tag:blogger.com,1999:blog-24956990672363235382026-05-05T08:24:16.160+08:00Bioinformatics for Proteomic Mass Spectrometry 生物資訊於蛋白質體的質譜資料分析散落一地的生物與資訊碎片， 能兜起來一個樣的有多少呢Unknownnoreply@blogger.comBlogger20125tag:blogger.com,1999:blog-2495699067236323538.post-80319905791735229242017-03-22T11:58:00.004+08:002017-03-22T11:59:37.675+08:00New features in Mascot Server 2.6 - administartor must know
Spectral library
spectral library creation is supported in database manager.
There are some default NIST and PRIDE spectral libraries.
You need to enable these and wait mascot download it automatically to use them.
You can also create your own spectral library from mascot results
Report Improvement
Report will only show significant results in default.
You can change it with Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-74915625934567559842015-07-17T15:21:00.003+08:002015-07-17T15:21:37.889+08:00improvement Byonic speedThere are two major reasons that why Byonic run so slow:
too large database and too many modifications.
[using Byonic funtion "Create focused database"]
http://www.proteinmetrics.com/wp-content/uploads/2014/10/AppNote-ByonicFocusedDatabase.pdf
Do Byonic search with few modificationsto to find possible proteins,
then using these proteins as new database to subsequent search with more Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-12679887107416837152012-09-27T15:18:00.001+08:002015-01-23T17:28:08.621+08:00Read Thermo RAW with MSFIleReader in C#Introduction
Thermo now provide free API called MSFileReader to access .RAW file.
This tutorial shows how to using C# to import MSFileReader .dll and call one of its function.
Step by Step
OS: Windows 7 x64
Visual Studio: 2010
MSFileReader: 2.2
Step 1. Install MSFileReader
http://sjsupport.thermofinnigan.com/public/detail.asp?id=703
Step 2. Create a project called "Unknownnoreply@blogger.com4tag:blogger.com,1999:blog-2495699067236323538.post-13990723674551080822011-11-24T12:19:00.009+08:002011-11-24T17:36:52.699+08:00Proteome Discoverer 1.3 InformationProteome Discoverer 1.3 new features includes:
*. phpsphoRS: PTM scoring
*. percolator : increase true positive PSM (peptide spectral match)
*. integrate proteinCenter: annotation
*. 64-bit windows support
Requirements:
Type Requirements
Disc Space Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-46859235202622616392011-09-26T10:01:00.000+08:002011-09-26T10:01:54.716+08:00Trans-Proteomic Pipeline (TPP) 4.5.0 releasehttp://tools.proteomecenter.org/wiki/index.php?title=TPP:4.5.0_Release_Notes
New Features New iModelParser.cgi tpp; fpr viewing iProphet models.
New PTMProphetParser tool.
New RTCatalogParser tool for cataloging retention times.
xinteract New features, report collision energy, report compensation voltage
InteractParser: New features, report collision energy, report Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-64071719078084296652011-09-15T10:00:00.000+08:002011-09-15T10:00:31.750+08:00MS File Reader 2.2 now support x64 Windows !MS File Reader finally support Windows x64.
Now you can use software that need MS File Reader, like MaxQuant, in Windows x64 with it.
Just downlaod the latest MS File Reader http://sjsupport.thermofinnigan.com/public/detail.asp?id=703 and install it.Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-59295115353953459122011-08-19T11:36:00.000+08:002011-08-19T11:36:01.470+08:00Using 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
zlib1donwloadhttps://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 Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-1579421813558618662010-10-08T18:47:00.005+08:002011-03-02T23:38:02.081+08:00How 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。
There are two ways to solve this issue.
因此可行的做法有2種，
One is to find the closest Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-52071977135317509222010-02-26T15:11:00.004+08:002010-12-30T21:27:15.487+08:00TPP 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。
而本文件除了試著將步驟說明翻譯成中文，並且加上些微的註解，最後附上實際操作畫面，希望能夠幫助初學者更快的應用 TPP !目錄:TPP Demo2009 - 1. Download and install the TPP (下載並安裝 TPP)TPP Demo2009 - 2. Download and install Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-71448438878362092782010-02-26T15:06:00.001+08:002010-12-30T21:07:20.541+08:00TPP 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Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-41252658096767752792010-02-26T15:04:00.001+08:002010-12-30T21:07:00.078+08:00TPP Demo2009 - 9. Peptide Quantitation with ASAPRatio 使用 ASAPRatio 定量 PeptideASAPRatio 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。
Click on the Analyze Peptides tab under the Analysis Pipeline section in Petunia to access the xinteract interface again.
將滑鼠移至上方的"Analysis Pipeline (Tandem)" 選項，並從跳出的視窗中，選擇"Analyze Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-22460383943081139252010-02-25T12:22:00.001+08:002010-12-30T21:06:46.173+08:00TPP 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。
Click on the Combine Analyses tab under the Analysis Pipeline section in Petunia to access the iProphet interface.
將滑鼠移至上方的"Analysis Pipeline (Tandem)" 選項，並從跳出的視窗中，選擇"Combine Analyses"選項以進入 iProphet的介面。
Select the Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-75158525154937493452010-02-25T12:21:00.003+08:002010-12-30T21:06:26.309+08:00TPP 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。
Under the Utilities -> Browse Files section in Petunia, navigate to the demo2009\tandem directory. (nB. you may already be in that directory.) You may also select the interact.pep.xml file under the spectrast folder.
將滑鼠移至上方的"Utilities" 選項，並從跳出的視窗中，選擇"Browse Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-2366302669875647142010-02-25T12:21:00.002+08:002010-12-30T21:06:14.887+08:00TPP 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。
Click on the Analyze Peptides tab under the Analysis Pipeline section in Petunia to access the xinteract interface.
回到首頁並選擇"Tandem"為分析流程後，將滑鼠移至上方的"Analysis Pipeline(Tandem)" 選項，並從跳出的視窗中，選擇"Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-17349714466892866372010-02-25T12:19:00.001+08:002010-12-30T21:06:04.322+08:00TPP 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 Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-32519672448005113252010-02-25T12:18:00.001+08:002010-12-30T21:05:54.250+08:00TPP 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。
First, make sure thatUnknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-43003828150545760542010-02-25T12:16:00.001+08:002010-12-30T21:05:42.944+08:00TPP 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。
If you downloaded the mzML files directly in step 2, skip to step 4.如果已下載 mzML 檔案，請跳過這個步驟並直接跳到步驟4。Mouse-over the Analysis Pipeline (Tandem) Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-26308952696452704742010-02-25T12:12:00.001+08:002010-12-30T21:05:23.961+08:00TPP 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。
If you would like to start the pipeline with the conversion of the vendor's Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-34016614215184533842010-02-25T11:23:00.001+08:002010-12-30T21:05:00.727+08:00TPP Demo2009 - 1. Download and install the TPP 下載並安裝 TPPTo 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。
Log into Petunia, the TPP GUI登入 TPP 的圖形介面 Petunia
As a way to verify Unknownnoreply@blogger.com0tag:blogger.com,1999:blog-2495699067236323538.post-79803657932995625702010-02-23T16:31:00.002+08:002011-03-09T17:07:15.810+08:00Using BioJava to Parsing FASTA 使用 BioJAVA 讀取 FASTA 檔案
Introudce簡介 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 &Unknownnoreply@blogger.com0