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。

Using BioJava to Parsing FASTA 使用 BioJAVA 讀取 FASTA 檔案

Introudce

簡介

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One of methods to parse FASTA in BioJava cookbook is using SeqIOTools which has been marked as deprecated.

BioJava 上的 Cookbook 範例有讀取 FASTA 的教學，不過所使用的 API "SeqIOTools" 在 Docs 上已經被標註為 Deprecated。

So, this example shows how to do it in other ways, like SequenceIterator and RichSequence.

因此以下的 Code 除了舊式寫法外，還包含了使用 SequenceIterator 以及 RichSequence 來達成

 

 

 

Code

原始碼

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import java.io.*;

import java.util.*;

import org.biojava.bio.*;

import org.biojava.bio.seq.*;

import org.biojava.bio.seq.db.*;

import org.biojava.bio.seq.io.*;

import org.biojava.bio.symbol.*;

import org.biojavax.bio.seq.RichSequence;

import org.biojavax.bio.seq.RichSequenceIterator;

public class ReadFasta {

  /**

   *  This is sample code for parsing FASTA by using BioJava 

   * 本程式測試如何使用 BioJava 取得 FASTA 序列並輸出

   */

  public static void main(String[] args) throws IOException, BioException {

    try {

 

      /* set up parameters

       * 設定必要參數 

       */

      String sFilename = "D:\\working\\cRAP_200905_prefixCON.fasta";

      String sSeqType="PROTEIN";

      String sFileType="FASTA";

 

      /* for Sequence DB

       * 給 SequenceDB 使用

       */

      BufferedInputStream is = new BufferedInputStream(new FileInputStream(sFilename));      

 

      /* for Sequence Iterator 

       * 給 SequenceIterator 與 RichSequenceIterator 使用

       */

      BufferedReader br = new BufferedReader(new FileReader(sFilename));         

 

      /* for SequenceDB 

       * 給 SequenceDB 使用

       */

      Alphabet alpha = AlphabetManager.alphabetForName(sSeqType);  

      /*  Parsing FASTA by SeqIOTools (Deprecated)

       *  使用舊型 SeqIOTools 來取得(已棄置)
       */

      /* get a SequenceDB of all sequences in the file

       * 使用 SequenceDB 方式取得: 會有序列不按照順序的問題

       */
      //SequenceDB db =  SeqIOTools.readFasta(is, alpha);
      //SeqIOTools.writeFasta(System.out, db);
      /*  Test method of Sequence

       *  測試 Sequence 的 method

       */
      //System.out.println("getClass: "+db.getClass());
      //System.out.println("ids: "+db.ids());
      //System.out.println("getName: "+db.getName());
      //System.out.println("getSequence: "+db.getSequence("CON_sp|ALBU_BOVIN|").seqString());
      //SeqIOTools.writeFasta(System.out, db);
     
      /* Parsing FASTA by SequenceIterator

       * 使用 SequenceIterator 方式取得       

       */
      SequenceIterator iter =(SequenceIterator) SeqIOTools.fileToBiojava(sFileType, sSeqType,br);

       /*
       int iCount=0;
       while (  iter.hasNext()  ){
          Sequence s = iter.nextSequence();

          //String name = s.getName();
          //s.length();
          //s.getAnnotation();
          System.out.println("\nName: "+s.getName());
          System.out.println("\tAnnotation: "+s.getAnnotation());
          System.out.println("\tSeq: "+s.seqString());
          iCount++;
         
        }
        System.out.println("\tCount for Seq: "+iCount);
       */

      /*  Parsing FASTA by RichSequence

       * 使用新的 RichSequence 方式來取得:

       */

       RichSequenceIterator rsIter = RichSequence.IOTools.readFastaProtein(br, null);

       while (rsIter.hasNext()){

          RichSequence rsSequence = rsIter.nextRichSequence();

          //String name = s.getName();

          //s.length();

          //s.getAnnotation();

          System.out.println("\tAccession: "+rsSequence.getAccession());

          System.out.println("\tDescription: "+rsSequence.getDescription());

          System.out.println("\tDivision: "+rsSequence.getDivision());

          System.out.println("\tName: "+rsSequence.getName());

          System.out.println("\tseqString: "+rsSequence.seqString());

      

       }

     

    }

    catch (BioException ex) {

      //not in fasta format or wrong alphabet

      ex.printStackTrace();

    }catch (NoSuchElementException ex) {

      //no fasta sequences in the file

      ex.printStackTrace();

    }catch (FileNotFoundException ex) {

      //problem reading file

      ex.printStackTrace();

    }

  }

}

 

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Reference 

參考

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Parsing FASTA by SeqIOTools

使用舊型的 SeqIOTools 來取得 FASTA 範例

http://www.biojava.org/wiki/BioJava:Cookbook:SeqIO:ReadFasta

Parsing FASTA by RichSequence

RichSequence.IOTools 的 API

http://www.biojava.org/docs/api/org/biojavax/bio/seq/RichSequence.IOTools.html