MZmine 2丨Waters raw data import

MZmine 2 something waters raw data import

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The software cannot recognize Waters raw data, the interface is as follows:

The software does not recognize Waters raw data, the interface is as follows:

After trying, it is found that the current version (MZmine 2.53) does not recognize the original Waters data, and the data needs to be formatted before uploading. The previous version (MZmine 2.52) can be recognized, as shown in the following figure. If necessary, you can download the old version from the software download address.

After trying it out, the current version (MZmine 2.53) does not recognize the raw Waters data and the data needs to be formatted before uploading. The previous version (MZmine 2.52) is recognized, as shown in the image below. If necessary, you can download an older version from the software download link.

Question 2: Chromatogram builder cannot be performed after importing the original data, as shown in the figure below.

Problem 2: After importing the raw data, the Chromatogram Builder cannot be executed, as shown in the image below.

It is speculated that the reason may be due to the inclusion of LockMass data in the original file. Right-click the file name→show TIC, as shown in the figure below, which is an overlay of three spectra.

Presumably, the reason might be the inclusion of LockMass data in the original file. Right-click on the filename → Show TIC, as shown in the image below, which is an overlay of the three spectra.

• The software cannot remove the signal generated by LockMass. During the experiment, in order to ensure the accuracy of the collected mass spectrometry data, even if the instrument has been calibrated, it is recommended to use LockMass for real-time calibration. 软件无法删除 LockMass 产生的信号。在实验过程中，为了确保采集到的质谱法数据的准确性，即使仪器已经校准，也建议使用 LockMass 进行实时校准

• If LockMass is not used in the experiment, the software should be able to process the data. 如果实验中没有使用 LockMass，软件应该能够处理数据

• If LockMass is used in the experiment, you need to format the data before importing the data. Here is a data conversion method. The software used is the Databridge software that comes with Waters MassLynx. 如果实验中使用了 LockMass，那么在导入数据之前需要对数据进行格式化。下面是一个数据转换方法。使用的软件是 Waters MassLynx 提供的 Databridge 软件

The data conversion process is as follows:

The data conversion process is as follows:

• Find MassLynx in the computer start menu → click Databridge 在计算机开始菜单中找到 MassLynx →单击 Databridge

• Open the software, the interface is as follows: Click Options→Select MassLynx→Select NetCDF→Click OK 打开软件，界面如下: 点击选项→选择 MassLynx →选择 NetCDF →点击确定

• File conversion: Click Select → select the file to be converted → select the destination file location → click OK 文件转换: 点击选择→选择要转换的文件→选择目标文件位置→点击确定

• Click Covert to convert, and the following prompt will pop up: The file contains different Functions, and different files will be generated according to different Functions during conversion, and then click OK. 单击 Covert 进行转换，将弹出以下提示: 文件包含不同的函数，在转换过程中将根据不同的函数生成不同的文件，然后单击 OK

• After the conversion is completed, you can see the converted files in the target folder, as shown in the figure below: The suffixes 01, 02, and 03 correspond to Function 1, Function 2, and Function 3 in the original file, respectively. 转换完成后，您可以在目标文件夹中看到转换后的文件，如下图所示: 后缀01、02和03分别对应于原始文件中的函数1、函数2和函数3(It can also be judged from the size of the three files) (也可以从三个档案的大小来判断)

Since the sample data is MSe data, the three Functions correspond to MS1 (low energy), MS2 (high energy) and LockMass information respectively, as shown in the figure below.

Since the sample data is MSe data, these three functions correspond to MS1 (low energy), MS2 (high energy), and LockMass information, respectively, as shown in the figure below.

We import the three files into MZmine 2 software and take a look at the spectral information contained in the files. The TIC corresponding to the three files is shown in the figure below. The data collected in the three Functions have been divided into three files, and then we can perform subsequent processing on the data.

We imported these three files into the mzmine2 software and looked at the spectral information contained in the files. The figure below shows the Internet Information Center corresponding to the three files. The data collected in these three functions is split into three files, and we can then perform subsequent processing on the data.

The sample data used in this article is MSe data, so there will be three Function files. When using this software for metabolomics preprocessing, we only need to import the data of Function 1 to generate a data list for subsequent statistical analysis.

The sample data used in this article is MSe data, so there will be three Function files. When using the software for metabolomics preprocessing, simply import the data from function 1 to generate a data list for subsequent statistical analysis.

Since MSe is a DIA acquisition mode, that is, no specific precursor ions are selected in the process of generating fragments, so the fragments generated in Function 2 are actually all ions detected at a certain point in time. Fragment stacking. If you want to select the parent ion → product ion information from it, you need a specific algorithm, and the software does not seem to be able to do this task at present. So if you want to observe the information of fragment ions from MSe, you can use the commercial Progenesisi QI or the open source MS-DIAL.

Since MSe is a DIA acquisition where no specific precursor ions are selected during fragmentation, the fragments produced in function 2 are actually all ions detected at a certain point in time. Debris piles up. If you want to select parent ion → product ion information from it, you need a specific algorithm, and the software currently doesn't seem to be up to the task. Therefore, if you want to observe fragment ion information from MSe, you can use the commercial progeny QI or the open source MS-DIAL.