TPP Demo2009 中文說明+操作畫面

TPP 官方 wiki 在 2009 年中製作了一份 TPP Demo2009 ，

http://tools.proteomecenter.org/wiki/index.php?title=TPP_Demo2009

裡面的內容從 TPP 軟體的初始下載到安裝，

以及基本的資料庫(X!Tandem)搜尋、檢驗分析結果(PeptideProphet, ProteinProphet)，

還有新增的功能(SpectraST搜尋)都有 Demo 說明，

是一個很好的 TPP 操作指引。

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。

TPP Demo2009 - 9. Peptide Quantitation with ASAPRatio 使用 ASAPRatio 定量 Peptide

ASAPRatio is a tool for measuring relative expression levels of peptides and proteins from isotopically-labeled samples (e.g. ICAT, SILAC, etc).

ASAPRatio 是一套用來測量以同位素標定樣本的工具，可計算出該 peptides 與 proteins 層級的相對表現量。

TPP Demo2009 - 8. Further peptide-level validation iProphet 使用 iProphet 做進一步的 peptide 層級檢驗

iProphet (or InterProphet) is a tool that provides statistical refinement of PeptidePropet results.

iProphet (或稱為 InterProphet) 工具能將 PeptidePropet 產生的結果檔合併並做更進一步統計上的檢驗。

TPP Demo2009 - 7. Visualize LC-MS/MS data using Pep3D 使用 Pep3D 來瀏覽 LC-MS/MS 圖譜

Pep3D is a tool for visualizing LC MS data, along with results from PeptideProphet.

Pep3D 是用來視覺化 LC MS 資料的工具，可搭配 PeptideProphet 的結果檔。

TPP Demo2009 - 6. Validation of Peptide-Spectrum assignments with PeptideProphet 使用 PetideProphet 檢驗 pepitde 與 Spectrum 對應的關係

PeptideProphet provides statistical validation of search engine results by assigning a probability to each peptide-spectrum match.

PeptideProphet 給予搜尋結果的每對 peptide 與 spectrum 一個機率，以統計模型來檢定是否為 false match。

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。

TPP Demo2009 - 4. Search data with X!Tandem 使用 X!Tandem 搜尋引擎

A custom version of the popular open-source search engine X!Tandem is bundled and installed with the TPP. It has been modified from the original distribution by adding the K-Score scoring function, developed by a team at the Fred Hutchinson Cancer Research Center.

TPP 本身包含客製化後的開放搜尋軟體 X!Tandem。
內含的 X!Tandem 已被更改並加入 K-Score 功能，該功能由Fred Hutchinson Cancer Research Center 所發展。

TPP Demo2009 - 3. Convert raw data to the mzML format 轉換 raw data 成 mzML 格式檔案

We have developed the TPP (and dozens of related tools) to read mass-spec data from a common, open data format. We must therefore first convert the proprietary raw data to this format, called mzML.

TPP 及其數種相關工具以共通的檔案格式當做來源，因此需要將原始的數據轉成該共通格式，稱為 mzML。

TPP Demo2009 - 2. Download and install the test data and database 下載並安裝測試資料

For this demo, we will be using a SILAC-labeled Yeast dataset, comprised of 2 runs on a high mass-accuracy Orbitrap instrument, along with a Yeast database appended with decoys. We also include a search parameters file.

Deom 所用的資料為 SILAC-labeled Yeast 資料，包含在高精準度 Orbitrap 儀器下的2組數據。序列資料庫為 Yeast 並包含 decoys。資料亦附上搜尋的參數檔。

TPP Demo2009 - 1. Download and install the TPP 下載並安裝 TPP

To install on your Windows system, please follow our Windows Installation Guide, making sure that you select to download the file "TPP_Setup_v4_3_JETSTREAM_rev_1.exe" from our Sourceforge download site.

從 Sourceforge download site.下載"TPP_Setup_v4_3_JETSTREAM_rev_1.exe"，並按照 Windows Installation Guide 指示安裝 windows 版本的 TPP。