Required
Precursor m/z & Ion Mode
This defines the precursor ion mass-to-charge ratio (m/z).
This defines polarity and ensures correct model selection.
Example: PRECURSOR_MZ=517.22098
IONMODE=positiveIONMODE=negative
DM
DeepMASS2 Documentation
Input Format Reference
DeepMASS2 Documentation Center
Comprehensive documentation for DeepMASS2 ncluding input format specifications, XCMS-based LC-MS/MS preprocessing, full annotation workflow, and result interpretation.
Data Processing for DeepMass
Before DeepMass annotation, raw LC-MS/MS data should be processed into DeepMass-compatible MSP or MGF files.
Batch Annotation
For large-scale annotation, use the local version.
Recommended local repository
https://github.com/hcji/DeepMASS2_GUI
Metadata Tags
These tags help DeepMASS2 parse spectra correctly, select the proper polarity-specific model, and assign meaningful output filenames.
Keep the input simple: each spectrum should include precursor m/z, ion mode, and the corresponding peak list.
Recommended
Automatic Naming & Adduct
Controls exported result filename and ion adduct. Defaults: [M+H]+ for positive, [M-H]- for negative.
DeepMASS2 uses this tag to define the output filename for the exported semantic similarity analysis.
If provided, the results will be saved as <COMPOUND_NAME>.csv.
Example: ADDUCT=[M-H]-
Example: COMPOUND_NAME=challenge_0
Optional
Molecular Formula
Adding the molecular formula helps the semantic similarity engine constrain potential chemical space, significantly improving the ranking accuracy of structurally related metabolites.
Example: FORMULA=C25H38O9
BEGIN IONS
PRECURSOR_MZ=194.04588176800002
COMPOUND_NAME=challenge_255
FORMULA=C9H9NO4
ADDUCT=[M-H]-
IONMODE=negative
132.0454 0.006008828855732822
134.0245 0.0022295306804225633
149.0483 0.00297960480724686
150.056 1.0
194.0459 0.36915136378467533
END IONS
DeepMASS2 Results Explanation
Formula Finder
Annotates possible chemical formulas for unknown spectra.
- Formula: Chemical formula, e.g.,
C9H9NO4 - Mass: Theoretical mass
- Error (mDa): Deviation between experimental and theoretical mass in millidaltons
Structure Finder
Predicts potential molecular structures with SMILES and structure scores.
- Title: Compound name
- MolecularFormula: Molecular formula
- CanonicalSMILES: Standardized SMILES
- InChIKey: Unique structure identifier
- Database IDs: Reference database IDs
- Formula Score, Structure Score, Consensus Score: Ranked from high to low, indicating likelihood
Reference Spectrums
- Name: Reference spectrum name
- Adduct: Ion form
- SMILES: Corresponding SMILES
- Parent Mass: Precursor ion mass
- Database: Source database
- Sorted by similarity, highest first
Spectrum Plot
Shows normalized intensity vs m/z, including unknown spectrum peaks and reference spectrum peaks for visual comparison.
