Identification Compare tool is used to compare search results in peptide or protein level. This tool does not calculate any statistical values (e.g. p- or q- values). This is a legacy tool, and we recommend users to try the Identification Stat Compare tool described in the next chapter. Both Identification Compare and Stat Compare use spectral count. For XIC peak area-based label-free analysis, please use the label-free tool described in separate chapter

To start such a comparison, you can click the “Project” tab to view all existing projects within a set of experiments.

Figure 10.1.1 Home Page.

The project tab lists the existing projects. Select “Demo Project c elegance” for example. Click “view” to list the existing experiments for this project.

Figure 10.1.2 List of Projects.

Click “identification©COMPARE” to list all existing comparisons. Once a user has created a new comparison, the result and relevant parameters will be saved on the server for further use.

Figure 10.1.3 List of Experiments.

Click “run new identificationCOMPARE” to build a new comparison.

Figure 10.1.4 List of Identification Comparison.

Select comparison level options, redundant options, and spectrum options. Then enter a name to save the comparison, search and select the experiments to compare. Click “run” to run the comparison.

Figure 10.1.5 Submit the Comparison Request to the Server

Once the comparison is completed, the page will redirect to the list of existing comparisons. The table of comparisons is sorted by date, so it is easy to locate the newly created comparison.

Figure 10.1.6 Updated List of Comparisons.

The user can view the comparison result either by clicking the “COMPARE file” link to open the result data or by clicking the “Venn Diagram” link to plot the result.

Figure 10.1.7 Venn Diagram for Identification Comparison

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