SIEVE User Guide

More documents

Recommendations

Info

B Understanding the Framing Process Aligning Peaks Aligning Peaks In this simplified representation of an experiment comparing three raw files (Controls) to three raw files (Treatments), SIEVE first consolidates the spectra in a multivariate space: Retention time versus m/z versus full-scan ms intensity (see Figure 23). Each of the control samples is represented by green spectral peaks on the map; each of the treatment samples is represented by red spectral peaks on the map. (In a real set of samples, thousands of peaks would populate this plane). Figure 23. SIEVE consolidates the spectra Notice that there are green outlying peaks to the left of each of the three main clusters. These peaks represent chromatographic shifts in retention time, requiring that the peaks first be aligned using the ChromAlign process. 36 SIEVE User Guide Thermo Fisher
Finding the Highest Peaks B Understanding the Framing Process Finding the Highest Peaks After alignment is complete, framing begins with the most intense MS peak. To find the first most intense peak, imagine a flat plane being lowered vertically over the 3D plot until a cluster of peaks with the highest intensity is found, triggering the creation of a frame. This iterative process is similar to the way data-dependent scanning operates in which the intensities of the MS peaks trigger MS/MS events. Using a proprietary algorithm (Recursive Base Peak Framing), SIEVE draws a frame around this cluster, which includes peaks from both the control and treatment samples (see Figure 24). The width and length of each frame depends on user-defined parameters selected before starting the SIEVE process, but the program suggests default values based on the type of instrument used to acquire the data. Figure 24. Finding peaks Thermo Scientific SIEVE User Guide 37
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 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 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

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?