Skip to content

ComFaceID-Fingerprint Prediction

Transforming MS2 features into molecular fingerprints enables the annotation of metabolites even when their spectral information is unavailable in current databases, substantially enhances the chemical structural interpretation of metabolomics data.

This module enables the prediction of molecular fingerprints from input MS2 spectra, and conduct library retrieval.

  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
    Filter By Mass: Relative molecular mass screening thresholds in pretreatment. 200
    Predict fingerprint or not Ture
    Filter By Formula: Choose false will accelerate the task. False
    Intensity threshold: Intensity threshold for fragments in MS2 spectra. Fragments from a normalized MS2 spectrum (intensity of the more intense fragment is normalized to 100) with intensity lower than this value are not used for analysis. 1
    rt: Delta retention time that is allowed when merging MS2 spectra within a sample. 30 (in seconds)
    ppm: ppm tolerance used to align precursor ions within a sample, determined mainly by the instrument type. 20
    MS Delta: Delta m/z that is allowed to align precursor ions within a sample. If set to 0, only the ppm parameter is used. 0.01 Da
    If merge samples by energy False
    Min m/z number 2
    Remove precursor Ture
    Output number: search results outnumber for 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.

  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 "res.csv" file will be provided.

  6. Data analysis.

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

    Columns Description
    precursor Precursor ions.
    file m/z and its corresponding source file.
    pred_fpr Predicted fingerprint for m/z.
    inchikey Search result for each m/z，copyable to PubChem https://pubchem.ncbi.nlm.nih.gov/ for structure lookup.
    name Name for matched compound.
    mass Exact mass for matched compound.
    formula Formula for matched compound.
    smiles Search result for each m/z，copyable to PubChem https://pubchem.ncbi.nlm.nih.gov/ or ChemDraw software for structure lookup.
    sim Fingerprint similarity between input and matched compounds.
    sim rank Fingerprint similarity rank.