TPP Demo2009 - 5. Search data with SpectraST 使用 SpectraST 搜尋圖譜數據

SpectraST is a search engine that compares acquired spectra against a library of pre-identified spectra to which peptide sequences have been assigned. In order to conduct the search, we must first download the appropriate spectral library.

SpectraST 為圖譜搜尋引擎，可經由事先建立的 peptide sequence 與 spectra 對應關系，取得實驗數據的比對結果。
為了建立該搜尋，需先下載適當的 spectral library。

• Go to the Home page, and switch the pipeline type to SpectraST.

按下位於網頁上方的"Home"連結，

再從選單中選擇"SpectraST"。

• Under the SpectraST Tools section of the navigation menu, select the Download Spectral Libraries menu item.

將滑鼠移至上方的"SpectraST Tools"選項，並從跳出的視窗中，選擇"Download Spectral Libraries"選項。

• You are now at at page that shows a list of spectral libraries available at PeptideAtlas, along with locally-installed/downloaded ones. Select the NIST_yeast_IT_v2.0_2008-07-11.splib.zip (yeast ion trap) library on the right pane, and click on Download Selected Libraries.

上述步驟完成後，會跳到一個列出 PeptideAtlas 的 spectral libraries 頁面，其中包含已安裝與可下載的。

請在右側欄位中勾選 NIST_yeast_IT_v2.0_2008-07-11.splib.zip 後按下"Download Selected Libraries"按鈕。

若完成下載，頁面上方的狀態欄會呈現橘色。

We also need to copy the mzML data files we converted in step 4 into the SpectraST data area. While this can be accomplished within Petunia, it is easier to use Windows file copy. Copy the two mzML files located at C:\Inetpub\wwwroot\ISB\data\demo2009\tandem into the directory C:\Inetpub\wwwroot\ISB\data\demo2009\spectrast (which you will need to create). Now we can move on to searching these data:

現在需要將 mzML 檔案複製到 SpectraST 的資料區域。
這裡我們使用 Windows 的檔案管理即可，將位於 C:\Inetpub\wwwroot\ISB\data\demo2009\tandem 目錄中的 mzML 複製到 C:\Inetpub\wwwroot\ISB\data\demo2009\spectrast (請自行建立該目錄)。




以下開始進行 SpectraST 搜尋。

• Mouse-over the Analysis Pipeline menu title in Petunia, and then click on the SpectraST Search menu item to access the SpectraST search interface.

將滑鼠移至上方的"Analysis Pipeline (SpectraST)" 選項，並從跳出的視窗中，選擇"SpectraST Search"選項。

• In section 1, select the two mzML data files under demo2009\spectrast and click Add Files.

選擇"Specify mzXML Input Files"區段中的"Add Files"按鈕。

勾選 demo2009\spectrast 下的2個 mzML 檔案後，按下"Select"按鈕。

• For section 2, select the NIST_yeast_IT_v2.0_2008-07-11.splib.splib spectral library file located under dbase\speclibs. This is the file you downloaded from PeptideAtlas above.

選擇"Specify Library FIle (not required if specified in params file below)"區段中的"Add Files"按鈕。

勾選 dbase\speclibs 下的 NIST_yeast_IT_v2.0_2008-07-11.splib.splib ，再按下"Select"按鈕。

• Finally, for section 3, select the yeast_orfs_all_REV.20060126.short.fasta sequence database, located under dbase.

序列資料庫選擇 dbase 下的 yeast_orfs_all_REV.20060126.short.fasta 。

• Leave the rest of the options on the page at their default values, and click on Run SpectraST to initiate the search.

其他的選項保持預設值，並按下"Run SpectraST"按鈕"開始執行搜尋。