I: Optimization and Exploratory Data Analysis.- 1 Development of an AI-Based Optimization System for Tandem Mass Spectrometry.- 1.1. Introduction.- 1.2. Problem Statement.- 1.3. Proposed Method of Solution.- 1.4. Evolution of TQMSTUNE.- 1.4.1. TQMSTUNE Version 1.- 1.4.2. TQMSTUNE Version 2.- 1.4.3. TQMSTUNE Version 3.- 1.5. Knowledge Representation in the TQMS Domain.- 1.5.1. Representation of InstrumentConstruction Knowledge.- 1.5.2. Representation of Procedural Tuning Knowledge.- 1.5.3. Representation of Output Evaluation Procedures.- 1.5.4. Representation of Interfacing Knowledge.- 1.6. Results.- 1.7. Conclusion.- References.- 2 Curve Fitting and Fourier Self-Deconvolution for the Quantitative Representation of Complex Spectra.- 2.1. Introduction.- 2.1.1. Quantitative Analysis of Highly Overlapped Spectra.- 2.1.2. Derivative Spectrometry.- 2.1.3. Fourier Self-Deconvolution.- 2.1.4. Curve-Fitting Unresolved Peaks.- 2.2. Synthetic Spectra.- 2.2.1. Isolated Bands.- 2.2.2. Band Multiplets.- 2.3. Application to Coal Spectrometry.- 2.4. Conclusion.- References.- 3 Evolutionary Factor Analysis in Analytical Spectroscopy.- 3.1. Introduction.- 3.2. Gemperline Method.- 3.3. Vandeginste, Derks, and Kateman (VDK) Method.- 3.4. Gampp, Maeder, Meyer, and Zuberbuhler (GMMZ) Method.- 3.5. Application of EFA to Circular Dichroism (CD) Spectra.- 3.6. Conclusions.- References.- 4 Numerical Extraction of Components from Mixture Spectra by Multivariate Data Analysis.- 4.1. Introduction.- 4.2. Factor Analysis.- 4.2.1. Geometrical Description.- 4.2.2. Mathematical Rationalization.- 4.2.3. Examples.- 4.3. Discriminant Analysis.- 4.3.1. Geometrical Description.- 4.3.2. Mathematical Rationalization.- 4.3.3. Examples.- 4.4. Graphical Rotation.- 4.4.1. Geometrical Description.- 4.4.2. Mathematical Rationalization.- 4.5. The Variance Diagram.- 4.5.1. Geometrical Description.- 4.5.2. Mathematical Rationalization.- 4.5.3. Examples.- 4.6. Calculation of Fractional Concentrations.- 4.6.1. Geometrical Description.- 4.6.2. Mathematical Rationalization.- 4.6.3. Examples.- References.- 5 Simultaneous Multivariate Analysis of Multiple Data Matrices.- 5.1. Introduction.- 5.2. Three-Mode Principal Components Analysis.- 5.2.1. Concepts.- 5.2.2. Algorithms.- 5.2.2.1. Tucker 1.- 5.2.2.2. Tucker 2.- 5.2.2.3. Tucker 3 (“Alternating Least Squares”).- 5.2.3. Examples.- 5.2.3.1. GC-MS of Crude Oils.- 5.2.3.2. Predicting Retention in HPLC.- 5.3. Generalized Procrustes Analysis.- 5.3.1. Concepts.- 5.3.2. Algorithms.- 5.3.3. Example: Comparison of Classifications of Staphylococcus Strains Using Binary (+ / -) Biochemical Tests or Fatty Acid Data.- References.- 6 Multivariate Calibration: Quantification of Harmonies and Disharmonies in Analytical Data.- 6.1. Introduction.- 6.1.1. Calibrating an Analytical Instrument Is Like Tuning a Musical Instrument.- 6.1.2. Quantitative Chemometrics.- 6.1.3. Notation.- 6.2. Interferences.- 6.2.1. Chemical Interference in the Samples.- 6.2.2. Physical Interference in the Samples.- 6.2.3. Experimental Interferences from the Measurement Itself.- 6.2.4. Determining Concentrations in the Presence of Interferences.- 6.2.5. The Danger of Outliers.- 6.3. Different Groups of Approaches.- 6.3.1. Linear-Nonlinear.- 6.3.2. Selection-Weighting.- 6.3.3. Different Types of Assumptions.- 6.3.3.1. Causal “Classical” Modeling.- 6.3.3.2. Traditional Statistical “Inverse” Calibration.- 6.3.3.3. Calibration on Latent Variables.- 6.4. Multivariate Calibration by Bilinear “Soft Modeling”.