MZmine 2-代謝組學(xué)數(shù)據(jù)處理軟件教程

Mzmine 2-metabonomics data processing software tutorial

軟件下載地址：?Software download https://link.zhihu.com/?target=https%3A//github.com/mzmine/mzmine2/releases

• 該軟件支持多種電腦系統(tǒng)，下載解壓即可。?The software supports a variety of computer systems, download decompression can

• 軟件運行：在安裝包內(nèi)找到下圖標(biāo)記的程序，雙擊即可運行。?Software run: in the installation package to find the following icon marked the program, double-click can run

• 軟件界面如下：?The software interface is as follows:

軟件操作步驟：

Software steps:

一、 Raw data import

原始數(shù)據(jù)導(dǎo)入

• 軟件支持多種格式的數(shù)據(jù)，包括通用數(shù)據(jù)mzML，mzXML，mzData，NetCDF；以及原始數(shù)據(jù)Thermo RAW，Waters RAW， Agilent CSV。?The software supports data in a variety of formats, including General Data MZML, mzXML, mzData, NetCDF; and RAW data Thermo RAW, Raw Waters, Agilent CSV

• 導(dǎo)入流程：Raw data method→Raw data import→選擇數(shù)據(jù)（這里以Thermo RAW為例）→點擊“打開”開始導(dǎo)入。軟件下方Task in progress框中會有進(jìn)度條顯示。?Import Process: RAW data method → RAW data import → select data (Thermo RAW in this case)→ click open to import. The progress bar is displayed in the Task in progress box at the bottom of the software

• 導(dǎo)入成功后，會顯示在Raw data files界面?After successful import, it will be displayed in the Raw data files interface

• 點擊文件前的+號，可以看到每個文件包含的譜圖信息。包含譜圖級別（MS1和MS2）、采集時間、數(shù)據(jù)形式（p輪廓圖或者c棒狀圖）以及采集模式（+正離子模式和-負(fù)離子模式）。?Click on the + sign in front of the file, you can see the spectrum information contained in each file. It includes spectral levels (MS1 and MS2) , acquisition time, data form (P profile or C bar) , and acquisition mode (+ + + And-minus)

二、Mass detection

質(zhì)量檢測

• 操作流程：Raw data methods→Feature detection→Mass detection?Something something something something: 原始數(shù)據(jù)方法→特征提取分析→質(zhì)量檢測

• 彈出菜單如下：?The pop up menu is as follows:

• 點擊①→All raw data files?Something 1→所有原始數(shù)據(jù)文件

• 點擊②→有五種方法可供選擇，其中Centroid適用于棒狀圖，其余四種適用于輪廓圖。實驗中采集的譜圖為c棒狀圖，所以在這一步選擇Centroid。?Click 2→ there are five options, Centroid for the bar chart and the other four for the outline chart. The spectrum collected in the experiment is a C-bar graph, so Centroid is chosen in this step

• 點擊③設(shè)置相應(yīng)參數(shù)?Click 3 to set the parameters

• 點擊“set filters”設(shè)置保留時間，MS等信息（由MS1更換為MS2時，要調(diào)整參數(shù)，特別是Noise level，因為MS2通常會比MS1低）。?Click on “Set filters”to set the retention time, MS, etc. . (when changing from MS1 to MS2, adjust the parameters, especially the Noise level, since MS2 is usually lower than MS1.)

