[Question] Adding 1/k0 information to selected precursor ions

[jspaezp]

Hello Joshua!

I hope everything is going well!
I had a question on the usage of the package. I am trying to write an mzML where the spectra
has ion mobility information and I was wondering if this was currently supported (or the option to pass a custom entry at a specific place). Let me know if you can point me to a place in the documentation where I could find that!

Here is a sample of the arguments I am trying to pass to the writer.

sample = {
            "mz_array": mz,
            "intensity_array": intensity,
            "scan_start_time": rt,
            "id": f"scan={i+offset}",
            "params": [
                "MSn Spectrum",
                {"ms level": 2},
                {"total ion current": sum(intensity)},
            ],
            "precursor_information": {
                "activation": [
                    "beam-type collisional dissociation",
                    {"collision energy": 25},
                ],
                "mz": quad_mid,
                "intensity": sum(intensity),
                "charge": 2,
                "isolation_window": [quad_low, quad_mid, quad_high],
                "scan_id": last_precursor_scan_id,
                "selectedIonList": [
                    {
                        ########## HERE ###########
                        "inverse reduced ion mobility": mobility_value,
                    }
                ],
            },
        }

with IndexedMzMLWriter("outfile.mzml") as out:
    ...
    out.write_spectrum(**sample)

And I would like the precursor list section of the mzml to look something like this:

            <precursorList count="1">
                <precursor>
                    <isolationWindow>
                        <cvParam cvRef="MS" accession="MS:1000827" name="isolation window target m/z" value="457.723968505859" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
                        <cvParam cvRef="MS" accession="MS:1000828" name="isolation window lower offset" value="1.5" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
                        <cvParam cvRef="MS" accession="MS:1000829" name="isolation window upper offset" value="0.75" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
                    </isolationWindow>
                    <selectedIonList count="1">
                        <selectedIon>
                            <cvParam cvRef="MS" accession="MS:1000744" name="selected ion m/z" value="457.723968505859" unitAccession="MS:1000040" unitName="m/z" unitCvRef="MS" />
                            <cvParam cvRef="MS" accession="MS:1000041" name="charge state" value="2" />
                            <cvParam cvRef="MS" accession="MS:1002815" name="inverse reduced ion mobility" value="1.078628" unitAccession="MS:1002814" unitName="volt-second per square centimeter"/>
                        </selectedIon>
                    </selectedIonList>
                    <activation>
                        <cvParam cvRef="MS" accession="MS:1000133" name="collision-induced dissociation" />
                        <cvParam cvRef="MS" accession="MS:1000045" name="collision energy" value="35.0"/>
                    </activation>
                </precursor>
            </precursorList>

[mobiusklein]

To accomplish this, you need to pass the ion mobility measure as part of the params list that most components take. The following is brain-compiled, so it may need to be adjusted but I don't think I'll have much time to answer in detail tomorrow.

"precursor_information": [ # note the enclosing list
    {
        "activation": [
            "beam-type collisional dissociation",
            {"collision energy": 25},
        ],
        "isolation_window": [quad_low, quad_mid, quad_high],
        "scan_id": last_precursor_scan_id,
        "selected_ion_list": [
            {
                "mz": quad_mid,
                "intensity": sum(intensity),
                "charge": 2,
                "params": [
                    {"inverse reduced ion mobility": mobility_value}
                ]
            }
        ],
    },
]

The ergonomics of building a precursor ion list are still really bad, in part because the way <precursorList> is substantially more complicated than regular DDA-MS2-focused tools need it to be. I added https://github.com/mobiusklein/psims/blob/master/psims/mzml/writer.py#L1124C19-L1124C19 which tries to make this easier, but merely ends up a little more terse, a little more opaque without much better documentation than I've had time to write as yet.

[jspaezp]

Ohhh I see, thanks a lot for the reply! (It is by no means something critical so dont worry too much about it, just wanted to make sure I was not overlooking a part of the docs)