Manual MSGet

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Latest revision as of 02:38, 4 February 2014

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MSGet Manual

Introduction

MSGet is a tool that exports mass chromatogram data and pda data in text files from the binary .raw data of Xcalibur software (ThermoFisher). Xcalibur is the control and data acquisition software for the mass spectrometers of ThermoFisher.

The resulted text files are used for input file for PowerGet tool.

System Requirement

MSGet is only allowed to run on a PC where Xcalibur software (ThermoFisher) is installed.

Operation of MSGet has been tested with the following conditions.

OS	Winodws XP
Software Required	Xcalibur 2.0

Install

Download MSGet from the KOMICS website.

Unzip the downloaded .zip file.

Double click the file "MSGet_VC.exe" to run the tool.

Uninstall

Delete the files uncompressed from the zip file. MSGet tool doesn't write registry entries.

Usage

Main window

The main window (right panel) appears when executing MSGet.

Browsebutton A dialog to selecet a .raw file appears.

Exitbutton or xbutton on the top-right MSGet quits.

After selecting a .raw file, the main window turns as shown in the right panel.

"Filters" field

The name of filters that represent the type of data acquisition method are listed. Check the filter(s) to export.
* The Filters field is disabled when "PDA" is selected at "ControllerType".

"Retention time (min)" field

The start and the end of scan time (minute) to output can be specified.

"Threshold"

The threshold value to output can be specified.

"ControlType"

The type of detector (MS or PDA) can be selected.
* Although all the controller types included in the .raw file are listed in the pull-down menu, MSGet supports only for MS and PDA.

Outputbutton

The output process starts.

Usage

Start MSGet by clicking the "MSGet_VC.exe" file.

Click Browsebutton to select a .raw file to process.

Select control type, filters, and set export parameters (time, threshold).

Click Outputbutton. The resulted text files are generated in the same folder of .raw file.

Output file

The resulted text files are generated in the same folder of .raw file.

File name

MS data

The file name is automatically assigned according to the number of filters selected and the threshold value.

The example shown in the table below is assumed that a file named "SAMPLE01.raw" was processed.

Filter	Threshold	File name
Single selection	0	The original file name (the string excluding ".raw") followed by the filter name with parentheses and ".txt". The speces included in the filter name are replaced by underscores "_". (Example) In the case a filter "ITMS + c EST d Full ms2" is selected, SAMPLE01(ITMS_+_c_EST_d_Full_ms2).txt
Single selection	> 0	The file name described above (excluding ".txt") followed by "_Th", the threshold value, and ".txt". (Example) In the case a filter "ITMS + c EST d Full ms2" is selected, and a threshold value 3000 is set, SAMPLE01(ITMS_+_c_EST_d_Full_ms2)_Th3000.txt
Multiple selection	0	The extension ".raw" is replaced by ".txt". (Example) SAMPLE01.txt
Multiple selection	> 0	The original file name (the string excluding ".raw") followed by "_Th", the threshold value, and ".txt". (Example) In the case threshold value 3000 is set, SAMPLE01_Th3000.txt

PDA data

The file name is automatically assigned according to the threshold value.

The example shown in the table below is assumed that a file named "SAMPLE01.raw" was processed.

Threshold	File name
0	The original file name (the string excluding ".raw") followed by "(PDA)" and ".txt". (Example) SAMPLE01(PDA).txt
0以外	The file name described above (excluding ".txt") followed by "_Th", the threshold value, and ".txt". (Example) In the case the threshold value 3000 is set, SAMPLE01(PDA)_Th3000.txt

File format

The result are exported in text file.

In the description below, "\t" means a tab, and "..." means a repetition of the information written just above it. Type of values are shown in the parentheses "[]".

MS data file

Multiple units of the data block shown below are exported in the order of the scan number. The format is independent of the number of filters selected.

: [Scan number]\t[Retention time]\t[Filter name]
[m/z]\t[intensity]
[m/z]\t[intensity]
 ...