• Mass list name：可以編輯列表名稱?Mass list name: You Can Edit the list name

• 點擊OK開始運行?Click OK to start




• 完成后，文件名上會有一個綠色的對號??When complete, the filename will have a green diagonal something

三、Chromatogram building

建立色譜圖

• 操作流程：Raw data methods→Feature detection→ADAP Chromatogram builder?Something something something something: 原始數(shù)據(jù)方法→特征提取分析→ ADAP 色譜構(gòu)建器

• 彈出菜單如下：?The pop up menu is as follows:

• 點擊①→選擇 All raw data files?Click 1→ select All raw data files

• 點擊②→選擇列表名稱（masses）?Click 2→ Select list names (masses)

• 接下來有四個參數(shù)：?Here are four parameters:

• Min group size in # of scans：在色譜圖中至少要有此數(shù)量的連續(xù)掃描點高于用戶設(shè)定的Group intensity threshold?Min Group size in # of Sharks: at least this number of consecutive scan points in the chromatogram is higher than the user-defined Group intensity threshold

• Group intensity threshold：強(qiáng)度閾值?Group intensity threshold

• Min highest intensity：在色譜圖中至少要有一個點的強(qiáng)度大于或等于此值?Min highest intensity: there must be at least one point in the chromatogram whose intensity is greater or equal to this value

• m/z tolerance：在連續(xù)掃描中質(zhì)荷比的最大偏差，用于構(gòu)建色譜圖?M/z tolerance: the maximum deviation of the mass-to-charge ratio in a continuous scan, used to construct a chromatogram

• 在suffix可以設(shè)置文件名后綴?You can set the filename suffix in suffix

• 點擊OK開始運行?Click OK to start




• 運行結(jié)束后，會在Feature list框中出現(xiàn)后綴為chromatogram的結(jié)果?At the end of the run, the result will appear in the Feature list box with the suffix chromatogram

三、Decovolution

Something、卷積

操作流程：Feature list method→Feature detection→Chromatogram deconvolution

Something something something something: 特征列表法→特征提取→色譜反褶積

• 彈出菜單如下：?The pop up menu is as follows:

• 點擊①→All feature lists?Something 1→所有特征列表

• 點擊②→選擇算法（本實驗選擇Wavelets ADAP）?Click 2→ select the algorithm (this experiment selects Wavelets ADAP)

注：如對界面中的參數(shù)有疑問，可以點擊Help，里邊對每一個選項都有專業(yè)解釋。

Note: If you have any questions about the parameters in the interface, please click Help. There is a professional explanation for each option.

四、Isotopic peak grouper

同位素峰石斑魚

• 操作流程：在Feature lists框中選中chromatograms后綴的文件→Feature list methods→Isotopes→Isotopic peaks grouper?Action Flow: select the file → list methods → ISOTOPS → topic peaks grouper from the chromatograms suffix in the Feature lists box

• 彈出對話框中填寫參數(shù)，點擊OK運行。?Pop-up dialog box to fill in the parameters, click OK to run
  

五、Alignment

Something、調(diào)整

• 操作流程：在Feature lists框中選中去同位素后的文件→Feature list→Alignment→Join aligner?Flow: in the Feature lists box, select the file after the isotope → Feature list → Alignment → Join Aligner

• 在彈出對話框中填寫參數(shù)，點擊OK運行。?In the pop-up dialog box to fill in the parameters, click OK to run

• 在Feature lists中獲得列表?Get the list in Feature lists

六、數(shù)據(jù)導(dǎo)出

Data Export

• 操作流程：選擇Aligned feature list→Feature list method→Export/Import→Export to CSV file（可以選擇需要的格式進(jìn)行導(dǎo)出）?Action Flow: select Aligned Feature list → Feature list method → Export/Import → Export to CSV file (Export in the desired format)

• 彈出菜單中選擇需要導(dǎo)出列表中包含的內(nèi)容，點擊OK導(dǎo)出。?From the pop-up menu, select what you want to include in the export list and click OK to export

• 目標(biāo)文件如下，可以將此文件導(dǎo)入到SIMCA等軟件進(jìn)行多元統(tǒng)計分析。?The object file is as follows, you can import this file into Simca and other software for multivariate statistical analysis

以上是MZmine的簡單操作流程，希望對大家處理數(shù)據(jù)有幫助。

The above is a simple operation of MZmine, I hope to help you deal with the data.

軟件還有很多其他的功能，大家可以探索使用。

There are many other features that you can explore.