Skip to content

Manual compound annotation

Feature table → right-click → Identification → Annotate manually

Lets you attach a compound identity to a single feature list row by filling in a form. Use this when you know the identity of a feature from external data (e.g. an internal standard or a reference compound) and want to record it without running an automated search module.

The annotation is stored as a CompoundDBAnnotation and labeled with the username of the person who created it.

Parameters

No standalone parameter dialog is shown to the user — the module is launched directly from the feature table context menu and presents its own input form.

Input form fields

Field Type Description
CCS Number Collision cross-section (Ų)
Comment String Free-text note
Compound Name String Primary human-readable compound name
Formula String Molecular formula (e.g. C6H12O6)
InChI String IUPAC International Chemical Identifier
InChIKey String Hashed InChI key
Ion Type / Adduct Ion type Adduct, e.g. [M+H]+
Precursor m/z Number Exact precursor mass-to-charge ratio
RT Number Retention time
SMILES String SMILES structure string

Entering a valid SMILES or InChI string displays a live 2D structure preview above the form.

Validation

The Save button stays disabled until both conditions are satisfied:

  1. At least one compound name identifier must be non-blank — any of: Compound Name, IUPAC Name, Internal ID, SMILES, InChI, InChIKey, Formula, or CAS.
  2. At least one m/z source must be provided — any of:
    • Precursor m/z entered directly, or
    • Formula + Ion Type (m/z calculated from these), or
    • SMILES + Ion Type (formula is first derived from the structure, then m/z is calculated).

Algorithm

On save

  1. A compound annotation is built from all non-empty form fields.

  2. Missing values that can be derived from what was entered are calculated automatically:

    Derived field Source
    Formula Derived from SMILES/InChI structure if not entered directly
    Precursor m/z Calculated from Formula + Ion Type if not entered directly
    Neutral mass Calculated from Precursor m/z and Ion Type
    Ion Type Best-match adduct inferred from neutral mass vs. row m/z if not specified
    m/z PPM difference Annotation m/z vs. row average m/z
    m/z absolute difference Annotation m/z vs. row average m/z
    RT absolute difference Annotation RT vs. row average RT (if RT was entered)
    CCS relative error (%) Annotation CCS vs. row average CCS (if CCS was entered)

  3. The Database Name field is set to "Annotated manually by <username>" (falls back to "unknown user" when no user is logged in).

  4. The annotation is added to the row and the feature table is refreshed.

Tip

If you know the SMILES or InChI of a compound, entering it together with an adduct is the most complete way to annotate: formula, m/z, neutral mass, and mass error are all derived automatically.

Warning

This module annotates exactly one selected row at a time. To annotate multiple rows, run the annotation for each row individually, or use an automated search module (e.g. local compound database search).

Steffen Heuckeroth