(Example)

: 1603	5.008621666667	ITMS + c ESI d Full ms2 224.98@35.00 [ 50.00-460.00]
98.206893920898 	5.572522640228
116.921920776367	6.633393287659
 ...
: 1604	5.014826666667	ITMS + c ESI Full ms [ 200.00-1500.00]
200.398406982422	960.902282714844
201.277923583984	1018.091125488281
 ...
: 1605	5.017761666667	ITMS + c ESI d Full ms2 436.16@35.00 [ 110.00-885.00]
148.928085327148	11.655914306641
198.879119873047	10.793945312500
 ...

PDA data file

The following data blocks are exported in the order of the scan number.

: [Scan number]\t[Retention time]\t
[Wave length (nm)]\t[Intensity]
[Wave length (nm)]\t[Intensity]
 ...

(Example)

: 751	5.003000000000	
200.000000000000	457963.000000000000
202.000000000000	452614.000000000000
 ...
: 752	5.009666666667	
200.000000000000	458963.000000000000
202.000000000000	453681.000000000000
 ...
: 753	5.016333333333	
200.000000000000	460016.000000000000
202.000000000000	454721.000000000000
 ...

Contributors

We acknowledge to the following people who are contributed to develop MSGet.

Mr. Takeshi Motegi
Dr. Ken-ichi Tanaka (Nara Institute of Science and Technology, past)
Dr. Yoshiyuki Ogata (Osaka Prefecture University)
Prof. Shigehiko Kanaya (Nara Institute of Science and Technology)

