In 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 previous configuration from a past analysis, press the “+” button underneath the “Create From Exisisting 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 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 intensy ratios. For example, 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 intensy ratios. One replicate nomalized intensity from sample2 divided by another replicate nomalized 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 sample. Please check protein abundance distribution graph by clicking the above button.

Figure 10.6.8.1 table view

Click on “View Graph” to see analysis results.

Figure 10.6.9 View Graph.

Click on a Protein and peptide to see its Chromotogram.

Figure 10.6.10 Chromotagram

Back on the Label Free Analysis page, press the “Change Status to Verification” link to change the experiment status.

Figure 10.6.11 Change Status To Verification

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