136, 137Fluorescence enhancement/detection, 262,

263, 264Fluticasone MS/MS fragmentation, 226. See

also Tandem mass spectrometry (MS/MS)

Fluticasone study, 225Food and Drug Administration (FDA), on

PEGylated drugs, 164Food and Drug Administration (FDA)

guidance, 116Forced degradation studies, 252Formalin-fixed paraffin embedded (FFPE)

samples, 293–294, 296Formalin-fixed tissue, 280Formic acid, analyte response and, 75Fourier transform (FT), 345Fourier transform–ion cyclotron resonance

(FT-ICR), 24–25, 115, 344–345. See also FT-ICR entries

Fourier transform–ion cyclotron resonance (FTICR)-MS, 19. See also Mass spectrometry entries

Fourier transform–ion cyclotron resonance (FT-ICR)-MS mass spectrometers, 245, 295

Fourier transform mass spectrometry (FT-MS), 24–27. See also Mass spectrometry entries

ion detection and, 25Fraction-collecting autosampling, 367–368Fragment-antibody binding (Fab) mAb

fragments, 152, 153. See also Fab regionFragmentation

of chemically modified oligonucleotides, 370

ion trap mass spectrometry and, 414of peptides, 406–407

Fragmentation pathways, 193–194, 247mapping, 248

Fragmentation patterns, 196Fragmentation process, alternative, 28Fragmentation spectra, 175Fragment-crystallizable (Fc) mAb

fragments, 152, 153. See also Monoclonal antibodies (mAbs)

Fragmented ions, intact protein ions and, 175

Fragmented peptides, 156Fragmented protein ions, 156Fragment identification, 208Fragment ions, 193, 194, 206

of GSH conjugates, 340, 342mass data on, 199

Free radicals, 340Free thiol content, reducing, 207Free thiols

investigating, 179mass spectrometric analysis of, 161

Frequency-sweep signal, 344–345Fresh frozen tissue samples, 279Frontal affinity chromatography, 261FT-ICR instruments, ECD and, 176–177FT-ICR mass analyzer, 344FT-Orbitrap, 115Full issue image analysis, 278Full scan acquisition, bioanalysis with,

105–106Full scan HRAM-based bioanalysis,

advantages of, 106. See also High-resolution accurate mass (HRAM) systems

Full scan HRMS, 415. See also High-resolution mass spectrometry (HRMS)

Full scan MS analysis, 120. See also Mass spectrometry

Full scan MS data, 43Full scan MS/MS experiments, 223Full scan tandem mass spectrometry, with

triple quadrupole instruments, 22Full width at half maximum (FWHM),

38–39, 79, 416Full width at half maximum units, 15

Gas chromatography (GC), 397Gas chromatography–mass spectrometry

(GC-MS), 391, 392, 394Gas phase chemistry, 28Gas-phase ionization process, 6, 7Gas phase ions, 5

INDEx 437

Gas-phase synthesis, controlled, 248Gene expression, post-transcriptional

control of, 357Generic data acquisition modes, 108Genomics, 388Global precursor scan, 28GLP preclinical multi-day toxicity testing,

42GLP-toxicology studies, 120Glucocorticoid receptor (GR) agonists

liquid extraction surface analysis and, 225

skin penetration for, 316–317Glucuronidation sites, derivatization

techniques for distinguishing, 141Glutamate (Glu), isoGlu residues from, 206Glutamine (Gln) residues, 204Glutathione (GSH), 258–259

reacting with electrophiles, 340–343for trapping/quantitation of reactive

metabolites, 351Glutathione (GSH) conjugates, 123. See

also GSH entriesGlutathione (GSH) drug conjugates, 46–48Glycan composition, correlation to

attachment site, 160Glycans

biosynthesis of, 158mass spectrometric fragmentation of,

159–160released from glycoproteins/

glycopeptides, 158Glycerophospholipids, 60, 61

classes of, 61Glycoforms, quantitation of, 158–159Glycopeptides, analysis of, 158Glycoproteins, analysis of, 158Glycosidic cleavage, 159–160Glycosylation, 179

of immunoglobulin G, 172Glycosylation analysis, 158–160Gradient effect, removing, 127Gradient methods, 250GSH adducts, 347, 349, 350. See also

Glutathione (GSH) entriesdetecting, 350MS/MS survey scan for, 343

GSH conjugate detection, 340–343GSH conjugates, 346–347

classes of, 343fragment ions of, 340, 342screening, 341, 346–347

GSH-metabolite detection, 229GSH-related species, detecting, 258Guanidine hydrochloride (GdnHCl),

211

“Hard” electrophiles, 340Hard ionization techniques, 306“Hard” nucleophiles, 340Hardware ruggedness, 39–40HC subunits, analyzing, 153. See also

Heavy chain (HC) mAb fragmentsH/D HPLC-MS exchange experiments,

195–196. See also High-performance liquid chromatography–mass spectrometry (HPLC-MS); Hydrogen deuterium (H/D) exchange (HDx)

HDx data analysis, automating, 173. See also Hydrogen deuterium (H/D) exchange (HDx)

HDx MS. See also Hydrogen deuterium (H/D) exchange MS

applications of, 171–173challenges related to, 173development of, 173

HDx MS experiments, basic principles of, 171

HDx studies, ion mobility MS and, 173Heart, visualizing molecular morphology

of chick, 285–286Heat-stabilized tissue, 279, 280Heavy chain (HC) mAb fragments, 152,

153, 154, 155Helium, as collision gas, 17, 18Hematoxylin and eosin (H&E) sections,

291–292Henion, Jack D., ix, 221Hepatocyte incubations, 130Hepatocytes, covalent binding in, 340Hepatotoxicity, 339Heterogeneous charge-transfer mechanism,

8Hexane, 67HFIP (1,1,1,3,3,3-hexafluoro-2-propanol),

366–367HFIP/TEA ion-pairing system, 366–367High-aqueous reversed-phase

chromatography, phase collapse and, 75–76

High-energy CID, 24. See also Collision-induced dissociation (CID)

High energy collision (HCD) cell, 26

438 INDEx

High-field asymmetric waveform ion mobility spectrometry (FAIMS), 80. See also Field asymmetric waveform ion mobility entries; Ion mobility spectrometry (IMS)

High mass ions, 21High MW therapies, 43–44. See also

Molecular weights (MWs)High organic mobile phase, 77High-performance liquid chromatography

(HPLC), 102–103. See also HPLC entries

chromatographic separations and, 396–397

hyphenation of, 262High-performance liquid chromatography–

high-resolution mass spectrometry (HPLC-HRMS), xi, 44

High-performance liquid chromatography–mass spectrometry (HPLC-MS), 1, 2, 7, 115, 120, 150, 249, 404. See also APCI HPLC-MS applications; HPLC-MS entries

applications of, 39–41coupled with in-line radioactive detector,

136with high-resolution mass spectrometers,

105–108in impurity/degradation product analysis,

213in PEGylated protein analysis, 167sensitivity and specificity of, 251

High-performance liquid chromatography–tandem mass spectrometry (HPLC-MS/MS), xi, 55, 77, 109–110, 150, 404. See also HPLC-MS/MS entries

in determining PEGylation site, 166importance of, 240in impurity/degradation product analysis,

213peptide mapping using, 211with triple quadrupole mass

spectrometers, 100–105High-performance liquid chromatography

(HPLC) with high-resolution accurate mass spectrometry (HPLC-HRAMS), 78–79. See also HPLC-HRAMS entries

ability to detect ions, 78for drug quantitation, 79HPLC-SRM vs., 78–79platforms for, 78

High resolution (HR), product ion selection at, 420

High-resolution accurate mass spectrometers, 77–78

High-resolution accurate mass spectrometry (HRAMS), 56, 77–79

High-resolution accurate mass (HRAM) systems, for metabolomics, 397. See also LC-HRAM

High-resolution instruments, improvements in, 405

High-resolution mass spectrometry (HRMS), xi, 40, 41, 43, 106, 343–345, 405. See also HRMS entries

for biological sample analysis, 414–415for biomarker discovery and compound

assessment, 42future trends in, 28implementation of, 40for new drug discovery applications,

37–54for peptide quantification, 414–420for regulated analysis, 41role in quantitative bioanalysis, 421technological advancements in, 37

High-resolution mass spectrometers (HRMSs), 49, 115

future trends in, 142for metabolite detection, 121–123for structural elucidation, 123–124use of, 121–124

High-resolution MS experiments, 192. See also Mass spectrometry

High-resolution MS hardware, 106High spatial/mass resolution system, 43High-throughput assay methods, rapid

implementation of, 249High-throughput indirect mass

spectrometric screening assays, 261High-throughput screening (HTS)

libraries, 239. See also HTS compound libraries

HILIC column technologies, 241. See also Hydrophilic interaction liquid chromatography (HILIC)

Hillenkampf, F., 11HIV-fusion inhibitor, 412HMDB library, 395Homogeneous/heterogeneous reaction

environments, coupling of MS to, 261Honing, Maarten, ix, 239Hopfgartner, Gérard, ix, 1

INDEx 439

HPLC-atmospheric pressure chemical ionization (APCI)-MS, 140

HPLC-electrospray ionization (ESI)-MS, 127

HPLC ESI-MS, 366. See also Electrospray ionization (ESI); High-performance liquid chromatography–mass spectrometry (HPLC-MS)

HPLC-ESI-MS/MS, 140. See also High-performance liquid chromatography–tandem mass spectrometry (HPLC-MS/MS)

HPLC-HRAMS bioanalytical methods, mass resolving power for, 78–79. See also High-performance liquid chromatography (HPLC) with high-resolution accurate mass spectrometry (HPLC-HRAMS)

HPLC-HRAMS parameters, evaluation of, 79

HPLC-MS analysis, 128. See also High-performance liquid chromatography–mass spectrometry (HPLC-MS)

HPLC-MS assays, 44HPLC-MSE, 156. See also MSE entriesHPLC-MS injections, 120HPLC-MS methods, performance of, 59HPLC-MS/MS-based assay methods, 251.