@@ Line 9: / Line 9: @@
 == Introduction ==
-MSGetは、Xcaliburソフトウェア（ThermoFishger社）で出力された.rawファイルから、全MSデータおよびPDAデータをテキスト形式で出力することができるソフトウェアです。XcaliburはThermoFisher社製の質量分析装置の標準制御ソフトです。
-このソフトウェアで出力したテキストファイルは、PowerGetツールで読み込み、解析することができます。
+MSGet is a tool that exports mass chromatogram data and pda data in text files from the binary .raw data of Xcalibur software (ThermoFisher). Xcalibur is the control and data acquisition software for the mass spectrometers of ThermoFisher.
+The resulted text files are used for input file for [http://www.kazusa.or.jp/komics/software/PowerGet PowerGet] tool.
 <br style="clear: both;" />
@@ Line 18: / Line 19: @@
 MSGet is only allowed to run on a PC where Xcalibur software (ThermoFisher) is installed.
-The functions of MSGet has been tested under the following conditions.
+Operation of MSGet has been tested with the following conditions.
-Winodws XP, 7,
+{| class="wikitable"
-Xcalibur 2.0
+|-
+!OS
+| Winodws XP
+|-
+!Software Required
+|Xcalibur 2.0
+|}
 == Install ==
-Download the MSGet tool from [http://www.kazusa.or.jp/komics/ja/tool-ja/66-msget.html the KOMICS website].
+Download MSGet from [http://www.kazusa.or.jp/komics/ja/tool-ja/66-msget.html the KOMICS website].
 Unzip the downloaded .zip file.
@@ Line 40: / Line 47: @@
 {{Manual_MSGet_MainWindow}}
-=== 処理の流れ ===
+=== Usage ===
-起動後{{Button|Browse}}ボタンを押して.rawファイルを選択したのち、各種条件を指定して、{{Button|Output}}ボタンを押します。出力ファイルは、選択した.rawファイルが存在するフォルダに生成されます。
+Start MSGet by clicking the "MSGet_VC.exe" file.
-== 出力ファイルについて ==
+Click {{Button|Browse}}button to select a .raw file to process.
-出力ファイルは選択した.rawファイルが存在するのと同じフォルダに生成されます。
+Select control type, filters, and set export parameters (time, threshold).
-=== ファイル名 ===
+Click {{Button|Output}}button. The resulted text files are generated in the same folder of .raw file.
-==== MSデータの場合 ====
-選択したフィルタの数とThresholdの値に応じて、下記の通り自動的に名前が付けられます。
+== Output file ==
-表中の【例】は「SAMPLE01.raw」という名の.rawファイルを処理した場合を示します。
+The resulted text files are generated in the same folder of .raw file.
+=== File name ===
+==== MS data ====
+The file name is automatically assigned according to the number of filters selected and the threshold value.
+The example shown in the table below is assumed that a file named "SAMPLE01.raw" was processed.
 <table class="wikitable">
 <tr>
-   <th>フィルタ</th>
+   <th>Filter</th>
    <th>Threshold</th>
-   <th>ファイル名の付き方</th>
+   <th>File name</th>
 </tr>
 <tr>
-   <td rowspan="2">単一選択</td>
+   <td rowspan="2">Single selection</td>
    <td>0</td>
-   <td>元のファイル名（.rawより前の部分）の後ろにフィルタの名前が括弧書きで加わり、拡張子が「.raw」から「.txt」に変わります。フィルタ名に含まれるスペースは、アンダースコア「_」に置き換えられます。<br/>
+   <td>The original file name (the string excluding ".raw") followed by the filter name with parentheses and ".txt". The speces included in the filter name are replaced by underscores "_".<br/>
-【例】「ITMS + c EST d Full ms2」というフィルタが選択されていた場合、<br/>
+<br/>
-SAMPLE01(ITMS_+_c_EST_d_Full_ms2).txt</td>
+(Example) In the case a filter "ITMS + c EST d Full ms2" is selected, <br/>
+'''SAMPLE01(ITMS_+_c_EST_d_Full_ms2).txt'''
+</td>
 </tr>
 <tr>
-   <td>0以外</td>
+   <td>&gt; 0</td>
-   <td>上記のファイル名（拡張子以外の部分）の最後に、「_Th」に加えてThresholdの値が加わります。<br/>
+   <td>The file name described above (excluding ".txt") followed by "_Th", the threshold value, and ".txt".<br/>
-【例】「ITMS + c EST d Full ms2」というフィルタ、<br/>
+<br/>
-Thresholdに「3000」が指定されていた場合、<br/>
+(Example) In the case a filter "ITMS + c EST d Full ms2" is selected, and a threshold value 3000 is set, <br/>
-SAMPLE01(ITMS_+_c_EST_d_Full_ms2)_Th3000.txt
+'''SAMPLE01(ITMS_+_c_EST_d_Full_ms2)_Th3000.txt'''
 </td>
 </tr>
 <tr>
-   <td rowspan="2">複数選択</td>
+   <td rowspan="2">Multiple selection</td>
    <td>0</td>
-   <td>拡張子を「.raw」から「.txt」に置き換えたものになります。<br/>
