Other utilities

1. MassQL in MS DIAL5

MassQL is a query language designed for mass spectrometry data. It enables users to search and filter mass spectrometry data using a structured query format, similar to how SQL is used for databases. MassQL allows for the extraction of specific information from complex datasets, making it easier for researchers and analysts to explore and interpret their mass spectrometry results. For more details, please refer to the MassQL Documentation.

The video below demonstrates how to perform peak filtering with MassQL from MS-DIAL5.

2. MSCleanR in MS-DIAL5

MS-CleanR is an R package that applies 1. general filtering and 2. feature clustering to the peak list of MS-DIAL4, then passes those peaks to MS-FINDER to obtain an annotated peak list.

We have made it possible to perform 1. general filtering inside MS-DIAL5. The video for using that feature can be found below.

4. Multivariate analysis in MS-DIAL5

5. Bridge to MRMPROBS for DIA-MS or GC/MS data sets

The purpose of this section is to announce the utility of ‘MRMPROBS’ instead of MS-DIAL for SWATH-MS or other DIA-MS data. MRMPROBS was originally developed for targeted metabolomics using triple quadrupole MS data (multiple reaction monitoring, MRM; selected reaction monitoring, SRM). It also supports the entire workflow from data import until statistical analysis as MS-DIAL does. Compared to the MS-DIAL program, MRMPROBS is optimized for targeted metabolomics:

  1. users can manually curate the peak left- and right edges of chromatographic peaks
  2. users can simultaneously check all samples’ peaks of a targeted compound, and 3) users can easily curate the identification results.

While the current MS-DIAL program always calculates the peak intensity (height) and peak area of compounds by the survey scan MS1 data, MRMPROBS can utilize the MS/MS chromatograms for metabolite quantifications. In addition, the tools for untargeted analysis like MS-DIAL will often provide the false positive things in the process of peak picking, deconvolution, and peak alignment. In contrast, users can easily parse the targeted compounds with the user-friendly graphical user interface. The ‘bridge’ from MS-DIAL to MRMPROBS is described in the video below. The workflow can also be utilized for GC/MS data. The detail of MRMPROBS is fully described in the tutorial of MRMPROBS program.

Required software program and dataset (to reproduce the video)

6. Molecular spectrum networking for metabolite annotations

This section introduces how to create molecular spectrum networking in MS-DIAL5. Molecular spectrum networking is a tool for creating networks that visualize the MS/MS similarities among metabolites.

To follow this video, please download the dataset and check the description in https://zenodo.org/communities/msdial?q=&l=list&p=1&s=10&sort=newest.

7. Console app

Download demo data from here.

  1. Download console app from MS-DIAL releases.
  2. Open your terminal or PowerShell.
  3. You can get help by typing “YourPathOfMSDIALCUI.exe”. fig1-1
  4. Type “YourPath.exe YourAnalysisType -i YourInputFolder -o YourOutputFolder -m YourLibraryFolder-p”. For example, ” ..exe lcms -i . -o . -m ._console_param4lipidomics.txt -p”
  5. It will take around a minute to start processing your data. fig1-2

The Workflow

  1. Download the dataset of “Molecular spectrum networking tutorial dataset” in https://zenodo.org/communities/msdial?q=&l=list&p=1&s=10&sort=newest
  2. Open *.mdproject in MS-DIAL5
  3. Follow the youtube video

You can get thses as outputs: 1. The molecular spectrum network that visualize the MS/MS similarities among metabolites. 2. The dataset to create the network in cytoscape 3. The molecular spectrum network that focusing on one metabolite.