Process Automation for Analytical Measurements Providing High Precise Sample Preparation in Life Science Applications Dissertation zur Erlangung des akademischen Grades Doktor-Ingenieur (Dr.-Ing.) der Fakultät für Informatik und Elektrotechnik der Universität Rostock Ellen Vorberg eingereicht am 25.02.2015 in Rostock verteidigt am 08.09.2015 in Rostock Supervisors 1. Prof. Dr.-Ing. habil. Kerstin Thurow, University of Rostock, Center for Life Science Automation 2. Prof. Dr.-Ing. Norbert Stoll, University of Rostock, Institute of Automation 3. Prof. Robin A. Felder, Ph.D., University of Virginia, School of Medicine, Department of Pathology, Charlottesville, VA Acknowledgment First of all, I would like to thank Prof. Dr. Kerstin Thurow for her continuous support throughout my PhD studies and dissertation work. I am truly grateful for her advices and suggestions and, moreover, for the excellent laboratory equipment. Furthermore, I would like to extend my thanks to all the staff members of celisca and the Institute of Automation. Especially, I would like to thank Sybille Horn, Dr. Heidi Fleischer, Dr. Thomas Roddelkopf, Lars Woinar, Heiko Engelhardt, Dr. Hui Liu, Dr. Sebastian Neubert, and Dr. Steffen Junginger for technical support. Most importantly, I thank my beloved husband, Mike Vorberg, for his love, support, and encouragement. Table of Contents Table of Contents List of Figures ............................................................................................................................................ i Sources of Figures ................................................................................................................................... iii List of Tables ............................................................................................................................................ iv List of Abbreviations ................................................................................................................................. v 1. Introduction ......................................................................................................................................... 1 2. State of the Art: Laboratory Automation ............................................................................................ 6 2.1 Automated Biological Sample Pretreatment Depending on Measurement Processes ................ 6 2.1.1 Automated Biological Processes Using Assay Detection Readers .......................................... 6 2.1.2 Automated Biological Processes Using Mass Spectrometers ................................................ 7 2.2 Approaches for Automated Analytical Sample Pretreatment and Measurement Processes ....... 9 2.3 Comparison and Conclusion of Automated Sample Pretreatment ............................................. 10 2.4 Automation Systems and Compounds ........................................................................................ 10 2.4.1 Workstations ........................................................................................................................ 10 2.4.2 Workstations with Embedded Autosamplers ...................................................................... 15 2.4.3 Comparison of Fully Integrated Systems and Traditional Workstations .............................. 20 2.5 Analytical Techniques of Measurement ...................................................................................... 24 2.5.1 Element-Specific Measurements .......................................................................................... 24 2.5.2 Structure-Specific Measurements ........................................................................................ 27 3. Scope of Work ................................................................................................................................... 29 3.1 Common Biological Processes ..................................................................................................... 29 3.2 Common Analytical Processes ‒ Comparison and Conclusion .................................................... 31 4. System Concept and Design .............................................................................................................. 34 Table of Contents 4.1 General Conspectus ..................................................................................................................... 34 4.2 Concept of Standardized Labware Design ................................................................................... 36 4.3 System Integrator ........................................................................................................................ 38 4.4 Liquid Handling ............................................................................................................................ 40 4.5 Sample Handling .......................................................................................................................... 42 4.5.1 Barcode Reading and Sample Storage.................................................................................. 42 4.5.2 (De-) Capping and MTP-Handling ......................................................................................... 42 4.5.3 Crimping and Individual Sample Handling............................................................................ 45 4.5.4 Housing ................................................................................................................................. 47 4.5.5 Weighing Station and Ionizer ............................................................................................... 48 4.6 Sample Treatment and Analytical Devices .................................................................................. 49 4.7 Software Integration ................................................................................................................... 54 4.8 Integration with External Stations (Mobile Robot Transport) .................................................... 58 5. Statistical Methods and Definitions .................................................................................................. 63 5.1 Validation Parameters ................................................................................................................. 63 5.1.1 Bias Error of the Measuring Instrument ............................................................................... 63 5.1.2 Repeatability Standard Deviation ......................................................................................... 63 5.1.3 Reproducibility Standard Deviation ..................................................................................... 63 5.1.4 Discrimination Threshold ..................................................................................................... 63 5.2 Further Definitions Considering the Acceptability of the Results ............................................... 64 5.2.1 Horwitz Definition ................................................................................................................ 64 5.2.2 Confidence Interval Using Student´s t-Distribution ............................................................. 64 5.2.3 David-Test ............................................................................................................................. 64 6. Application I: Element-Specific Analytical Measurements ................................................................ 65 6.1 Process Description Including Motivation and Process Steps ..................................................... 65 6.2 Automation Concept: Automation Requirements and Process Adaption .................................. 67 6.3 Results: Manual Validation Sequence – Element-Specific Measurement .................................. 73 6.3.1 Bias Error of the Measuring Instrument ............................................................................... 73 6.3.2 Repeatability Standard Deviation ......................................................................................... 73 6.3.3 Reproducibility Standard Deviation ..................................................................................... 73 6.3.4 Discrimination Threshold ..................................................................................................... 73 Table of Contents 6.4 Results: Automated Validation Sequence – Element-Specific Measurement ............................ 74 6.4.1 Bias Error of the Measuring Instrument ............................................................................... 74 6.4.2 Repeatability Standard Deviation ......................................................................................... 74 6.4.3 Reproducibility Standard Deviation ..................................................................................... 74 6.4.4 Discrimination Threshold ..................................................................................................... 74 6.5 Comparison and Conclusion of the Validation Sequences – Element-Specific Measurement ... 74 6.6 Further Element-Specific Measurements.................................................................................... 77 7. Application II: Structure-Specific Analytical Measurements ............................................................. 81 7.1 Process Description Including Motivation and Process Steps ..................................................... 81 7.2 Automation Concept: Automation Requirements and Process Adaption .................................