TPP Demo2009 - 10. Protein-level validation with ProteinProphet 使用 ProteinProphet 做 protein 層級的檢驗

ProteinProphet is a tool that provides statistical validation of Protein identifications, and is based on PeptideProphet results.

ProteinProphet 是一套基於 PeptideProphet 結果檔的檢驗工具，
以統計模型來檢定 Protein Identifications 是否為 false match。

• Click on the Analyze Proteins tab under the Analysis Pipeline section in Petunia to access the ProteinProphet interface.

將滑鼠移至上方的"Analysis Pipeline (Tandem)" 選項，並從跳出的視窗中，選擇"Analyze Proteins"選項以進入 ProteinProphet 介面。

• Select the interact.pep.xml file in the directory demo2009. Make sure that there is only one file selected for analysis; you can edit the selections using the checkboxes and Remove button on the right-hand side.

加入 demo2009 目錄下的 interact.pep.xml 檔案。

• Leave all other options set to their defaults, and click on Run ProteinProphet at the bottom of the page to run ProteinProphet.

保留其他預設值，再按下"Run proteinProphet"按鈕以執行 ProteinProphet。

• once the command finishes running, you can click on the view results link that appears in the Command Status box to view and analyze the results. Protein groups are sorted in descending order by Probability so that the groups at the top of the page are the most confident identifications. The protein probabilities are the red numbers listed next to each protein group. IMG:Protxml

一旦執行完畢，按下"Command Status"區塊下的"here"連結，

再按下"Output Files"區塊下的"View"連結瀏覽結果。

Protein groups 預設以機率從大到小排序，因此第一個 Protein group 為最可信。

而機率以紅色數字顯示在 Protein 名稱的右側。