SIEVE User Guide

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2 Setting up a Procedure Setting Parameters Table 1. Set Parameters dialog box values, continued Parameter Definition LTQ default Retention time stop (min) Type the end of the retention time for the chromatogram in minutes. Values: The minimum value is the minimum retention time in the first control raw file. The maximum value is the maximum of RT in the first control raw file. Threshold Enter a value to determine the lowest MS intensity that triggers framing. Perform SEQUEST search Parameters file name Enter Max. # of frames to search Values: 1 to 1E10 . IMPORTANT If you set this value too low, SIEVE might examine the total amount of frames before finding significant peaks Click Yes to search a protein database using SEQUEST. Values: Yes or No. Select a SEQUEST parameter file (.params) to be used for a SEQUEST search. See the BioWorks User’s Manual for further details. The default is C:\Xcalibur\system\programs\SIEVE\params\ SIEVE.params. Type a maximum number of frames to be searched by SEQUEST. Values: 1 to 10000. The default value is 100. pValue Type the lowest pValue for a frame to be sent for a SEQUEST search. Xcorr vs. charge state filter Values: The minimum value is 0. The maximum value is 1. The default minimum value is 1.00E -08 . Specifies the ID threshold for the filter criteria to improve the number of valid positive entries in the results. This filter combines the peptide properties, using the peptide charge and the Xcorrelation score from SEQUEST. Values: (+1) = 1.5 [0.1 to 10.0] (+2) = 2.5 [0.1 to 10.0] (+3) = 3.7 [0.1 to 10.0] (+4) = 4.5 [0.1 to 10.0] Maximum of RT in the first control raw file. 50 000 500 000 for LTQ FT 1E 6 for Orbitrap Yes Yes SIEVE.params 100 100 LTQ FT and Orbitrap default 14 SIEVE User Guide Thermo Scientific
Tips for Improving the Process Analyzing Files Use the following guidelines to improve the SIEVE process when comparing files: 2 Setting up a Procedure Analyzing Files • To improve processing speed, narrow the retention time range to the area of the chromatogram where components (for example, peptides and metabolites) have eluted. • Pick the file with the best chromatogram as the first control file, since all other files are compared to this reference chromatogram. To submit files for analysis and display initial results 1. After selecting files and setting parameters, click Next on the Set Parameters window to send the raw data from the files to the ChromAlign process. For a description of the alignment process, see Appendix A, “Understanding the ChromAlign Process.” The Submit Analysis dialog box appears. Figure 8. Options for submitting analysis Thermo Scientific SIEVE User Guide 15
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: Table 1. Set Parameters dialog box
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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