See also High-performance liquid chromatography–tandem mass spectrometry (HPLC-MS/MS)

improved sensitivity of, 249HPLC-MS/MS bioanalysis, 55–56, 75

lysophospholipids in, 68–69quantitative, 85

HPLC-MS/MS bioanalytical methods, development of, 82

HPLC-MS/MS method development, 100HPLC/MS/MS peptide mapping analysis,

204–206HPLC-MS/MS quantification, of amyloid

peptides, 413HPLC-MS/radiometry, sample analysis

using, 136–139HPLC-MS response, 127HPLC-MS techniques

advances in, 142in structural elucidation, 140

HPLC-NSI-MS, 127HPLC separation, coupling ESI-TOF with,

151HPLC separation methods, 116

HPLC-SRM bioanalytical methods, 77. See also Selected reaction monitoring (SRM) entries

HPLC-HRAMS vs., 78–79HPLC systems, to remove gradient effect,

127HPLC-UV–based purity assays, 252. See

also Ultraviolet (UV) entriesHPLC-UV-MS, 245HPLC-UV quantitative analysis, 251HRAM mass spectrometers, for

metabolomics, 397HRAMS resolving power, 78–79. See also

High-resolution accurate mass spectrometry (HRAMS)

HR-HPLC/MS/MS experiments, 196, 213. See also High-performance liquid chromatography–tandem mass spectrometry (HPLC-MS/MS); High resolution entries

HR-LC/MS/MS experiments, 196. See also Liquid chromatography–tandem mass spectrometry (LC-MS/MS)

HRMS instruments, 121, 420, 421. See also High-resolution mass spectrometry (HRMS)

for quantitative bioanalysis, 414HRMS research, future trends in, 48–49HRMS spectral data, transformation of raw,

419–420HRMS SRM strategy, 420. See also Selected

reaction monitoring (SRM) entriesHRMS systems, 38–39HRMS technologies, 345–346, 405

advances in, 343, 351HSH trapped adducts, rapid detection of,

349HSQC NMR spectrum, 264. See also

Nuclear magnetic resonance (NMR)HTS compound libraries, 251–252. See also

High-throughput screening (HTS) libraries

Human ADME studies, 132. See also Absorption, distribution, metabolism, and excretion (ADME) entries

Human cancer tissue, investigations of, 288

Human circulating metabolites, 128profile of, 118

Human metabolism data, 117–118Human metabolite testing, qualifications

regarding, 116

440 INDEx

Human metabolome consortium projects, 395

Human Metabolome Project, 395Human Plasma Metabolome (HuPMet),

395Human plasma phospholipids, techniques

for monitoring, 63Hybrid FT-ICR instruments, 345. See also

Fourier transform–ion cyclotron resonance (FT-ICR)

Hybrid ion activation techniques, 370Hybrid mass spectrometers, 19, 22, 27, 120Hydrazine-based derivatives, 327Hydrochlorothiazide, 232Hydrodynamic instability, 4–5Hydrogen deuterium (H/D) exchange

(HDx), 140, 171–173, 180, 213combined with MALDI-MS, 211, 260–261

Hydrogen/deuterium exchange experiments, 48

Hydrogen deuterium (H/D) exchange MS, 252. See also HDx MS entries

Hydrophilic interaction liquid chromatography (HILIC), 77, 241, 397

Hydrophobicity, ion-pairing reagents with increasing, 366–367. See also siRNA hydrophobicity

Hydroxy acid drugs, 70–71, 72lactone metabolites of, 73

ICH: M3(R2) guidance, 116ICR cell, 345. See also Fourier transform–

ion cyclotron resonance (FT-ICR)Idiosyncratic drug reactions, electrophile-

associated, 46IgG1 antibody, 208. See also

Immunoglobulin entriesIgG2 disulfides, 161–162IgG2 isoform composition, 162IgG2 mAb, modified form of, 154–155. See

also Monoclonal antibodies (mAbs)Imaging, unconventional applications for,

323–326. See also Autoradiography imaging; DESI imaging; Drug/metabolite imaging application; Drug imaging; Magnetic resonance imaging (MRI); MALDI imaging entries; Mass spectrometry imaging entries; Semi-quantitative imaging technology; SIMS imaging; Tissue images

Imaging analysis, matrix applications for, 281

Imaging-capable MS platforms, 304Imaging data, quantification of, 328–329Imaging mass spectrometry (IMS). See also

IMS entries; Ion mobility mass spectrometry (IMMS, IMS); Ion mobility spectrometry (IMS); Mass spectrometry imaging (MSI)

abscesses examined by, 291applications to bacterial imaging, 290–292applications to cancer research, 288–290applications to histology, 284–288in classifying HER2 status, 289for drugs and metabolites, 303–337fundamentals of, 312–315future developments in, 326–329imaging via, 277lens protein distribution and, 287–288methodology of, 278–284molecular morphology visualization

using, 285–286peptide analysis via, 294–296of proteins/peptides, 277–302in redefining brain regions, 286–287sample preparation for, 278–280

Imaging technologiesconventional, 304–305optimizing and advancing, 277

Imatinib, distribution/quantitation of, 328Iminium ions, cyanide-trapped reactive, 350Immunoglobulin G (IgG), glycosylation of,

172. See also IgG entriesImmunoglobulin (Ig) molecules, 152Immunological assays, drug development

programs and, 403–404Impurities

characterization of, xii, 191cysteine-related, 207profiling and identification of, 251in small-molecule pharmaceuticals/

biologics, 191–220Impurity ions, characterization of, 194–197Impurity profiling, 243–245

of large biomolecules, 419Impurity structures, 197IMS instrumentation, 281–283. See also

Imaging mass spectrometry (IMS); Ion mobility mass spectrometry (IMMS, IMS); Ion mobility spectrometry (IMS)

IMS technology, as a tool for in situ molecular assays, 296

IMS-TOF device, 48, 50. See also Time-of-flight (TOF) entries

INDEx 441

Incubation/analysis, 107Incubations, microsomal and hepatocyte,

130Incurred sample applications, in method

development, 80–82Incurred sample extract, analysis of, 84Incurred sample reanalysis (ISR), 56. See

also ISR conceptIncurred samples, 56

for method testing, 83–84pooled, 81

Induced degradation, 212Inductively coupled plasma (ICP), 13–14Inductively coupled plasma–atomic

emission spectroscopy (ICP-AES), 325–326

Inductively coupled plasma mass spectrometry (ICP-MS), 1, 13–14

“Industrial validation,” 262Information assembly, 82Information-dependent analysis (IDA),

108Information-dependent analysis (IDA) MS

experiments, 223–224Infrared (IR) lasers, 10Infrared (IR) multiphoton dissociation

(IRMPD), 176, 370Ingelse, Benno, ix, 239Inhaled tiotropium (ITP), spatial

distribution of, 316Initial metabolism assessment, strategy for,

130Injection solvents, 85In-line radioactive detector, HPLC-MS

coupled with, 136Inorganic ions, analysis of, 3In situ digestion, 292In-source decay (ISD), 284

in determining PEGylation site, 166In-source fragmentation (ISF), 124

in determining PEGylation site, 166In-source fragmentation spectra, 175Instrumentation, 38–39, 115. See also

Analytical instrumentation; FT-ICR instruments; High-resolution instruments; HRMS instruments; Hybrid FT-ICR instruments; Ion cyclotron resonance instrument; Ion mobility instruments; Ion trap instruments; LIT-FT-ICR instruments; MALDI-TOF instruments; Mass spectrometric approaches/instruments;

MS instrumentation; NanoMate™ instruments; Orbital trapping instruments; Q-trap instrument; Quadrupole instruments; Quadrupole-time-of-flight (QqTOF) instruments; TOF instruments; TOF trapping instruments; Triple quadrupole (QqQ, QQQ) instruments

Instrumentation duty cycles, impact of, 420–421

Intact duplex detection, disadvantages of, 375

Intact endogenous peptides, 294–296Intact glycoproteins, analysis of, 158Intact lysozyme, bioanalysis of, 418–419Intact mAb molecules, HPLC-MS analysis

of, 153–154Intact mass analysis, 151–155, 179Intact protein analysis, applications of,

284–292Intact protein ions, fragmented ions and,

175Intelligent data-dependent acquisition

processes, 142“Intelligent” data mining tools, in screening

reactive metabolites, 339–355Interference, 69–74Intermediate formation, 258Internal standards (IS, ISTD), 410

radiolabeled peptides as, 178In vitro ADME assay automation, 109. See

also Absorption, distribution, metabolism, and excretion (ADME) entries

In vitro ADME assays, mass spectrometry for, 97–113

In vitro ADME assay samples, analyses of, 99

In vitro ADME bioanalysis, 99–100, 102In vitro ADME profiling, 110In vitro ADME sample reduction, through

cassette incubation/analysis, 104In vitro ADME samples, analyses of, 103In vitro ADME support, 100, 102–103, 106,

109In vitro experiments, 97In vitro incubations, 258In vitro–in vivo correlations (IVIVCs), 97In vitro metabolic stability assays, 107In vitro metabolism profiles, comparing,

375–376In vitro screening assays, 249

442 INDEx

In vitro studies, with radiolabeled test article, 130

In vivo AME studies, dose administration and sample collection in, 131

In vivo cassette dosing, 40In vivo DDI potentials, 99In vivo fixed tissue, 279In vivo imaging technologies, 304In vivo MRI, 326. See also Magnetic

resonance imaging (MRI)In vivo studies, with radiolabeled test

article, 130–136Ion accumulation, 18Ion chromatograms, 348Ion cyclotron frequency (f), 344–345Ion cyclotron resonance instrument, 25Ion cyclotron resonance mass systems, 2Ion detection, 14–15, 25Ion/electron molecule reactions, 9Ion evaporation, 5Ion evaporation model (IEM), 4, 5Ion exchange (IEx) chromatography, 162,

171Ion filtering devices, 48Ion-flight-time equation, 343Ionic compounds, 11Ion/ion reactions, 370Ionization, of peptides, 406–407Ionization efficiency, 241

of analytes, 225of DESI, 311enhancement of, 407reduction in, 362

Ionization methods, alternative, 28Ionization process, 7Ionization suppression, 108–109Ionization techniques, 1, 2–14, 21

improvements in, 245variety in, 252

Ionization technologies, future trends in, 142

Ion mobility, 28differences in, 80

Ion mobility instruments, 174, 282Ion mobility mass spectrometry (IMMS,

IMS), 27, 173–174, 180, 404. See also IMS entries; Ion mobility spectrometry (IMS)

advantages of, 174HDx studies and, 173

Ion mobility separation (IMS), 48, 50. See also IMS entries

Ion mobility separation, 173–174, 283Ion mobility spectrometry (IMS), 173–174,

180. See also IMS entriescoupled with MS instruments, 173–174

Ion motion, 14in quadrupoles, 14

Ion-pairing (IP) reagents, 362with increasing hydrophobicity, 366–367

Ion-pair reversed-phase HPLC (IP-RP-HPLC), 366

Ions, electrostatically trapped, 38Ion separation, 27Ion signal intensity, 170Ionspray, 2. See also Electrospray entriesIon suppression, 60Ion trap instruments, 413–414. See also

