SIEVE User Guide

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© 2007 Thermo Fisher Scientific Inc. All rights reserved. Microsoft ® Windows ® XP is a registered trademark of Microsoft Corporation in the United States and other countries. SIEVE, ChromAlign, LTQ XL, LTQ Orbitrap, LTQ FT Ultra, and BioWorks are trademarks and Xcalibur ® is a registered trademark of Thermo Fisher Scientific Inc. DecisionSite is a trademark and Spotfire ® is a registered trademark of Spotfire, Inc. SEQUEST ® is a registered trademark of the University of Washington. Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the product operation. This document is copyright protected and any reproduction of the whole or any part of this document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc. The contents of this document are subject to change without notice. All technical information in this document is for reference purposes only. System configurations and specifications in this document supersede all previous information received by the purchaser. Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or errorfree and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that might result from any use of this document, even if the information in the document is followed properly. This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of Sale shall govern all conflicting information between the two documents. Release history: For Research Use Only. Not regulated for medical or veterinary diagnostic use by U.S. FDA or other competent authorities.
Contents Thermo Scientific SIEVE User Guide iii C Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .v SIEVE User Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Viewing the Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi Getting a License. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Getting a New License Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Installing a New License Code. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix Safety and Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x Chapter 1 Overview to SIEVE. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1 Understanding SIEVE. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 About the SIEVE Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Chapter 2 Setting up a Procedure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5 Starting a New Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 Setting Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Analyzing Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Framing the Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 Identifying Proteins and Peptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 Viewing a Saved Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Appendix A Understanding the ChromAlign Process. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .27 Outlining the ChromAlign Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 Starting the ChromAlign Process. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 ChromAlign First Level Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 ChromAlign Second Level Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 Aligning Over Different Abundance Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 Aligning Over Chromalign Time Shifts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Page 1: XCALI-97186 Revision B July 2007 Fo
Page 5 and 6: Preface SIEVE User Guide Viewing th
Page 7 and 8: Getting a License Getting a New Lic
Page 9 and 10: Installing a New License Code Once
Page 11 and 12: Overview to SIEVE SIEVE software pe
Page 13 and 14: About the SIEVE Procedure 1 Overvie
Page 15 and 16: Setting up a Procedure The followin
Page 17 and 18: 2. Click Get Started to display exp
Page 19 and 20: 2 Setting up a Procedure Starting a
Page 21 and 22: 10. Click Add to add the files to t
Page 23 and 24: Table 1. Set Parameters dialog box
Page 25 and 26: Tips for Improving the Process Anal
Page 27 and 28: Spotfire displays a screen similar
Page 29 and 30: 2 Setting up a Procedure Framing th
Page 31 and 32: 2. Make changes to the parameters a
Page 33 and 34: Viewing a Saved Experiment 2 Settin
Page 35: 2 Setting up a Procedure Viewing a
Page 38 and 39: A Understanding the ChromAlign Proc
Page 46 and 47: B Understanding the Framing Process
Page 49 and 50: Using Spotfire to View Analysis Res
Page 51 and 52: Spotfire Range Sliders Frame Detail
Page 53 and 54:
Protein ID View C Using Spotfire to
Page 55:
Table 4. Parameter definitions for
Page 58:
Index: P P parameters framing 37 se
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