MZmine 2-代谢组学数据处理软件教程
MZmine 2-代谢组学数据处理软件教程
Mzmine 2-metabonomics data processing software tutorial
软件下载地址： Software download https://link.zhihu.com/?target=https%3A//github.com/mzmine/mzmine2/releases
该软件支持多种电脑系统，下载解压即可。 The software supports a variety of computer systems, download decompression can
软件运行：在安装包内找到下图标记的程序，双击即可运行。 Software run: in the installation package to find the following icon marked the program, double-click can run
软件界面如下： The software interface is as follows:
软件操作步骤：
Software steps:
一、 Raw data import
原始数据导入
软件支持多种格式的数据，包括通用数据mzML，mzXML，mzData，NetCDF；以及原始数据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
导入流程：Raw data method→Raw data import→选择数据（这里以Thermo RAW为例）→点击“打开”开始导入。软件下方Task in progress框中会有进度条显示。 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
导入成功后，会显示在Raw data files界面 After successful import, it will be displayed in the Raw data files interface
点击文件前的+号，可以看到每个文件包含的谱图信息。包含谱图级别（MS1和MS2）、采集时间、数据形式（p轮廓图或者c棒状图）以及采集模式（+正离子模式和-负离子模式）。 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
质量检测
操作流程：Raw data methods→Feature detection→Mass detection Something something something something: 原始数据方法→特征提取分析→质量检测
弹出菜单如下： The pop up menu is as follows:
点击①→All raw data files Something 1→所有原始数据文件
点击②→有五种方法可供选择，其中Centroid适用于棒状图，其余四种适用于轮廓图。实验中采集的谱图为c棒状图，所以在这一步选择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
点击③设置相应参数 Click 3 to set the parameters
点击“set filters”设置保留时间，MS等信息（由MS1更换为MS2时，要调整参数，特别是Noise level，因为MS2通常会比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：可以编辑列表名称 Mass list name: You Can Edit the list name
点击OK开始运行 Click OK to start
完成后，文件名上会有一个绿色的对号✔ When complete, the filename will have a green diagonal something
三、Chromatogram building
建立色谱图
操作流程：Raw data methods→Feature detection→ADAP Chromatogram builder Something something something something: 原始数据方法→特征提取分析→ ADAP 色谱构建器
弹出菜单如下： The pop up menu is as follows:
点击①→选择 All raw data files Click 1→ select All raw data files
点击②→选择列表名称（masses） Click 2→ Select list names (masses)
接下来有四个参数： Here are four parameters:
Min group size in # of scans：在色谱图中至少要有此数量的连续扫描点高于用户设定的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：强度阈值 Group intensity threshold
Min highest intensity：在色谱图中至少要有一个点的强度大于或等于此值 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：在连续扫描中质荷比的最大偏差，用于构建色谱图 M/z tolerance: the maximum deviation of the mass-to-charge ratio in a continuous scan, used to construct a chromatogram
在suffix可以设置文件名后缀 You can set the filename suffix in suffix
点击OK开始运行 Click OK to start
运行结束后，会在Feature list框中出现后缀为chromatogram的结果 At the end of the run, the result will appear in the Feature list box with the suffix chromatogram
三、Decovolution
Something、卷积
操作流程：Feature list method→Feature detection→Chromatogram deconvolution
Something something something something: 特征列表法→特征提取→色谱反褶积
弹出菜单如下： The pop up menu is as follows:
点击①→All feature lists Something 1→所有特征列表
点击②→选择算法（本实验选择Wavelets ADAP） Click 2→ select the algorithm (this experiment selects Wavelets ADAP)
注：如对界面中的参数有疑问，可以点击Help，里边对每一个选项都有专业解释。
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
同位素峰石斑鱼
操作流程：在Feature lists框中选中chromatograms后缀的文件→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
弹出对话框中填写参数，点击OK运行。 Pop-up dialog box to fill in the parameters, click OK to run
五、Alignment
Something、调整
操作流程：在Feature lists框中选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
在弹出对话框中填写参数，点击OK运行。 In the pop-up dialog box to fill in the parameters, click OK to run
在Feature lists中获得列表 Get the list in Feature lists
六、数据导出
Data Export
操作流程：选择Aligned feature list→Feature list method→Export/Import→Export to CSV file（可以选择需要的格式进行导出） Action Flow: select Aligned Feature list → Feature list method → Export/Import → Export to CSV file (Export in the desired format)
弹出菜单中选择需要导出列表中包含的内容，点击OK导出。 From the pop-up menu, select what you want to include in the export list and click OK to export
目标文件如下，可以将此文件导入到SIMCA等软件进行多元统计分析。 The object file is as follows, you can import this file into Simca and other software for multivariate statistical analysis
以上是MZmine的简单操作流程，希望对大家处理数据有帮助。
The above is a simple operation of MZmine, I hope to help you deal with the data.
软件还有很多其他的功能，大家可以探索使用。
There are many other features that you can explore.
