LC-Inspector comes with several lists of metabolites and commonly searched compounds predefined.

However, the user can define any number of custom ion lists. All the lists (including the default ones) can be freely saved, modified, and deleted -- they will be persisted in JSON format in the file config.json. This file is present in the _internal folder on Windows and on macOS it is accessible via right-clicking on the LC-Inspector package -> Show package contents -> Contents -> Resources -> config.json.

The ion lists can contain any number of compounds, with each compound containing any number of comma-separated m/z values to be traced. Additional information about each m/z value can be specified in the column Add. info. The format should also be comma-separated and in the same order as the m/z values.

The lists can be added easily via the graphical user interface of LC-Inspector or manually, by editing the config.json file.

Editing via the user interface

The user interface of LC-Inspector enables the user to define their ion lists through the same menu box as when they choose the m/z values to target during processing.

The ion table is editable, and so you can input whatever compounds or fragments you want to trace. Every row represents one compound or fragment to be traced and accepts multiple m/z values per compound, each with their own short description in the Add. info column.

Example:

Manually editing the JSON file

The lists are defined in the following format in the JSON file:

"Short-chain fatty acids": { 
        "Formate": { 
            "ions": [47.0128, 44.9982, 91.0026], 
            "info": ["Formate-(+)", "Formate-(-)", "Formate dimer (+)"] 
        }, 
        "Acetate": { 
            "ions": [61.0284, 59.0139], 
            "info": ["Acetate-(+)", "Acetate-(-)"] 
        }, 
        "Butyrate": { 
            "ions": [89.0597, 87.04515], 
            "info": ["Butyrate-(+)", "Butyrate-(-)"] 
        }, 
        "Propionate": { 
            "ions": [75.0441, 73.0295], 
            "info": ["Propionate-(+)", "Propionate-(-)"] 
        } 
    }, 

New lists can be added manually following JSON formatting and existing lists can be freely modified.

[!WARNING] As of v0.8.4, LC-Inspector does not perform polarity checks, so it's important to remember to double-check that the correct compound is detected for the given polarity mode and not an isomeric/isobaric compound with the same m/z.