Using ReAdW to convert Thermo .RAW files to mzXML

To run ReAdW, you need to install Xcalibur first.

1. download program:

ReAdW program download:

http://sourceforge.net/projects/sashimi/files/ReAdW%20%28Xcalibur%20converter%29/ReAdW-4.3.1/ReAdW-4.3.1.zip/download

zlib1donwload

https://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-3-0/win_lib/zlib123-dll/zlib1.dll

2. put the readw.exe and zlib1.dll in the same directory.

3. input something like below by command line:

ReAdW -v --mzXML test.raw

 

Reference:

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

How to find/build the closest specie sequence database 如何在序列資料庫中找到最接近的目標物種

Take "Vibrio parahaemolyticus" for exmaple.
以腸炎弧菌(Vibrio parahaemolyticus)為例，

We cannot find this specie on common sequence database, ex: NCBInr.

一般在序列資料庫(如NCBInr)沒有細分到這一層，

If we cannot reduce possible sequence database pool, we'll get too much results too difficult to analysis.

如果不分類就搜尋的話，可能導致花費大量的時間在搜尋過程或結果的過濾上。

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。