- 6.4.1. Introduction.- 6.4.2. Principal Component Regression.- 6.4.3. Partial Least-Squares Regression.- 6.4.4. Outlier Detection (Error Warnings).- 6.5. Example from NIR Diffuse Reflectance Spectroscopy.- 6.6. Conclusion.- References.- II: Spectral Interpretation and Library Search.- 7 Automated Spectra Interpretation and Library Search Systems.- 7.1. Introduction.- 7.2. The Mathematical Model.- 7.3. The General Algorithm.- 7.3.1. Overview.- 7.3.2. Structure Inference.- 7.3.3. Consistency Check.- 7.3.4. Structure Assembly.- 7.3.5. Spectra Prediction and Comparison.- 7.3.6. Discussion.- 7.4. Library Search Systems.- 7.4.1. Overview.- 7.4.2. The Model.- 7.4.3. Spectral Feature Selection.- 7.4.4. Implementation.- 7.4.5. Composition of the Reference Data Base.- References.- 8 Carbon-13 Nuclear Magnetic Resonance Spectrum Simulation.- 8.1. Introduction.- 8.2. Methodology.- 8.2.1. Data Entry and Problem Definition.- 8.2.2. Molecular Mechanics Model Building.- 8.2.3. Molecular Structure Descriptor Generation.- 8.2.4. Development and Evaluation of Chemical Shift Models.- 8.2.5. Spectrum Simulation.- 8.3. Example Studies.- 8.3.1. Steroids.- 8.3.2. Substituted Cyclopentanes and Cyclopentanols.- 8.4. Conclusion.- References.- 9 The Evolution of an Automated IR Spectra Interpretation System.- 9.1. Introduction.- 9.2. Early Explorations.- 9.3. The Research Phase.- 9.4. Unsatisfactory Results.- 9.5. Steps toward Interpretation.- 9.6. Separation of Interpretation and Search.- 9.7. The Experts.- 9.8. Product Development.- 9.9. An Applications Example.- 9.10. Conclusion.- References.- 10 Novel Advances in Pattern Recognition and Knowledge-Based Methods in Infrared Spectroscopy.- 10.1. Identifying a Compound by IR Spectroscopy.- 10.1.1. Searching Collections of Spectra.- 10.1.1.1. The Role of Computers in Spectral Searching.- 10.2. Interpretation of IR Spectra.- 10.2.1. Carboxylic Acid Interpretations.- 10.2.2. The Role of Computers in IR Spectral Interpretation.- 10.2.2.1. Pattern Recognition.- 10.2.2.2. Knowledge-Based Systems.- 10.3. Current Status of PAIRS Package.- 10.3.1. PAIRS Interpretation of Carboxylic Acids.- 10.4. Conclusion.- References.- 11 Library Storage and Retrieval Methods in Infrared Spectroscopy.- 11.1. Introduction.- 11.2. Existing Computerized Databases.- 11.3. Storage Methods for Infrared Spectra.- 11.3.1. Magnetic Tape.- 11.3.2. High-Performance Disk Drives.- 11.3.3. Small Winchester Disk Drives.- 11.3.4. Floppy Disk Drives.- 11.3.5. CD ROM Disk Drives.- 11.4. Spectral Searching and Retrieval Methods.- 11.5. Spectral Information Management Systems.- 11.6. Conclusion.- References.- 12 Synergistic Use of Infrared, 13C Nuclear Magnetic Resonance, and Mass Spectral Data in Analysis Schemes for the Identification of Organic Mixture Components.- 12.1. Identification Schemes for Multisource Spectral Data.- 12.2. Algorithms for IR and MS Data.- 12.2.1. GC/IR/MS Instrumentation.- 12.2.2. Combined IR and MS Library Search Results.- 12.2.3. IR/MS Algorithms with Auxiliary MS Data.- 12.2.3.1. Chemical Ionization IR/MS.- 12.2.3.2. Accurate Mass Measurement IR/MS.- 12.3. 13C NMR Applications in Organic Mixture Analysis.- 12.3.1. Quantitative 13C NMR for the Analysis of Mixtures.- 12.3.2. NMR Data Used for the Identification of Unknowns.- 12.3.3. Use of 13C NMR to Confirm GC/MS Search Results.- 12.3.3.1. MS/NMR Algorithm.- 12.3.3.2. MS/NMR Applications to Mixtures.- 12.3.4. Analysis of Petroleum Distillates by Q13C NMR.- References.