Acquisition modes

The TDF format records a small set of acquisition modes. OpenTimsTDF identifies them through the Frames.ScanMode / MsMsType columns and exposes the mode-specific metadata via dedicated reader methods.

ScanMode describes the acquisition method, while MsMsType describes the role of an individual frame. They are not interchangeable: in the repository corpus, PASEF acquisitions contain MS1 frames with ScanMode = 8 and MsMsType = 0. Spectrum projection therefore dispatches on MsMsType and keeps ScanMode as exposed acquisition metadata. The documented legacy MsMsType = 2 has no fixture in the corpus, so projecting it requires a clean-room fixture containing that value plus a decision about its expected spectrum/precursor representation; until then it remains unsupported rather than being guessed from ScanMode.

Mode	Detection	Reader entry point
MS1 only	MsMsType = 0	reader.frame(id)
PASEF DDA	MsMsType = 8	reader.pasef_msms_info_for_frame(id) + reader.precursor(id)
diaPASEF	MsMsType = 9	reader.dia_windows_for_frame(id)
prm-PASEF	MsMsType = 10	reader.prm_msms_info_for_frame(id) + reader.prm_target(id)

The bundle is not constrained to a single mode: prm-PASEF and diaPASEF runs both interleave MS1 frames with mode-specific MS2 frames.

diaPASEF

if let Some(fw) = reader.dia_windows_for_frame(frame.id)? {
    for w in &fw.windows {
        println!(
            "scan_begin={:>4} scan_end={:>4} mz={:.2} width={:.1} ce={:.1}",
            w.scan_num_begin, w.scan_num_end,
            w.isolation_mz, w.isolation_width, w.collision_energy,
        );
    }
}

PASEF DDA

for info in reader.pasef_msms_info_for_frame(frame.id)? {
    let prec = reader.precursor(info.precursor_id)?.unwrap();
    println!(
        "precursor {} mz={:.4} z={:?} parent_frame={}",
        prec.id, prec.mono_mz, prec.charge, prec.parent_frame_id,
    );
}

prm-PASEF

for entry in reader.prm_msms_info_for_frame(frame.id)? {
    if let Some(target) = reader.prm_target(entry.target_id)? {
        println!(
            "target id={} external={} mono_mz={:.4} charge={}",
            target.id, target.external_id, target.monoisotopic_mz, target.charge,
        );
    }
}