+   <td>The extension ".raw" is replaced by ".txt". <br/>
-【例】SAMPLE01.txt</td>
+(Example)<br/>
+'''SAMPLE01.txt'''
+</td>
 </tr>
 <tr>
-   <td>0以外</td>
+   <td>&gt; 0</td>
-   <td>拡張子を「.raw」から「.txt」に置き換え、拡張子以外のファイル名部分の最後に、「_Th」に加えてThreshold値が加わります。<br/>
+   <td>The original file name (the string excluding ".raw") followed by "_Th", the threshold value, and ".txt".<br/>
-【例】Thresholdに「3000」が指定されていた場合<br/>
+(Example) In the case threshold value 3000 is set, <br/>
-SAMPLE01_Th3000.txt</td>
+'''SAMPLE01_Th3000.txt'''
+</td>
 </tr>
 </table>
-==== PDAデータの場合 ====
+==== PDA data ====
-Thresholdの値に応じて、下記の通り自動的に付与されます。
+The file name is automatically assigned according to the threshold value.
-表中の【例】は「SAMPLE01.raw」という名の.rawファイルを処理した場合を示します。
+The example shown in the table below is assumed that a file named "SAMPLE01.raw" was processed.
 <table class="wikitable">
 <tr>
    <th>Threshold</th>
-   <th>ファイル名の付き方</th>
+   <th>File name</th>
 </tr>
 <tr>
    <td>0</td>
-   <td>元のファイル名（.raw以外の部分）の後ろに「(PDA)」が加わり、拡張子が「.raw」から「.txt」に置き換わったものになります。<br/>
+   <td>The original file name (the string excluding ".raw") followed by "(PDA)" and ".txt".<br/>
-【例】SAMPLE01(PDA).txt</td>
+(Example) <br/>
+'''SAMPLE01(PDA).txt'''
+</td>
 </tr>
 <tr>
    <td>0以外</td>
-   <td>上記のファイル名（拡張子以外の部分）の後ろに、さらにThresholdの情報が「_Th」に加えて付け足されたものになります。<br/>
+   <td>The file name described above (excluding ".txt") followed by "_Th", the threshold value, and ".txt".<br/>
-【例】Thresholdに「3000」を指定した場合、<br/>
+(Example) In the case the threshold value 3000 is set, <br/>
-SAMPLE01(PDA)_Th3000.txt</td>
+'''SAMPLE01(PDA)_Th3000.txt'''
+</td>
 </tr>
 </table>
-=== <span id="FileFormat"></span>ファイルフォーマット ===
+=== <span id="FileFormat"></span>File format ===
-テキスト形式で出力されます。
+The result are exported in text file.
-下記説明中、「\t」はタブを、「...」はその上の行と同様な情報の繰り返しを意味します。
+In the description below, "\t" means a tab, and "..." means a repetition of the information written just above it. Type of values are shown in the parentheses "[]".
-==== MSデータファイル ====
+==== MS data file ====
-選択したフィルタが単一であっても、複数であっても、以下の情報がスキャン番号順に出力されます。
+Multiple units of the data block shown below are exported in the order of the scan number. The format is independent of the number of filters selected.
 <pre>
-: スキャン番号\t溶出時間\tフィルタ名
+: [Scan number]\t[Retention time]\t[Filter name]
-質量電荷比\tシグナル強度
+[m/z]\t[intensity]
-質量電荷比\tシグナル強度
+[m/z]\t[intensity]
   ...
 </pre>
-【例】
+(Example)
 <pre>
 : 1603	5.008621666667	ITMS + c ESI d Full ms2 224.98@35.00 [ 50.00-460.00]
@@ Line 149: / Line 170: @@
 </pre>
+==== PDA data file ====
-==== PDAデータファイル ====
+The following data blocks are exported in the order of the scan number.
-スキャン番号順に下記の情報が出力されます。
 <pre>
-: スキャン番号\tリテンションタイム\t
+: [Scan number]\t[Retention time]\t
-吸収波長（nm）\tシグナル強度
+[Wave length (nm)]\t[Intensity]
-吸収波長（nm）\tシグナル強度
+[Wave length (nm)]\t[Intensity]
   ...
 </pre>
-【例】
+(Example)
 <pre>
 : 751	5.003000000000
@@ Line 176: / Line 197: @@
 </pre>
-== 開発者 ==
+== Contributors ==
-MSGetの開発には以下の方々にご協力をいただきました。
+We acknowledge to the following people who are contributed to develop MSGet.
-*茂木岳 様
+*Mr. Takeshi Motegi
-*田中健一 様　（元 奈良先端大学）
+*Dr. Ken-ichi Tanaka (Nara Institute of Science and Technology, past)
-*尾形善之 様　（現 大阪府立大学准教授）
+*Dr. Yoshiyuki Ogata (Osaka Prefecture University)
-*金谷重彦 様　（奈良先端大学教授）
+*Prof. Shigehiko Kanaya (Nara Institute of Science and Technology)

Manual MSGet

Latest revision as of 02:38, 4 February 2014

Contents

Introduction

System Requirement

Install

Uninstall

Usage

Main window

Usage

Output file

File name

MS data

PDA data

File format

MS data file

PDA data file

Contributors

Personal tools

Namespaces

Variants

Views

Actions

Search

Navigation

Toolbox