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Table of Contents
Preface ........................................................................................................ 7
Chapter 1: Getting Started with Scaffold............................................... 11
Chapter 2: Identifying Proteins with Scaffold ....................................... 23
Chapter 3: Loading Data in Scaffold ...................................................... 37
Chapter 4: The Scaffold Window............................................................ 61
Chapter 5: The Load Data View ............................................................ 111
Chapter 6: The Samples View............................................................... 121
Chapter 7: Quantify View ...................................................................... 143
Chapter 8: Protein Grouping and Clustering ...................................... 151
Chapter 9: Quantitative Methods and tests......................................... 163
Chapter 10: Precursor Intensity Quantitation ..................................... 179
Chapter 11: Reports............................................................................... 189
Appendix................................................................................................. 205
Scaffold User’s Manual
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