SIEVE User Guide

More documents

Recommendations

Info

1 Overview to SIEVE About the SIEVE Procedure Step 5: Analyze the data using SEQUEST to identify proteins Select SEQUEST to perform a database search only on frames determined to have confident pValues. This step identifies peptides and proteins that might represent differential expression. Using SIEVE to pre-filter data greatly reduces the number of spectra that need to be searched, significantly decreases the time spent identifying proteins, and increases the throughput of complex sample sets. Step 6: Review Interactive Results SIEVE provides interactive results using several different Spotfire plots, specifically chosen to maximize the information extracted from these types of biomarker discovery experiments. Breakpoints after ChromAlign, Recursive Base Peak Framing, and SEQUEST provide the option of checking intermediate results before proceeding or adjusting parameters. 4 SIEVE User Guide Thermo Scientific
Setting up a Procedure The following sections describe setting up and running a procedure for SIEVE using two sets of raw files: • Starting a New Experiment • Setting Parameters • Analyzing Files • Framing the Data • Identifying Proteins and Peptides • Viewing a Saved Experiment Thermo Scientific SIEVE User Guide 5 2
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: About the SIEVE Procedure 1 Overvie
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

SIEVE User Guide

Create successful ePaper yourself

Delete template?

Save as template?