Orbitrap™ entries; Q-trap instrumentIon trap mass spectrometers, 255. See also

IT mass spectrometersIon trap mass spectrometry, 413–414Ion traps (ITs), 17–20, 115. See also Linear

ion traps (LITs); Quadrupole ion trap entries; Two-dimensional (2D) ion traps (LTQs)

linear quadrupole, 38mass ranges of, 18

Ion trap technology, published reports on, 414

IS addition, 69Isoaspartate (isoAsp, iso-Asp)

amount in proteins, 167–168Asp products vs., 177

Isoaspartate (isoAsp) residues, 206Isobaric metabolites

identification of, 123–124interference from, 71–73

Isobaric phase 2 metabolites, 124, 125Isobaric phosphate prodrugs, 73Isobaric structures, differentiating between,

159Isocratic elution, 65Isoelectric focusing (IEF), 204Isoglutamate (isoGlu) residues, 206Isomeric metabolites, 82

interference from, 71, 72Isopropyl alcohol elution, 63–65Isotope envelopes, 375Isotope pattern filter (IPF), 350–351Isotopic metabolites, interference from,

70–71, 72, 73Isotopic peaks, 416Isotopic ratios, 27–28

INDEx 443

ISR concept, 81. See also Incurred sample reanalysis (ISR)

ISTD peptides/proteins, 179IT mass spectrometers, 120–121. See also

Ion trap entriesIT-TOF hybrid mass spectrometer, 344. See

also Time-of-flight (TOF) entries

Jemal, Mohammed, ix, 55Jetstream™ spray device, 41

Karas, M., 11Ketone metabolites, 73Kidney abscesses, examined by IMS, 291“Kinetic” assays, 250–251Kinetic energy, in TOF analysis, 20–21“Kinetic method,” 248Kits, absolute metabolite quantitation,

393Korfmacher, Walter A., ix, xiiKretschmer algorithm, 378

Label/tracer requirements, 305Lactone group, 56–57Lactone metabolites, of hydroxy acid drugs,

73Lactones, chromatographic separation

interference due to, 70–71, 72Ladder sequence ions, 407Large biomolecules, impurity profiling of,

419Large peptides, direct analysis of, 158Larger molecule therapies, analysis of, 326Larger proteins, quantitative workflows for,

404Laser ablation electrospray ionization

(LAESI), 10–11, 109Laser beams, to probe tissue, 43Laser desorption, 10Laser diode array thermal desorption

(LDTD), 109Laser-induced dissociation (LID) MS/MS,

24Laser ionization, 11Lasers, 282–283LC-ARC system, 139. See also Liquid

chromatography entriesLC column effect, 66LC-ESI-MS, 279. See also Electrospray

ionization (ESI); Mass spectrometry entries

LC-fluorescence, 263

LC-HRAM, 106. See also High-resolution accurate mass (HRAM) systems

LC mobile/stationary phases, screening of, 83

LC-MS chromatograms, 263. See also Liquid chromatography–mass spectrometry (LC-MS)

LC-MS data, 118fingerprinting analysis of, 391, 392

LC-MS/MS bioanalysis, avoiding pitfalls in, 56–80. See also Liquid chromatography–tandem mass spectrometry (LC-MS/MS)

LC-MS/MS ion chromatogram, 346LC-MS/MS methods, in analyses of small

molecules from biological matrices, 372

LC-MS/MS platforms, 303LC-MS/MS quantitation data, discrepancies

in, 329LC-MS/MS screening, development of, 248LC-MS peptide maps, mirror plots of, 157LC-MS platforms, 243LC-MS response, influence of

oligonucleotide sequence/chemical modifications on, 362–364

LC-MS spectra, 124LC-MS (FT) spectra, 125. See also Fourier

transform mass spectrometry (FT-MS)LC-MS techniques, siRNA-related, 366–368LC-MS total ion chromatogram, 193LC platforms, 243LC-Q-TOF MS/MS, 242. See also Fast

scanning Q-TOF MS/MS systems; Time-of-flight (TOF) entries

LC-SRM, 106. See also Selected reaction monitoring (SRM) entries

LC-SRM technique, 77LC subunits, analyzing, 153LC/UV chromatograms, 199. See also

Ultraviolet (UV) entriesLead compound, discovery of, 239–240Lead optimization (LO) compounds, 243Lean thinking initiative, 240Lens protein distribution, 287–288LESA applications. See also Liquid

extraction surface analysis (LESA)additional, 229–233in drug discovery/development, 224–229future for, 232

LESA-LC approach, 233. See also Liquid chromatography entries

444 INDEx

LESA-LC-MS approach, 233. See also Liquid chromatography–mass spectrometry (LC-MS)

LESA-MS profiling, 225. See also Mass spectrometry entries

LESA-MS-SRM, 227, 228. See also Selected reaction monitoring (SRM) entries

LESA sampling process, 227–229LESA schematic, 223LESA spatial resolution, 233LESA system operation, 233Libraries, web-based, 395, 396Light chain (LC) mAb fragments, 152, 153,

155. See also Monoclonal antibodies (mAbs)

“Limited” throughput issue, solutions to, 245Limit of quantification (LOQ), 178. See also

Lower limit of quantitation (LLOQ)of siRNAs, 362

Linear ion traps (LITs), 1–2, 18–19, 120, 344, 405. See also LIT entries

quadrupole ion traps vs., 17Linear quadrupole ion trap, 38, 120Lipid analysis, 229Lipid nanoparticles (LNPs), 44–45Lipinski “rule of five,” 246Lipophilicity, assessment of, 249–250Liquid chromatography (LC), coupled with

triple quadrupole mass spectrometer, 100. See also LC entries

Liquid chromatography–high-resolution mass spectrometry (LC-HRMS), in screening reactive metabolites, 339–355

Liquid chromatography–mass spectrometry (LC-MS), 242, 305, 391, 392, 394. See also LC-MS entries

quadrupoles used for, 15of siRNAs, 362

Liquid chromatography (LC) separation, 170

Liquid chromatography–tandem mass spectrometry (LC-MS/MS). See also LC-MS/MS entries

approaches for reactive metabolite screening, 340–343

for quantification of therapeutic mAbs, 178

Liquid extraction probe, 9Liquid extraction surface analysis (LESA),

xii, 221–238. See also LESA entriesin automatic analyte extraction, 231–232DART vs., 229–231glucocorticoid receptor agonists and, 225

for identifying pesticides, 229interest in, 234outlook and future development of,

233–234shotgun lipidomic approaches and, 229spatial resolution of, 224whole-body drug distribution and,

225–227Liquid extraction surface analysis mass

spectrometry (LESA-MS), 222. See also LESA-MS entries

advantages and limitations of, 234–235applications of, 234applied to toxicological samples, 231extraction efficiency of, 227–229

Liquid extraction surface analysis (LESA) process, 222–224

Liquid junction, 224Liquid–liquid extraction (LLE), 57, 58, 84,

134, 366. See also LLE entriesfor drug and metabolite extraction, 66–69

Liquid microjunction surface sampling probe (LMJ-SSP), 9–10, 222

Liquid scintillation counting (LSC), 28LIT/FT-CR combination, 25. See also

Fourier transform mass spectrometry (FT-MS); Linear ion traps (LITs)

LIT-FT-ICR instruments, 345. See also Fourier transform–ion cyclotron resonance (FT-ICR) entries

LIT MALDI, 13. See also Linear ion traps (LITs); Matrix-assisted laser desorption/ionization (MALDI)

LIT-TOFMS, 19. See also Mass spectrometry entries; Time-of-flight (TOF) entries

LLE extract, 65. See also Liquid–liquid extraction (LLE)

LLE-SPE combination extraction method, 365–366. See also Solid phase extraction (SPE)

LLOQ chromatograms, for Enfuvirtide, 417. See also Lower limit of quantitation (LLOQ)

LLOQ peak areas, 410, 411Locked nucleic acids (LNAs), 361Lock masses, 22LockSpray, 22Loss of adduct, 159–160Lower limit of quantitation (LLOQ), 38, 40,

41, 66, 78, 82, 99, 408–412. See also LLOQ chromatograms

Low mass ions, 21

INDEx 445

Low molecular weight compounds (LMWCs), 1, 12. See also Molecular weights (MWs)

analysis of, 13LTQ-FT, 44. See also Fourier transform

mass spectrometry (FT-MS); Two-dimensional (2D) ion traps (LTQs)

LTQ-Orbitrap, 26–27LTQ-Orbitrap mass spectrometers, 121, 347

advantages of, 193Lung tumor tissue, protein profiles from,

288Lx-0722, 122Lyso-PC, in LLE plasma extracts, 67–68Lyso-PC phospholipid class, 61, 62. See also

Phosphatidylcholine (PC) phospholipid class

in HPLC-MS/MS bioanalysis, 68–69Lyso-PC species, 68Lysophospholipids, 61, 62, 65Lysozyme, bioanalysis of, 418–419

M + 1/M + 2 isotopic contributions, 73M10 metabolite, 124Ma, Shuguang, x, 339mAb fragments, 151–152. See also

Monoclonal antibodies (mAbs)mAb ISTD, 178mAb quantification methods, improvements

in, 178mAb therapeutic proteins, structure of, 153Macromolecule exclusion, 59Magnetic resonance imaging (MRI),

304–305. See also In vivo MRI; MRI contrast agent

Magnetron motion, 25MALDI analyses, 281, 282–283. See also

Matrix-assisted laser desorption/ionization (MALDI)

MALDI images, 319, 320as complementing autoradiography, 323in whole-body sections, 321–322

MALDI imaging, 233, 310, 329derivatization for, 327DESI imaging vs., 311development of, 326future developments in, 326–329unconventional applications for, 323–326

MALDI imaging analysis, 323MALDI imaging experiment, 227, 229MALDI ion production process, 23MALDI lasers, 312MALDI mass spectrometric imaging, 306

MALDI mass spectrometry, H/D exchange and, 260–261. See also MALDI MS entries; MALDI-TOF MS; Matrix-assisted laser desorption/ionization–mass spectrometry (MALDI-MS)

MALDI matrices, 11, 12, 280MALDI-MS/MS imaging, of astemizole,

316, 317. See also MALDI mass spectrometry; Matrix-assisted laser desorption/ionization–mass spectrometry (MALDI-MS); Tandem mass spectrometry (MS/MS)

MALDI MS platform, 304MALDI spectra, 159MALDI/SRM, 109. See also Selected

reaction monitoring (SRM) entriesMALDI-TOF instruments, 21, 283, 312–313.

