10.6 Label-free Analysis using XIC

In the project page, click the Label-Free Analysis button on the menu

Figure 10.6.1: Link for Quantitative Comparison.

The Label-Free Analysis Page will show previous analysis results.
To run a new Label-Free Analysis, click on “Run Label-Free Analysis” on the top right.
To load the previous configuration from a past analysis, press the “+” button underneath the “Create From Existing Configuration” column.

Figure 10.6.2 View of the Label-Free Analysis Page

Run Label-Free Analysis

Figure 10.6.3: Selecting Groups.

Type a name for the sample group and select multiple samples (typically replicates) from below. Press “Add to Group” to finish group selection.

Figure 10.6.4 Naming and selecting sample groups.

Name a second group and select the experiments to add to this group. The previous group will be listed at the top of the page. Repeat to add as many groups as necessary.

Figure 10.6.5 Add as many groups as necessary.

Click “Next” at the bottom of the page once the desired groups are added.
Name the experiment analysis before submission.

Figure 10.6.6 Final Interface before Submission.

Press the “Submit” button to begin the analysis.

Figure 10.6.7 Submit Button.

After pressing the submit button, the page will be redirected to the Label-Free Analysis page, with the submission results on the top of the table.

Figure 10.6.8 Main Page

Each column description:

accession: protein accession
gene: name
intensity p-value: t-test for 2 samples or ANOVA test for more than 2 samples
intensity q-value: BH correction value
ratio p-value: p-value using multiple intensity ratios. For example, the ratio is calculated like this: Ratio 1 = peptide intensity from 1st replicate experiment from sample 2 / peptide intensity from 1st replicate experiment from sample 1. Ratio 2 = peptide intensity from 2nd replicate experiment from sample 2 / peptide intensity from 2nd replicate experiment from sample 1, and so on. One sample t-test is done using all these ratios.
One replicate intensity from sample2 divided by another replicate from sample 1 is one ratio, for example.
ratio q-value: corresponding BH correction value
norm ratio p-value: p-value using multiple normalized intensity ratios. One replicate-nomalized intensity from sample2 divided by another replicate normalized intensity from sample 1 is one ratio, for example.
norm ratio q-value: corresponding BH correction value
log intensity p-value: t-test p-value from log2 (intensity)
log intensity q-value: corresponding BH correction value
norm log intensity p-value: t-test p-value from log2 (norm intensity)
norm log intensity q-value: corresponding BH correction value
protein abundance: log10 (total peptide intensity sum/protein length). This value can be used as protein abundance in the sample. Please check the protein abundance distribution graph by clicking the above button.