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ComFaceID-Library Search

Spectral library search is the foundational and most frequently used approach in MS-based analysis. It identifies compounds or their structural analogues by finding reference library spectra that most closely match an unknown query spectrum, based on the principle that similar spectra indicate similar chemical structures.

This module performs library search function for MS/MS spectra.

  1. Please log in and upload files before use.

    Data preparation is described in the MSConvert Usage section.

  2. Check the parameter settings.

    The default parameters settings are designed to be compatible with Q-TOF systems from different manufacturers, such as Waters, SCIEX, Thermo, etc. Users may modify these parameters as needed for their particular analytical purposes.

    Parameter & Description Default Setting
    rt: Retention time. 30
    MS2 delta 0.01
    Filter by mass: Relative molecular mass screening thresholds in pretreatment. 200
    Compound library to search: Contains GNPS and HMDB Default
    Search batch sizes: output number of each m/z. 20

  3. Upload the corresponding files under the option.

    For Input files option (Required), please insure that the input file contains valid MS/MS information;

    For Peaktable file option (Optional), select the peak table file corresponding to mzXML.; it supports the .csv format and must contain two columns named “mz” and “rt”. This table is optional and provides the m/z and retention time (in seconds) for precursor ions of interest. For the sample of interest, only MS2 spectra corresponding to the targeted precursor ions are included in the analysis.

    Note: when uploading a peak table, please ensure that the converted file (.mzXML) from the same original data file and its corresponding peak table (.csv) are named exactly the same.

  4. Enter a task name to start your analysis journey.

    Click "Tasks" at any time to check your analysis progress.

  5. Data output.

    After the task finishes, a "final_results.csv" file will be provided.

  6. Data analysis.

    A brief explanation of the key output results is provided below.

    Columns Description
    sid m/z and the corresponding source file
    Precursor Precursor ions
    Cosine Score Cosine distance between two embeddings
    PubChem_InChIkey Search result for each m/z，copyable to PubChem https://pubchem.ncbi.nlm.nih.gov/ for structure lookup.