See also Time-of-flight (TOF) entriesMALDI-TOF MS

in characterizing PEGylated proteins, 165in detecting siRNA duplexes, 362

MALDI-TOF reISD MS, 166. See also Reflectron entries

Mammalian gene expression, altering, 357Mammalian systems, investigating for

neuropeptide distribution, 295Mass accuracy data, 196–197Mass analyzers, 14–28, 115, 240. See also

FT-ICR mass analyzerchoosing, 253coupled to MALDI sources, 281for MS analysis, 26quadrupole, 14, 15, 16–17, 407–408TOF, 11, 13, 22, 23, 344variety in, 252

Mass-based data mining tools, for reactive metabolite screening, 345–351

Mass-based pattern isotope filter, 351Mass chromatograms, 105Mass data, on fragment ions, 199Mass defect, 347Mass defect filtering (MDF), 46, 121. See

also MDF entriesMass defect filters (MDFs), 256, 347–348

drug metabolite identification using, 45–48

Mass determination, effects on, 22Mass extraction window (MEW), 416–419

centroid mode and, 420effect of, 79

Mass ladders, 368–369Mass measurements, metabolite

differentiation and, 375, 376

446 INDEx

Mass-MetaSite, 108Mass reflectron, 21Mass resolution, 25, 46Mass resolving power

for HPLC-HRAMS bioanalytical methods, 78–79

influence on quantification, 416–419Mass-selective axial instability mode,

17–18Mass-selective ejection, 17Mass spectral interference, 56Mass spectrometers (MSs), 241

in drug discovery/development, 1–35for metabolite profiling studies, 121for metabolomics experiments, 397miniaturization of, 28

Mass spectrometric approaches, to molecular structure elucidation, 246–247

Mass spectrometric approaches/instruments, in drug metabolism studies, 126

Mass spectrometric detection, enhancing, 77–80

Mass spectrometric imaging (MSI) applications, 13

Mass spectrometric interference, 69–73, 81Mass spectrometric monitoring, of

phospholipids, 61–62Mass spectrometric (MS) techniques

for biologics applications, 213future development of, 170–179success of, 124

Mass spectrometry (MS), 43. See also APCI-MS

ADME assays and, 99–100advantages of, 303analyzing siRNAs by, 364application to drugs/metabolite

distribution in tissues, 329of biological drugs, proteins, and peptides,

149–190broad application of, 142capabilities of, 221–222in characterizing PEGylated therapeutic

proteins, 164–165coupled to (semi)-preparative LC/SFC,

242–243coupling of homogeneous/heterogeneous

reaction environments to, 261for cysteine connectivity determination,

161future trends in, 28

as the generic platform for model compounds, 262

metabolite identification using, 115–147for protein quantification, 177in PTM characterization, 167quantitative analysis of peptides using,

403–425for quantitative in vitro ADME assays,

97–113role in chemical structure elucidation,

245–248role in pharmaceutical R&D, 303role in protein structure investigation,

179role of, 240of siRNAs, 357–385siRNA sequencing by, 368–372in therapeutic protein discovery/

development, 149–150utility of, xi–xii

Mass spectrometry (MS) applicationsin biological drug discovery/development,

150supporting medicinal chemistry sciences,

239–275Mass spectrometry–based techniques, for

ambient surface profiling, 221–238Mass spectrometry imaging (MSI), xii, 1.

See also Imaging mass spectrometry (IMS)

sample preparation for, 313–315use of, 303–304

Mass spectrometry imaging (MSI) techniques, 221–222

Mass spectrometry imaging (MSI) technologies, for drug discovery, 305–312

Mass spectrometry metabolomics, 387–401

chromatographic/nonchromatographic solutions for, 396–397

Mass spectrometry sensitivity, lack of, 362Mass spectrum (spectra), 15. See also

MALDI spectradeconvoluted, 209generating, 18, 21

Matrix (matrices). See also Biological matrices; Biomatrices; MALDI matrices

applying to tissue surfaces, 314–315deposited on tissues, 281for drug analysis, 314

INDEx 447

used for matrix-assisted laser desorption/ionization, 12

used in MALDI-MS analysis, 368Matrix applications, 280–281Matrix-assisted laser desorption/ionization

(MALDI), 1, 11–13, 391, 394. See also MALDI entries

development of, 109, 312ESI vs., 13introduction of, 277protein identification and, 22sample preparation for, 365–366SIMS vs., 312siRNA chemistries and, 361

Matrix-assisted laser desorption/ionization ESI (MALDIESI), 10. See also Electrospray ionization (ESI)

Matrix-assisted laser desorption/ionization–mass spectrometry (MALDI-MS), 12–13, 192. See also MALDI mass spectrometry; MALDI-MS entries

acid hydrolysis and, 369H/D exchange combined with, 211of siRNA, 368

Matrix-assisted laser desorption/ionization–time of flight (MALDI-TOF), 13, 151, 179. See also MALDI-TOF entries

in optimizing PEGylation reaction, 165–166

Matrix effects, 59–69assessment of, 60plasma phospholipid association with,

60–65Matrix-free laser desorption/ionization, 11Matrix interference peaks, 417Matrix parameters, 280–281Matrix/solvent system, analyte-appropriate,

314Matthieu equations, 14, 17MDF-based acquisition, 123. See also Mass

defect filtering (MDF)MDF templates, 347Medicinal chemistry

in drug discovery process, 239new methodologies in, 241

Medicinal chemistry support, 239Medicinal chemistry sciences, MS

applications supporting, 239–275Mehl, John, x, 149Metabolic activity samples, quantitation of,

106Metabolic clearance, rapid, 258

Metabolic hotspot screening, 253–258Metabolic pathways, 253Metabolic profile data, 49Metabolic profiles, in animals, 130Metabolic stability assays, 97, 106, 253–254,

255Metabolism

role in drug safety profile, 116systematic evaluation of, 55

Metabolism assays, 98. See also Metabolic stability assays

Metabolite characterization, 115Metabolite conversion, 74Metabolite coverage, understanding, 129Metabolite detection, 132, 139–140

HRMS for, 121–123Metabolite detection approaches, 120–121Metabolite detection/identification, data

mining tools for, 256–258Metabolite differentiation, mass

measurements and, 375, 376Metabolite exposure level, 45Metabolite exposures, estimating, 119Metabolite extraction, LLE for, 66–69Metabolite formation, 124Metabolite identification, xi–xii, 48, 106. See

also Drug metabolite identification; Metabolite profiling/identification

future trends in, 141–142siRNA chemistries and, 361using mass spectrometry, 115–147

Metabolite imaging applications, imaging mass spectrometry for, 315–326

Metabolite interference, 73, 80–81due to conversion to parent drug, 73–74

Metabolite mass spectrometric interference, 69–73

MetabolitePilot™, 108Metabolite/prodrug interference, 72Metabolite profiles, 139Metabolite profiling, 121

categories of, 116–117outline of studies conducted during drug

development, 117radiolabeled test articles for, 139in studies without radiolabeled test

article, 117–129in studies with radiolabeled test article,

130–141Metabolite profiling/identification, 115–116Metabolite quantitation, 73

from nonradiolabeled studies, 124–129

448 INDEx

Metabolite quantitation kit, 393Metabolites

characterization of, 46chemically reactive, 339containing ester groups, 74drug generation from, 70, 80, 82imaging in whole-body sections, 321–322imaging mass spectrometry for, 303–337in silico prediction of, 256instability of, 56, 133ionization efficiencies of, 127MS in-source conversion of, 80qualitative analysis of, 414unstable, 133

Metabolite screeningusing scanning MS, 255–256using targeted MS, 254–255

Metabolite screening studies, design of, 254Metabolite sequences, identified, 377Metabolites in safety testing (MIST), 116Metabolite SRM table, 84. See also Selected

reaction monitoring (SRM) entriesMetabolite steady state, 119Metabolome, defined, 387–388Metabolome measurement, 388

analytical approaches for, 390–395, 396main approaches to, 390MS techniques for, 390–391

Metabolome studies, procedure for, 389Metabolomic biomarkers, 42Metabolomic experiments, steps in, 389–390Metabolomic libraries, 395, 396Metabolomic profiling, 388Metabolomics, xii, 388

defined, 387in drug discovery, 388–390future trends in, 397–398mass spectrometry for, 387–401MS instrumentation for, 397

Metabolomic studies, success of, 390MetaboLynx xS with MassFragment™, 108Metabonomics, 387Metaiodobenzylguanidine (MIBG),

intratumor biodistribution of, 307Metal-enhanced SIMS (MetA-SIMS), 307.

See also Secondary ion mass spectrometry (SIMS)

Methanol, 74in sample extraction, 134, 135

Methionine (Met) oxidation, 206–207, 212Methionine (Met) residues, oxidation of,

170

Method design, 74Method development

incurred sample applications in, 80–82steps in, 83–85

Method validation, 84–852-Methyl-1-butanol, 67Methyl ester group, 74Methyl ether group, 73Methyl-tert-butyl ether (MTBE), 67, 68, 69METLIN library, 395Met sulfoxide, 207. See also Methionine

(Met) entriesMicrochannel plate (MCP) electron

multipliers, 21–22Microplate scintillation counter, 137, 138Microplate scintillation counting (MSC),

136Microsomal incubations, 130Microsomal metabolites, profiling of,

121–123Microspotted arrays, for imaging, 281Middle-down experiments, 176Mid-infrared (mid-IR) lasers, 10Minimally fixed tissue samples, 279Minimal resolving power, 419Mirror plots, 157MIST-related risks, 116MMCD library, 395Mobile phase screening, 74–75Modified chromatographic conditions,

81–82Modified siRNAs, quantification of, 373.

