SIEVE User Guide

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2 Setting up a Procedure Analyzing Files 2. Specify a new experiment name and define break points for various steps so that you can evaluate the intermediate results and make changes. See the following table for information about the options. SIEVE displays interactive windows for any break points you select. If you don’t select any break points, SIEVE finishes the entire process without interruption. Table 2. Submit Analysis parameters Experiment Name ChromAlign break point Framing break point Show advanced progress info Type the name of the experiment, using the following criteria: • Do not type the name of an existing experiment. • Do not us a name with spaces or special characters. • Use an underscore (_) to separate parts of the file name. If you enter an existing experiment name or an invalid file name, SIEVE displays an error message. Select this option to pause after the ChromAlign process so that you can evaluate the results. This option opens a Spotfire display after the chromatograms in all control and sample files have been aligned. Use the display to view alignment and to determine whether to continue or to start over with different files. Select this option to pause the procedure after the framing process so that you can evaluate the results. This option opens a Spotfire report that includes all framing information before you start a SEQUEST search. This report provides all comparative information, including intensity ratios and pValues for each frame. Click this option to display a DOS window that displays the procedure progress (see Figure 10). 3. Click Run to start the analysis and align the chromatograms. If you selected Show advanced progress info in the Submit Analysis view, a DOS window displays the progress of the procedure. 16 SIEVE User Guide Thermo Scientific
Spotfire displays a screen similar to Figure 9 with the aligned chromatograms. Figure 9. ChromAlign results 2 Setting up a Procedure Analyzing Files Thermo Scientific SIEVE User Guide 17
Page 1 and 2: XCALI-97186 Revision B July 2007 Fo
Page 3 and 4: Contents Thermo Scientific SIEVE Us
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: Tips for Improving the Process Anal
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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