Console app

While the standard MS-DIAL version provides a graphical user interface (GUI) primarily for Windows, the Console app allows users to perform high-throughput data processing across multiple operating systems, including Windows, Linux, and macOS.

Key Features and Capabilities

  • Automation and Scripting: Designed for users who need to automate large-scale data processing or integrate MS-DIAL into bioinformatics pipelines.
  • Core Processing Steps: It performs essential data analysis tasks without the GUI, including:
    • Peak Detection: Identifying signals from complex mass spectrometry raw data.
    • Deconvolution: Separating overlapping peaks to identify individual compounds.
    • Alignment: Matching peaks across different samples for comparative analysis.
    • Identification: Annotating metabolites using spectral libraries (e.g., MSP format files).
  • Supported Data Formats: The app can process various raw data formats such as mzML, wiff, raw, and D, and it supports multiple instruments (GC/MS, LC/MS/MS) and vendors.
  • Outputs: It generates 3 metabolome table formats (.mdalign, .mdmsp, .mzTab) and 2 types (.mdmsp, .mdpeak) peak annotation data formats used for downstream/statistical analysis.

Console app in action

Download our demo mzML files and a Console app configuration file (we call it method file) from https://zenodo.org/records/18336159.

(Below is an example of using the Console app for Linux.)

  1. Download Console app for Linux (MSDIAL5-Console-ubuntu-latest-net8.zip) from MS-DIAL nightly build
  2. Run mkdir msdial5console && mv MSDIAL5-Console-ubuntu-latest-net8.zip msdial5console/ && cd msdial5console/ && unzip MSDIAL5-Console-ubuntu-latest-net8.zip
  3. Download the demo dataset from https://zenodo.org/records/18336159
  4. Unzip the zenodo18336159.zip
  5. Run mv zenodo18336159 msdial5console/ && cd msdial5console
  6. Run ./MSDIALCUI lcms -i zenodo18336159/consoleapp_demo_csvimportfiles.csv -o zenodo18336159/output/ -m zenodo18336159/zenodo18336159_method.txt -p

The -i option stands for input. The -i option takes the path to the raw data and the path to the CSV file containing its metadata as arguments. The contents of the input CSV file will be as follows.

file_path file_name file_type class_id acquisition_type batch_order analytical_order factor Included
zenodo18336159/20230406_blank_NEG_1.mzML 20230406_blank_NEG_1 Blank Blank DDA 1 1 1 TRUE
zenodo18336159/20230406_feces_1_NEG.mzML 20230406_feces_1_NEG Sample feces DDA 1 2 1 TRUE
zenodo18336159/20230406_feces_2_NEG.mzML 20230406_feces_2_NEG Sample feces DDA 1 3 1 TRUE
zenodo18336159/20230406_feces_3_NEG.mzML 20230406_feces_3_NEG Sample feces DDA 1 4 1 TRUE
zenodo18336159/20230407_plasma_1_NEG.mzML 20230407_plasma_1_NEG Sample plasma DDA 1 5 1 TRUE
zenodo18336159/20230407_plasma_2_NEG.mzML 20230407_plasma_2_NEG Sample plasma DDA 1 6 1 TRUE
zenodo18336159/20230407_plasma_3_NEG.mzML 20230407_plasma_3_NEG Sample plasma DDA 1 7 1 TRUE

The first 8 columns of the header row must be file_path, file_name, file_type, class_id, acquisition_type, batch_order, analytical_order, factor

Information in 9th column and beyond will be ignored.

The file_path column can contain either an absolute or relative path to the raw data. Relative paths will be relative to the MSDIALCUI file.

The -o option specifies the output destination. The Console app at the path specified by the -o option outputs alignment results in 3 formats (mzTab, mdalign, mdmsp) and peak annotation results for each raw data set in 2 formats (mdpeak, mdmsp).

If you give the zenodo18336159 dataset to the Console app, the output file will look like this:

20230406_blank_NEG_1.mdmsp   20230406_feces_2_NEG.mdmsp   20230407_plasma_1_NEG.mdmsp   20230407_plasma_3_NEG.mdmsp      AlignResult-20261221921.mzTab
20230406_blank_NEG_1.mdpeak  20230406_feces_2_NEG.mdpeak  20230407_plasma_1_NEG.mdpeak  20230407_plasma_3_NEG.mdpeak     Project-2601220721.mdproject
20230406_feces_1_NEG.mdmsp   20230406_feces_3_NEG.mdmsp   20230407_plasma_2_NEG.mdmsp   AlignResult-20261221921.mdalign
20230406_feces_1_NEG.mdpeak  20230406_feces_3_NEG.mdpeak  20230407_plasma_2_NEG.mdpeak  AlignResult-20261221921.mdmsp

The -m option specifies the path to a configuration file called the method file.

The important parts of the method file are the first few lines below.

MS1 data type: Centroid
MS2 data type: Centroid
Ion mode: Negative
Target omics: Lipidomics
Ionization: ESI
Machine category: LCMS
Instrument type:
Instrument:
Authors:
License:
Comment:
Msp file path: ./zenodo18336159/MSMS-Public_all-neg-VS19.msp
Lbm file path: ./zenodo18336159/Msp20241113163720_NCDK-TUAT-FastLC_converted_dev.lbm2
Text DB file path: ./zenodo18336159/20200121_MsdialTxtDB_Neg_EquiSPLASH_rapid.txt
Isotope text DB file path:
Compounds library file path for target detection:
Compounds library file path for RT correction:

Below we will explain some of the most important lines.

Ion mode: Negative

Please set the ion mode to either Positive or Negative. If the mode is different from the actual mode of the raw data, the process will not complete.

Msp file path: ./zenodo18336159/MSMS-Public_all-neg-VS19.msp
Lbm file path: ./zenodo18336159/Msp20241113163720_NCDK-TUAT-FastLC_converted_dev.lbm2
Text DB file path: ./zenodo18336159/20200121_MsdialTxtDB_Neg_EquiSPLASH_rapid.txt

Please set the path to the library used for metabolite or lipid annotation. Absolute and relative paths can be used for the library path. Relative paths are relative to the MSDIALCUI file. In addition to the well-known msp file format, MS-DIAL’s dedicated lbm file or a text file in a proprietary text format can be used. See https://systemsomicslab.github.io/compms/msdial/main.html#MSP for details on those file formats.

This concludes the explanation of the Console app. If there is anything missing from the explanation, please add an issue to https://github.com/systemsomicslab/msdial5tutorial/issues.