See also Small interfering RNAs (siRNAs)

Modulated RF voltage, 22. See also Radio frequency (RF)

Molecular constitution, 252–253Molecular weights (MWs), 192. See also

High MW therapies; MW informationmedicines with high, 43of peptide degradants, 205

Mometasone furoate, 193–194, 197Monoclonal antibodies (mAbs), 151. See

also mAb entriesintact mass analysis of, 151–152quantitative analysis of, 177–179therapeutic, 149top-down MS for, 176trisulfide modifications in, 208truncation sites in, 208–210

Monolithic capillary columns, 367Monolithic columns, 59

INDEx 449

MRI contrast agent, distribution of, 325–326. See also Magnetic resonance imaging (MRI)

MS2 trap CID, 18, 19–20. See also Collision-induced dissociation (CID); Mass spectrometry entries

MS acquisition schemes, 28MS analysis

of free thiols, 161of IgG2 disulfides, 161–162of peptides, 406

MS-based quantification, of peptides, 404MS-based quantitation, 109–110MS-based strategies, 192MS-based technologies, potential of, 259MS data, evaluating, 252MS-directed purification, 242MSE experiments, 348MSE methodology, 371–372MSE mode, 108, 255–256MS hardware, high-resolution, 106MS (HRAM), bioanalysis using, 106. See

also High-resolution accurate mass (HRAM) systems

MSI absolute quantitative data, 233–234. See also Mass spectrometry imaging (MSI) entries

MSI methods, advantages of, 234MS instrumentation, 312–313

advancement in, 180IMS coupled with, 173–174for metabolomics, 397

MS methodologies, potential of, 248MS-MS (IT) spectra, 125. See also Tandem

mass spectrometry (MS/MS)MS/MS acquisition schemes, 28MS/MS analysis, advantages of, 313MS/MS data, 121–123MS/MS fragmentation, 253

siRNAs and, 364MS/MS fragmentation pattern, 315MS/MS imaging, of astemizole, 316, 317MS/MS in space, 16MS/MS spectrum (spectra), 20, 123, 124, 247MS/MS survey scans, for GSH adducts, 343MSn data, 121MSn experiments, 120MS response, 127MS techniques

for metabolome measurement, 391recent developments in, 255

MS technology, xii

MTBE LLE extracts, 68. See also Liquid–liquid extraction (LLE); Methyl-tert-butyl ether (MTBE)

Multichannel electrospray inlets, 245Multichannel plate detector (MCP), 21Multiple chromatographic systems,

nontarget metabolomic approaches utilizing, 394

Multiple MDF templates, 347Multiplexed HPLC-MS/MS system, 103. See

also High-performance liquid chromatography–tandem mass spectrometry (HPLC-MS/MS)

Multiplexed LC, 102. See also Liquid chromatography entries

MultiQuant™ software, 107Multistage MS systems, 246. See also Mass

spectrometry entriesMW information, for degradants, 198–199.

See also Molecular weights (MWs)Mycobacterium tuberculosis study, 291–292

Nanoelectrospray (nESI), 4. See also Nano-ESI entries; Nanospray ionization (NSI) technique; nESI chip

Nanoelectrospray (nESI) emitters, 222–223Nanoelectrospray LC-MS, 367. See also

Liquid chromatography–mass spectrometry (LC-MS)

Nanoelectrospray normalization techniques, 124–127

Nano-ESI interfaces, 245. See also Nanoelectrospray (nESI) entries

Nano-ESI-QqTOF, 369. See also Time-of-flight (TOF) entries

NanoMate™ instruments, 108, 118, 137NanoMate™ system, 9, 10Nanospray ionization (NSI) technique, 127.

See also Nanoelectrospray entriesNd:YAG laser, 11Nd:YVO4 laser, 282–283Nebulizer probe, 6Negative ESI, 83. See also Electrospray

ionization (ESI)Negative ESI response, 75Negative ion mode, 410, 412–413Negative precursor ion scan technique, 62nESI chip, 234. See also Nanoelectrospray

(nESI) entriesNeuropeptides, analysis of, 295Neutral loss (NL) scanning, 16, 17, 120,

346–347

450 INDEx

Neutral matrices, 368New biological entities (NBEs), 239

synthesis and identification of, 240–248New chemical entities (NCEs), 239

synthesis and identification of, 240–248New drug discovery applications, high-

resolution mass spectrometry for, 37–54

New molecular entities (NMEs), 97, 99New synthesis approaches, implementation

of, 241NIST (National Institute of Standards and

Technology) library, 395Nitrogen lasers, 11, 282N-linked glycans, 158, 160NMR technologies, 259–260. See also

Nuclear magnetic resonance (NMR)Noise reduction algorithm (NoRA),

background subtraction with, 348–350Nonchromatographic approaches, to mass

spectrometry metabolomics, 396–397Nonradiolabeled studies, metabolite

quantitation from, 124–129Nonsteroid glucocorticoid receptor (GR)

agonists, skin penetration for, 316–317

Nontargeted metabolomic analytical techniques, 394–395, 396

Nontargeted metabolomic approaches, utilizing multiple chromatographic systems, 394

Nontargeted metabolomics, 390, 394–395, 396

annotation in, 395, 396Normalization techniques, 124–127“No sample wasted” approach, 136–137N-terminal acetylation, 412Nuclear magnetic resonance (NMR),

241–242, 391, 392, 394. See also NMR technologies

Nuclease cleavage, 375Nuclease protection, 374Nucleobase modifications, incorporating

into siRNAs, 360Nucleophiles, 340

Offline plasma extraction, 57–58Olanzapine, 321Oligonucleotide desalting technique, 365Oligonucleotide extraction, 373Oligonucleotide sequences, influence on

LC-MS response, 362–364

Oligonucleotide sequencing, 368, 370by MS/MS, 369, 378rapid, 378

Oligonucleotide sequencing software, 376O-linked glycans, 158, 160“-omics” cascade, 387, 388Oncology drugs, tumor penetration by,

318–319One-column system, 59Online extraction column, 58Online extraction HPLC-MS systems, 59.

See also High-performance liquid chromatography–mass spectrometry (HPLC-MS)

Online plasma extraction, 58–59Open-access analysis, 240–242Oppenheimer, Stacey R., x, 303Optimal cutting temperature (OCT),

313–314Optimized RP-HPLC, combined with

ESI-TOF, 153. See also Reversed-phase (RP) entries; RP-HPLC-MS

Optimize software, 100–102Orbital trapping instruments. See also Ion

trap entriesfor quantitative bioanalysis, 414TOF trapping instruments vs., 418

Orbitrap™, 48Orbitrap™ instruments, 421Orbitrap™ mass spectrometers, 38, 255,

345Orbitrap™ mass systems, 2, 19, 26–27Orbitrap™ resolution, 26Orbitrap™ technology, 78, 106Organic solvents

effect of, 69in sample extraction, 133–134used in LLE, 67

Organisms, biochemical state of, 387Organs/tissues, imaging drugs and

metabolites in, 315–320Orthogonal acceleration TOF (oaTOF),

421. See also Time-of-flight (TOF) entries

Orthogonal chromatography, 81Orthogonal gas phase separation, 48Orthogonal MALDI (o-MALDI) TOF, 23.

See also MALDI entries; Matrix-assisted laser desorption/ionization (MALDI); Time-of-flight (TOF) entries

Orthogonal techniques, 403, 404

INDEx 451

Oxidationfrom analysis of mAb molecules,

153–154of methionine residues, 170as a modification in proteins, 206–207in therapeutic proteins, 170

Oxidation sites, derivatization techniques for distinguishing, 141

Oxidative deamination, 73Oxidative defluorination, 124Oxidative degradation pathway, 199–201

Pancreatic cancer tissue microarray, 293IMS analysis of, 294

Parallel artificial membrane permeability assay (PAMPA), 106, 107, 250

Parent drugs, metabolite interference due to, 73–74

Parent/fragment information, 46Parent/metabolite quantitation, 108Parkinson brain biomarkers, 294Paul’s trap, 26PC species, 68. See also Phosphatidylcholine

(PC) phospholipid classPeak areas, 410, 411Peak picking algorithm, 351PEG-SOD, 165. See also Poly(ethylene

glycol) (PEG)PEGylated protein therapeutics, 179PEGylated therapeutic proteins, 164PEGylation analysis, 164–167PEGylation site, determining, 166Penner, Natalia, x, 115Penning’s trap, 26Peptide analysis, 13, 292–294, 294–296

mass-spectrometric, 149–190quantitative, xii, 403quantitative mass-spectrometric,

403–425using full scan HRMS, 415

Peptide biomarkers, in disease assessment, 403

Peptide degradants, molecular weights of, 205

Peptide drug candidates, quantitative methods for, 412

Peptide fragmentation, 412Peptide fragments, 295–296Peptide mapping, 155–158, 174

artificial degradation in, 211–213drawbacks of, 155–156improving, 156

steps in, 155therapeutic protein characterization and,

155using HPLC-MS/MS, 211

Peptide mapping approach, 210Peptide mapping HPLC-MS/MS analysis,

207, 211. See also High-performance liquid chromatography–tandem mass spectrometry (HPLC-MS/MS)

Peptide mass mapping, 179Peptide quantification

high-resolution mass spectrometry for, 414–420

selected reaction monitoring for, 407–414

Peptide quantification approaches, 405Peptides

as degradation products, 212disulfide-containing, 160in drug development programs, 403–404fragmented, 156imaging mass spectrometry of, 277–302ionization and fragmentation of,

406–407lower ion intensities of, 408MS-based quantification of, 404

Peptide separation, 406Peptide SRM methods, 404. See also

Selected reaction monitoring (SRM) entries

Peptidic HIV-fusion inhibitor, 412Permeability assays, 97–99pH, of plasma samples, 57Pharmaceutical compounds, analysis of,

74–75Pharmaceutical mapping, in tissues, 312Pharmaceutical products, small molecule

impurities in, 193Pharmaceutical relevant molecules,

fragmentation behavior of, 247Pharmaceuticals. See also Drug entries;

Therapeutic entriesdegradation profiling of, 198derivatizing, 326–327impurities and degradation products in

small-molecule, 191–220MS role in R&D of, 303

Pharmacokinetic (PK) parameters, therapeutic siRNAs and, 372

Pharmacokinetic (PK) predictions, 39Pharmacokinetic (PK) profiles/profiling, 40,

132, 136

452 INDEx

Pharmacokinetics (PK), 97imaging data quantification for, 328–329improving, 164systematic evaluation of, 55

Pharmacokinetic (PK) studies, 44Phase 2 metabolites, 48Phase collapse, aqueous mobile phase and,

75–76Phosphate prodrugs, 71–73Phosphatidic acid (PA) phospholipid class,

61, 62Phosphatidylcholine (PC) phospholipid

class, 61, 62Phosphatidylethanolamine (PE)

phospholipid class, 61, 62Phosphatidylglycerol (PG) phospholipid

class, 61, 62Phosphatidylinositol (PI) phospholipid

class, 61, 62Phosphatidylserine (PS) phospholipid class,

61, 62Phospholipid avoidance strategies, 65–69Phospholipid chromatographic elution

profiles, 64Phospholipid detection, all-inclusive

technique in, 62Phospholipid extraction, 68Phospholipid removal, during sample

extraction, 66–69Phospholipids

chromatographically separating analytes from, 65

chromatographic elution behavior of, 62–65

chromatographic fate of, 67–68collision-induced dissociation of, 61–62mass spectrometric monitoring of, 61–62rapid elution of, 65

Phospholipid structures, 61Phosphorothionate-modified siRNAs, 360.


Photoionization probe, 7Photostability testing, 251–253Physical degradation, 210–211Physicochemical properties, assessment of,

99, 248–259PK/metabolite characterization, 48. See also

Pharmacokinetic (PK) entriesPK/pharmacodynamic (PD) correlations,

42Placebo samples, 119

Plasma. See also Serum entriescollection and storage of, 56–57pooling approaches for, 135–136

Plasma concentration–time profiles, 131, 132

Plasma extractionoffline, 57–58online, 58–59

Plasma phospholipidsassociation with matrix effects, 60–65bioanalytical risks posed by, 67

Plasma pooling, volume calculation for, 135Plasma sample collection, 132Plasma sample extraction procedures,

evaluating, 84Plasma samples, 118

pH of, 57profiling, 129

“Plug and play” formats, 407Pneumatically assisted electrosprays, 2Pneumatic nebulization, 5Polar analytes

retention and separation of, 75–77reversed-phase columns for, 75–77

Polar metabolites, structural elucidation of, 140

Poly(ethylene glycol) (PEG), 164, 165. See also PEG- entries

Polymerase chain reaction (PCR). See qPCR techniques; Q-RT-PCR methods; RT-qPCR entries; siRNA qPCR concentrations

Polymeric sorbents, 58, 59Pooled incurred samples, 81Pooled placebo samples, 119Pooling, of biological samples, 135–136. See

also Sample poolingPorous graphitic carbon (PGC), 75–76Posaconazole (SCH 56592), degradation

products of, 198–201Positive electrospray (ESI) selected

reaction monitoring (SRM), 61–62Positive ESI, 83Positive ESI response, 75Positive ion mode, 410, 412Positive/negative mode electrospray

analyses, 394Positive neutral loss scan technique, 62Positive precursor ion scan technique, 62Positron emission tomography (PET), 304Positron-emitting nuclides, 304Post-acquisition data filtering, 121

INDEx 453

Post-acquisition data processing software, 40

Post-acquisition data processing software tools, 121

Post-analysis processing software tools, 121, 142

Post-column analyte addition, 60Post-column infusion system, 60Post-ion/ion trap CID spectrum, 371. See

also Collision-induced dissociation (CID)

Post-run data mining, 123Postsource decay (PSD), 284Post-transcriptional gene regulation,

357–358Post-translational modifications (PTMs),

150, 180. See also PTM analysisin proteins/peptides, 203

Potassium adducts, 3Prakash, Chandra, x, 115Pramanik, Birendra N., x, 239Pravastatin, 74Pravastatin lactone, 74Preclinical ADME programs, investment in,

131. See also Absorption, distribution, metabolism, and excretion (ADME) entries

Precursor ion approach, 346–347Precursor ion mode, 16–17, 23Precursor ions (PIs), 20

isolation of, 22isolation window of, 24mass measurements of, 26

Precursor ion (PI) scans, 22, 23, 62, 120, 346–347

Primary sequence characterization, 151–158Principal component analysis (PCA), 391,

392Principal component analysis (PCA)

followed by discriminant analysis (DA) (PCA-DA), 293

Pristatsky, Pavlo, x, 149Probe-specific analysis, 99Prodrugs, 133

instability of, 56, 57Product ion mass spectra, 194, 195, 197,

201–203. See also Product ion spectraProduct ion mode, 16Product ions, 16, 22Product ion selection, at high resolution,

420Product ion spectra, 205–206

Profile data, 419–420ProMass software, 377–378Proof-of-concept LESA-MS analysis, 232Proof-of-concept (POC) studies, 129Property assays, 98Prostate tissue marker, 289Protein affinity selection mass spectrometry,

261Protein aggregation, 210Protein A strategy, 178–179Protein binding assays, 106Protein characterization, 192Protein degradation, 279

in tissues, 295–296Protein denaturing, urea for, 211Protein drug candidates, preclinical stage of,

150Protein drug discovery/development,

149–150Protein drugs

sample denaturing for dissociating, 178therapeutic properties of, 171

Protein exclusion mechanism, 59Protein folding defects, 210Protein glycosylation, 158Protein heterogeneity, analysis of, 151Protein identification, 283–284

MALDI and, 22Protein ions, fragmented, 156Protein modification analysis, ECD/ETD in,

177Protein oxidation, 206–207Protein precipitation (PPT), 57, 58, 133,

134Protein profiles, from lung tumor tissue,

288Protein–protein interactions, 210Protein quality, evaluating, 150Protein quantification, mass spectrometry

for, 177Proteins. See also Peptide entries; Proteins/

peptidesdeamidation of, 168–170detected in situ, 283disulfide bonds in, 160HDx in, 172imaging and identifying, 285imaging mass spectrometry of, 277–302isoAsp in, 167–168modifications/degradations of, 167,

202–204MS analysis of, 149–190

454 INDEx

quantitative workflows for larger, 404RISC core, 358therapeutic, 151

Protein signals, identifying, 284Proteins/peptides

affinity-based enrichment of, 210post-translational modifications in, 203

Protein structures, 210Protein therapeutics, characterizing, 176Protein therapies, 43–45Proteolytic degradation, 279Proteomic experiments, 283–284Proteomics, 388Proton exchange, 9Proton transfer ion/ion reactions, 370Pseudo–MS/MS data sets, 348. See also

Tandem mass spectrometry (MS/MS)“Pseudo” neutral loss approach, 346–347Pseudo-Rayleigh ion release (PRIR), 5Pseudo-SRM, 404. See also Selected

reaction monitoring (SRM) entriesPTM analysis, 155, 167–170. See also

Post-translational modifications (PTMs)

Pulmonary granulomas, 291–292Pure ion evaporation (PIE), 5Purity analysis, 243–245

Q Exactive, 26qPCR techniques, 361. See also Q-RT-PCR

methods; RT-qPCR entries; siRNA qPCR concentrations

QqQ instruments. See Triple quadrupole (QqQ, QQQ) instruments

QQQ mass spectrometers, 115. See also Triple quadrupole (QqQ, QQQ) instruments

QqTOF instruments, 281, 283. See also Quadrupole-time-of-flight (QqTOF, Q-TOF) instruments; Time-of-flight (TOF) entries

Q-RT-PCR methods, 44. See also qPCR techniques; RT-qPCR entries; siRNA qPCR concentrations

Q-TOF MS, 46. See also Fast scanning Q-TOF MS/MS systems; Mass spectrometry entries; Quadrupole time-of-flight (Q-TOF)

Q-trap instrument, 120QTRAP mode, 19–20Quadrupole CID spectra, 19–20

Quadrupole fields, 14Quadrupole instruments, operation of, 408Quadrupole (3D) IT mass spectrometers,

120Quadrupole ion trap (QIT) mass

spectrometer, 17Quadrupole ion traps (QiTs, QITs), 16,

17–20, 344. See also Linear quadrupole ion trap

in qualitative analysis, 18Quadrupole mass analyzer modes, 16–17Quadrupole mass analyzers, 14, 15, 407–408Quadrupole mass filters, 17Quadrupole settings, 16Quadrupole time-of-flight (Q-TOF), 40. See

also Q-TOF MSQuadrupole-time-of-flight (QqTOF,

Q-TOF) instruments, 22, 23, 255, 344. See also QqTOF instruments

schematic of, 23Qualitative analysis

of biological drugs, xiiof drugs/metabolites, 414

Qualitative/quantitative (Qual/Quan) workflows, 40. See also QUAL/QUAN workflows

in drug metabolism, 38–41Quality control (QC) samples, 56, 80, 82, 85Qual/Quan experiments, 41QUAL/QUAN workflows, 28. See also

Qualitative/quantitative (Qual/Quan) workflows

QuanOptimize™, 100Quantification, mass resolving power as

influencing, 416–419Quantification strategy, best, 408Quantitative analysis

of biological drugs, xiiof peptides, xii, 403of peptides using mass spectrometry,

403–425Quantitative bioanalysis

HRMS instruments for, 414role of HRMS in, 421

Quantitative data, response factors for obtaining, 127–129

Quantitative HPLC-MS/MS bioanalysis, research activities in, 85. See also Tandem mass spectrometry (MS/MS)

Quantitative informationcapturing analyte, 394derived for imaging data, 329

Proteins (cont’d)

INDEx 455

Quantitative mass spectrometry, in a regulated environment, 55–95

Quantitative methods, for peptide drug candidates, 412

Quantitative whole-body autoradiography (QWBA), 221–222. See also QWBA analysis

Quantitative whole-body autoradiography imaging, 321

Quaternary ammonium glutathione analog (QA-GSH), 351

QuickQuan™, 100, 102QWBA analysis, 323. See also Quantitative

whole-body autoradiography entries

Radial ejection, axial ejection vs., 19Radioactive detector, HPLC-MS coupled

with, 136Radioactive samples, biotransformation

analysis of, 136, 137Radiochromatograms, 138Radiochromatographic profiles, 136Radio frequency (RF), magnetic field

produced via, 14. See also RF entriesRadiolabeled ADME studies, 130. See also

Absorption, distribution, metabolism, and excretion (ADME) entries

Radiolabeled compounds, 130Radiolabeled drug products, testing, 131Radiolabeled drugs, 116Radiolabeled drug studies, 136Radiolabeled material studies, 117Radiolabeled peptides, as internal

standards, 178Radiolabeled samples, for estimating

metabolites, 128–129Radiolabeled studies, uses for, 130Radiolabeled test articles, metabolite

profiling in studies with, 130–141Radiolabeled trapping agents, 351Radiometric detector technology, 139Radioprofiles, 130RAM-based online extractions, 59RapidFire system, 103, 106

schematic of, 104Rapid mass analysis, 18Rapid metabolic clearance, 258Rapid oligonucleotide sequencing, 378Rapigest surfactant, 211Raw HRMS spectral data, transformation

of, 419–420. See also High-resolution mass spectrometry (HRMS)

Rayleigh limit, 4Reaction monitoring mode, 20Reactive iminium ions, cyanide-trapped, 350Reactive intermediate formation, 258Reactive metabolite formation, 352

quantitation of, 351Reactive metabolites

classification of, 340, 343detection and characterization of, 341detection and identification of, 352in vitro trapping of, 340

Reactive metabolite screening, xii, 339–355challenges of and future perspectives on,

351–352LC-MS/MS approaches for, 340–343mass-based data mining tools for,

345–351Reactive metabolite screening workflow,

123Reactive species, 339Real time (RT). See Direct analysis in real

time (DART); Q-RT-PCR methods; RT-qPCR entries

Real-time dynamic background subtraction, 123

Reconstitution solvents, 85Reduced mAbs, mass analysis of, 153, 154.

See also Monoclonal antibodies (mAbs)

Reducing agents, 212Reference standards, 128Reflectron, 21

trajectories in, 21Reflectron mode ISD (reISD), 166. See also

In-source decay (ISD)Reflectron technology, 344Regulated environment, quantitative mass

spectrometry in, 55–95Regulatory authorities, 116Reily, Michael D., x, 387Relative standard deviation (RSD), 85Renal elimination studies, 119Research and development (R&D), 239

DESI role in, 308–309MS role in pharmaceutical, 303

Resolution (R), 27. See also Mass resolution; Resolving power

in DESI imaging, 311increasing, 21in MALDI imaging, 311Orbitrap, 26transient time and, 25

456 INDEx

Resolving power, 416–419. See also Resolution (R)

defined, 416effect of, 44of experiments, 396minimal, 419

Resonant mass ejection, 18Response–concentration relation, 59–60Response factors

calculating, 128for obtaining quantitative data, 127–129

Response normalization techniques, 124–127

Restricted access media (RAM), 59Reversed-phase (RP) chromatography,

62–65, 74–75. See also Flow-injection RP-HPLC-MS technique; RP entries

Reversed-phase (RP) columns, for polar analytes, 75–77

Reversed phase (RP)-HPLC separation, 151–152, 396–397

Reyzer, Michelle L., x, 277RF/DC potentials, 15, 17, 19. See also Radio

frequency (RF)RF mode, 16RF-only mode, 22RF voltage, 15

modulated, 22Ricin A-chain (RTA), 165–166RISC core proteins, 358. See also RNA-

induced silencing complex (RISC)Rising-multiple-dose (RMD) studies,

117–119Rising-single-dose (RSD) studies, 117–119RNAi biology, advances in, 378RNA-induced silencing complex (RISC),

357–358RNA interference (RNAi) mechanism,

357–358RNAi therapies, complete sequence

coverage of, 370–371RNA oligonucleotides, sequence coverage

of, 370RP-HPLC-MS, 152, 153. See also High-

performance liquid chromatography–mass spectrometry (HPLC-MS); Reversed-phase (RP) entries

RP phase modifications, 75RT-qPCR–based assays, 361. See also qPCR

techniques; Q-RT-PCR methods; siRNA qPCR concentrations

RT-qPCR hybridization technique, 367

“Rule of five,” 246, 249Run-to-run assay, 66

Safety, of drug candidates, 116. See also Drug safety

Safety risks, 45Sample analysis, using HPLC-MS/

radiometry, 136–139Sample collection, 131–132

based on a stability profile, 119in in vivo AME study, 131

Sample denaturing, for dissociating protein drugs, 178

Sample extraction, phospholipid removal during, 66–69

Sample extraction methods/techniques, 66, 133–135

Sample instability, 56–57Sample pooling, 104. See also Pooled

entries; PoolingSample preparation, 56, 132–135

for imaging mass spectrometry, 278–280for MALDI, 365–366for mass spectrometry imaging, 313–315in metabolomic experiments, 390refinements in, 178

Sample pretreatment, for imaging mass spectrometry, 278–279

Samples, reanalysis of, 129. See also Biological samples; Blood samples; “Dosed” samples; Fixed tissue samples; Formalin-fixed paraffin embedded (FFPE) samples; Fresh frozen tissue samples; Incurred samples; In vitro ADME assay samples; In vitro ADME samples; Metabolic activity samples; Minimally fixed tissue samples; Placebo samples; Plasma sample entries; Pooled incurred samples; Pooled placebo samples; Quality control (QC) samples; Radioactive samples; Radiolabeled samples; Spiked QC samples; Steady-state plasma samples; Tissue samples; Toxicological samples; Untreated water-rich biological samples; Urine samples

Sample stabilization, common approaches for, 133, 134

Scanning MS, metabolite screening using, 255–256. See also Mass spectrometry entries

Scan numbers, comparison of, 102

INDEx 457

Scan/scanning modes, 16, 255Scan types, 115SCH 56592. See Posaconazole (SCH 56592)Screening assays

for reactive metabolites, 339–355target–ligand, 259–262, 263, 264

“Sealing” surface sampling probe (SSSP), 9Secondary ion mass spectrometry (SIMS),

306–307application to tissue imaging, 307for drug and metabolite, 307imaging via, 277MALDI vs., 312

Secondary ions, 306Secondary metabolites, 291Segmented post-column analyte addition,

60Selected ion monitoring (SIM), 404Selected reaction monitoring (SRM). See

also SRM entriesfor peptide quantification, 407–414TOF-based approaches vs., 420–421

Selected reaction monitoring (SRM) mode, 13, 16, 17, 77

Selected reaction monitoring (SRM) technique, xi, 37, 40–41, 43, 223, 342, 404

Selective sample extraction, 55Selectivity, in HRMS experiments, 405(Semi)-preparative LC/SFC, 242–243. See

also Liquid chromatography (LC); Supercritical fluid chromatography (SFC)-MS

Semi-quantitative imaging technology, 304Separation techniques, 161Sequence mass ladders, 368–369Sequencing. See De novo sequencing;

Metabolite sequences; Oligonucleotide sequencing entries; Primary sequence characterization; siRNA sequencing

Sequential window acquisition of all theoretical fragment-ion spectra (SWATH), 28, 41

Serum, siRNA degradation in, 374–375Serum sample enrichment strategies,

178–179SFC-MS system, 243. See also Supercritical

fluid chromatography (SFC)-MSSFC-UV chromatogram, 244. See also

Ultraviolet (UV) entriesSFC-UV system, 243, 244Shipkova, Petia, x, 387

Shotgun lipidomic approaches, liquid extraction surface analysis and, 229

Shou, Wilson Z., x, 97“Signature peptides,” 404Silica-based RP columns, characterizing,

74–75. See also Reversed-phase (RP) entries

Silica-based sorbents, 58–59Simple Oligonucleotide Sequencer (SOS),

378SIMS imaging, 306–307, 329. See also

Secondary ion mass spectrometry (SIMS)

SIMS isotope images, 308Single ion monitoring (SIM), 16Single MS mode, 22. See also Mass

spectrometry entriessiRNA analysis, future trends for, 378–379.


siRNA applications, mass spectrometry for, xii

siRNA degradation, in serum, 374–375siRNA duplexes, 361–362, 373–375

collision-induced dissociation of, 364, 369–370

siRNA duplex intensities, measured by MALDI-MS, 368

siRNA hydrophobicity, ESI efficiency and, 364

siRNA metabolites, 44, 376characterizing duplex, 373–375

siRNA molecules, characterizing, 44siRNA qPCR concentrations, 44. See also

qPCR techniques; Q-RT-PCR methods; RT-qPCR entries

siRNA quantitation methods, 360siRNA-related LC-MS techniques, 366–368siRNA sequencing, by mass spectrometry,

368–372siRNA stability, 360siRNA strands, elucidating, 378siRNA therapeutic formulations,

accumulation of, 373siRNA-type oligonucleotides, desalting, 365Six sigma initiative, 240Size-exclusion chromatography (SEC), 208,

210–211, 261Skin penetration, for nonsteroid

glucocorticoid receptor agonists, 316–317

Small cations, effects of, 60

458 INDEx

Small interfering RNAs (siRNAs). See also siRNA entries

ADME properties of, 364analytical methodologies for, 360–361chemical modifications of, 358–360complete sequencing of, 364de novo sequencing of, 369double-stranded characteristic of, 361–362extracting from biological matrices,

365–366isolation from biomatrices, 364MALDI-MS of, 368mass spectrometry of, 357–385qualitative and quantitative analyses of,

372–376quantification of modified and

unmodified, 373tandem mass spectrometry fragmentation

and, 364of UPLC-MS/MS, 370–371

Small interfering RNA (siRNA) therapies, 43–45

Small molecule degradation products, characterization of, 198–201

Small molecule impurities, characterization of, 193–198

Small molecule metabolites, 387–388Small-molecule pharmaceuticals/biologics,

impurities and degradation products in, 191–220

Small molecule quantification, HRMS and, 405

Small molecules, LC-MS/MS analyses of, 372

Sodium adducts, 3“Soft” electrophiles, 340“Soft” nucleophiles, 340Software

advancement of, 376–378for metabolomic studies, 390

Software development, 108Software ease of use, 39–40Software tools. See also Statistical tools

development of, 106–107for post-acquisition data processing, 121for post-analysis processing, 142

Solid-phase extraction (SPE), 57, 58, 66, 68, 103–104, 134, 229, 366. See also SPE entries

Solid-phase extraction (SPE)-NMR, 262, 263, 264

Solid-state lasers, 282

Solid-supported LLE, 58Solubility, defined, 250Solubility assay methods, 250Solution phase hybridization, 361Solvents

in drug extraction, 224–225reconstitution, 85

Sonic spray, 4Sorbents, 58–59Spatial resolution, 305

of LESA, 224Special-isotope-requirement technologies,

304–305Specialized phases, 75–76Spectrometers, for intact mass analysis, 151SPE method, 412. See also Solid-phase

extraction (SPE) entriesSPE systems, 103Sphingomyelin (SM) phospholipid class, 61,

62Sphingomyelins (SMs), 60, 61Spiked QC samples, 80. See also Quality

control (QC) samplesSporulation delaying protein (SDP), 291Sporulation killing protein (SKP), 291Spotted arrays, for imaging, 281, 282SRM analysis, 100. See also Selected

reaction monitoring (SRM) entriesSRM assays, 37SRM-based method development, for

peptides, 408SRM chromatograms, 408–409

in negative ion mode, 413SRM conditions, optimized, 102SRM development, solutions for, 100–102SRM LLOQ chromatograms, 409. See also

Lower limit of quantitation (LLOQ)SRM methods, 177

for metabolomics, 397SRM mode, 372SRM systems, 46SRM transitions, 80, 83, 84, 104–105, 254,

409, 410SRM workflow, 405“Stability indicating,” development of, 252Stability profile, sample collection based on,

119Stability testing regimen, 85Stabilizing reagents, 57“Staggered parallel” approach, 102–103Standalone linear ion trap, 19“Standard assays,” 260

INDEx 459

Standard-free quantitative techniques, 129STAT3 compound, 326, 327Static extraction process, 234–235Stationary phase screening, 74–75Statistical tools, 391Steady-state plasma samples, analyzing, 118Stress-testing methods, 198Structural elucidation, 139–140

chemical derivatization for, 140–141Structure–activity relationships (SARs), 46,

246Structure–liability relationship (SLR), 97Structure–property relationships (SPRs),

246Subtraction routines, 46Sulfate metabolites, 71–73Supercritical fluid chromatography (SFC)-

MS, 242, 243Supernatants, 134Super oxide dismutase (SOD), 164, 165SUPREx (stability and unpurified proteins

from H/D exchange) method, 260–261Surface analysis, 13

application of MS to, xiiSurface enhanced laser desorption/

ionization (SELDI), 13Surface sampling ionization MS platforms,

305Synapt G2™ ion mobility–TOF mass

spectrometer, 39. See also Time-of-flight (TOF) entries

Synthesized compounds, screening, 253Systematic method development, protocol

for, 82–85

Tandem mass spectrometry (MS/MS), 15, 18, 19–20, 44. See also MS/MS entries; Trap MS/MS

in chemical structure elucidation, 245–246oligonucleotide sequencing by, 369, 378

Tandem mass spectrometry (MS/MS) experiments, 192

Tandem mass spectrometry (MS/MS) techniques, to monitor phospholipids, 62

Tandem MS mode, 22. See also Mass spectrometry entries

Tandem TOF combinations (TOF/TOF), 23. See also Time-of-flight (TOF) entries; TOF/TOF analyzers

Tandem TOF/TOF geometries, 24Target characterization, 259

Targeted enhanced multiple charge scanning (tEMC), 405

“Targeted” high-throughput screening (HTS) libraries, 239

Targeted ion parking (TIP), 405Targeted metabolomic analyses,

endogenous biomarker measurement assays vs., 393–394

Targeted metabolomics, 390, 392–394Targeted MS, metabolite screening using,

254–255. See also Mass spectrometry entries

Targeted profiling, 278Target–ligand interactions, 259–262, 263, 264

kinetics/energies involved in, 260Target–ligand screening assays, 259–262,

263, 264Target quantitation, bioanalytical methods

for, 78Taylor cone, 2TEA/HFIP buffer system, 367. See also

HFIP/TEA ion-pairing system; Triethylammonium (TEA)

Terfenadine, 225–227, 321LESA-MS-SRM analysis of, 228

Test compounds, purity of, 244–245Therapeutic discovery, antisense

oligonucleotide, 372Therapeutic mAbs, in drug development,

177. See also Monoclonal antibodies (mAbs)

Therapeutic protein characterization, peptide mapping and, 155

Therapeutic protein drug candidates, 179Therapeutic proteins, 151, 164

deamidation of, 168–170modifications/degradations of, 202–204oxidation in, 170

Therapeutic proteins/peptides, in drug portfolios, 403

Therapeutic siRNAs, ADME and PK parameters and, 372

“Thermodynamic” assays, 250–251Thermogravimetric analysis (TGA), 249Thiol content, reducing, 207Thiols

investigating, 179mass spectrometric analysis of, 161

Three-dimensional (3D) ion traps (ITs), 120Timed ion selector (TIS), 23–24Time-of-flight (TOF) analysis, 20–24,

343–344. See also TOF entries

460 INDEx

Time-of-flight (TOF) design, 39Time-of-flight (TOF) mass systems, 2, 13Time-of-flight (TOF) mass spectrometer, 21Time-of-flight (TOF) technology, 78Time-point pooling method, 136Time-to-digital converter (TDC), 344Tiotropium, in vivo transport of, 315. See

also Inhaled tiotropium (ITP)Tissue, as pharmacological target, 43. See

also TissuesTissue distribution studies, application of

DESI to, 309Tissue images, 8, 303Tissue microarrays (TMAs), 293Tissue preservation, 278–279Tissues

pharmaceutical mapping in, 312protein degradation in, 295–296

Tissue samplesabsolute quantitation from, 233–234fresh frozen or minimally fixed, 279

Tissue sectionsapplying enzymes to, 284identifying protein signals from, 284matrix added to, 280protein identification in, 292–293

Tissues/organs, imaging drugs and metabolites in, 315–320

Tissue surfacesapplying matrix to, 314–315drug detection from, 312

T-L complex, 261TOF-based approaches, SRM vs., 420–421.

See also Time-of-flight (TOF) entriesTOF-based HPLC-HRAMS methods, 78.

See also High-performance liquid chromatography (HPLC) with high-resolution accurate mass spectrometry (HPLC-HRAMS)

TOF-based MS systems, quantitative output of, 421. See also Mass spectrometry entries

TOF instruments, 21–22, 105–106, 115, 344for quantitative bioanalysis, 414

TOF mass analyzer(s), 11, 13, 22, 23advantages of, 344

TOF systems, resolving power of, 27TOF technology, 255TOF/TOF analyzers, 281. See also Tandem

TOF entriesTOF trapping instruments, 414–415

orbital trapping instruments vs., 418

Top-down mass spectrometry (MS), 174–176, 180, 192

Total adduct burden, 352Total ion chromatograms (TICs), 79, 349,

363Total ion current (TIC) chromatograms, 415Toxicity, assessing and preventing, 99Toxicity prediction, 45Toxicological samples, LESA-MS applied

to, 231Toxicology studies, 116–117

use of samples from, 117–119Trajectory stability, in Orbitrap, 26Transcriptomics, 388Transient time (T), resolution and, 25Transmission mode, 16Transporter assays, 98Transporter-related liabilities, 99Trap CID spectra, 19–20. See also Collision-

induced dissociation (CID)Trap MS/MS, 18. See also Tandem mass

spectrometry (MS/MS)Trapped ions, detecting, 344–345Trapping agents, 258

bromine in, 341radiolabeled, 351

Trapping assays, 258–259Traveling-wave ion mobility mass

spectrometry (TWIMS), 27Traveling waves (T waves), 174Triethylammonium (TEA), 366–367Triethylammonium bicarbonate (TEAB),

366Trifluoroacetic acid (TFA), 410Triple quadrupole (QqQ, QQQ) instruments,

13, 15–16, 22, 77, 115, 407–413fast scanning, 410full scan tandem mass spectrometry with,

22QiTs vs., 18schematic of, 16

Triple quadrupole linear ion trap (QqQLIT), 19–20

operation modes of, 20Triple quadrupole mass spectrometers

(TQMSs), 37, 40, 110, 120HPLC-MS/MS with, 100–105

Triple quadrupole MS systems, 1, 13, 14–17Triple quadrupoles, for metabolomics, 397Tris(2-carboxyethyl) phosphine (TCEP),

161, 212Trisulfide bonds, detection of, 162

INDEx 461

Trisulfide linkages, 207–208Trisulfides, 162–164TriVersa-NanoMate robotic ion source, 222,

223Troglitazone metabolites, 46, 47Trypsin digestion, 212–213Tryptic digestion, 156Tumor blood vessel destruction, 319–320Tumor margins, IMS studies of, 289–290Tumor penetration, by oncology drugs,

318–319T-wave IMMS, 174. See also Ion mobility

mass spectrometry (IMMS, IMS); Traveling wave entries

Two-dimensional (2D) ion traps (LTQs), 120

Two-dimensional (2D) quadrupole field, 14Two-dimensional (2D) trap, 19Tymiak, Adrienne A., x, 191

Ultrafast ADME sample analysis, 106. See also Absorption, distribution, metabolism, and excretion (ADME) entries

Ultrafiltration-ESI-MS, 261. See also Electrospray ionization (ESI); Mass spectrometry entries

Ultra-high pressure liquid chromatography (UHPLC), 102–103, 397

Ultra-high vacuum, 345Ultra-performance liquid chromatography

(UPLC), 121, 241. See also UPLC entries

Ultra-performance liquid chromatography (UPLC)-HRMS systems, 40, 42. See also High-resolution mass spectrometry (HRMS)

Ultraviolet (UV)-based techniques, 129Ultraviolet (UV) detectors, 46Ultraviolet (UV) lasers, 10Unlocked nucleic acids (UNAs), 361Unmodified siRNAs, quantification of, 373Unstable drugs/metabolites, 56Unstable metabolites, 133

effect of, 73–74

Untreated water-rich biological samples, analysis of, 10

UPLC-MS/MS, 405. See also Tandem mass spectrometry (MS/MS); Ultra-performance liquid chromatography (UPLC)

of siRNA, 370–371UPLC technology, 178UPLC-UV assay, 251Urea, for protein denaturing, 211Urine samples, 118–119

value of, 119

Vacuum-MALDI, 13. See also Matrix-assisted laser desorption/ionization (MALDI)

“Vaporization problem,” 4Veterinary drugs, 40Vinblastine, 321

Wash step, 66, 67Water washes, 278WBA experiments, 321. See also Whole

body autoradiography (WBA)WBA imaging, 311Web-based libraries, 395, 396Wei, Hui, x, 191Wet chemistry techniques, 142Whole body autoradiography (WBA),

309–311. See also Quantitative whole-body autoradiography entries; WBA entries

Whole-body sections, imaging drugs and metabolites in, 321–322

Wide band excitation, 18

xenobiotics, metabolism of, 339xia, Yuan-Qing, x, 55x-ray therapy (xRT), 318, 320

Zebrafish, pharmaceutical distribution in, 323–324, 325

Zgoda-Pols, Joanna, x, 115Zhang, Jun, x, 97Zhang, Nanyan Rena, x, 37