name: xic file_type: xic_file primary_key: [xic_id] doc: "Extracted-ion chromatograms (XIC) for DIA and targeted acquisitions — one row per traced precursor or fragment ion per run" fields: # Identity xic_id: type: string required: true doc: "Opaque identifier of one chromatogram trace. Producer-supplied (e.g. ||||) and unique within the file; the primary key of this view." run_file_name: type: string required: true doc: "Raw data file containing the trace (without extension); links to run_file_name in the run, feature, psm, and mz views." label: type: string required: true doc: "Channel label. Use 'LFQ' for label-free DIA, or the reporter/plex channel name (e.g. 'TMT126') for multiplexed traces. Matches feature.intensities[].label." feature_ids: type: "list" optional: true nullable: true doc: "Optional links to the feature.feature_id rows this trace supports. A trace is precursor-level evidence and can support several candidate peak groups, so this is a list rather than one feature id." feature_scores: type: "list" optional: true nullable: true doc: "Per-feature scores for this trace, for producers whose fragment scores depend on the feature (e.g. area, apex intensity/RT, mass error or shape scores). Use trace-level additional_scores for scores that do not depend on a feature." compensation_voltage: type: float32 optional: true nullable: true doc: "FAIMS compensation voltage of the trace, when the acquisition uses FAIMS; part of the trace identity because one precursor can be traced at several voltages." # Precursor identity precursor_id: type: string required: true doc: "The producer's precursor identifier (DIA-NN pr: modified sequence plus charge, e.g. 'PEPTM(UniMod:35)IDEK2'). Preserved as reported so a trace can be traced back to the source file." peptidoform: type: string required: true doc: "Precursor peptidoform in ProForma notation; links to feature.peptidoform and psm.peptidoform." charge: type: int16 required: true doc: "Precursor charge state." # Traced ion transition: type: string required: true doc: "Transition annotation: 'ms1' for the precursor trace, or a fragment label such as 'y7^1' or 'b4^2'. Fragment annotations should follow mzPAF (the PSI peak annotation format) where the producer supports it; ms1 is reserved for the precursor trace." transition_type: type: string required: true doc: "Kind of trace: 'ms1' for the precursor (MS1) trace, 'fragment' for a fragment-ion (MS2) trace." fragment_type: type: string optional: true nullable: true doc: "Fragment-ion series (e.g. 'b', 'y'). Null for an ms1 trace or a fragment the producer did not annotate." fragment_number: type: int16 optional: true nullable: true doc: "Fragment-ion ordinal measured from its terminus (y7 -> 7). Null when the transition carries no fragment annotation." fragment_charge: type: int16 optional: true nullable: true doc: "Charge of the traced fragment ion (y7^1 -> 1). Null when the producer does not report it." neutral_loss: type: string optional: true nullable: true doc: "Neutral-loss annotation of the traced ion (e.g. '-H2O'). Null when the trace has no neutral loss." isotope: type: int16 optional: true nullable: true doc: "Isotope index of the traced ion: 0 is monoisotopic, 1 is M+1, and so on. Applies to both precursor (ms1) and fragment traces; null when the producer does not report isotope resolution." target_mz: type: float32 optional: true nullable: true doc: "m/z the trace was extracted at: the precursor m/z for an ms1 trace, or the product-ion m/z for a fragment trace. Null when the producer does not report it." target_rt: type: float32 optional: true nullable: true doc: "Expected/target retention time of the trace in seconds, when the producer reports one (e.g. the library or predicted apex)." rt_start: type: float32 optional: true nullable: true doc: "Start of the extraction window in seconds. Null when the producer does not report the window or the whole run was extracted." rt_stop: type: float32 optional: true nullable: true doc: "End of the extraction window in seconds. Null when the producer does not report the window or the whole run was extracted." target_ion_mobility: type: float32 optional: true nullable: true doc: "Target ion-mobility value of the trace (1/K0), when the acquisition is ion-mobility coupled and the producer reports it." ion_mobility_start: type: float32 optional: true nullable: true doc: "Start of the ion-mobility extraction window (1/K0), when applicable." ion_mobility_stop: type: float32 optional: true nullable: true doc: "End of the ion-mobility extraction window (1/K0), when applicable." library_intensity: type: float32 optional: true nullable: true doc: "Library or predicted relative intensity of this fragment, when available; useful as an ML feature or for transition prioritisation." used_for_quantification: type: bool optional: true nullable: true doc: "True when the producer used this trace for quantification or scoring, false when it was only extracted for inspection. Null when the producer does not mark it." # Measurement rt: type: "list" required: true doc: "Raw retention times of the trace in seconds, strictly increasing and in acquisition order. Not aligned or iRT-corrected. MUST have the same length as intensity and, when present, mz." intensity: type: "list" required: true doc: "Raw intensity at each retention time, as exported by the producer; zero-intensity points are kept and QPX does not smooth them. MUST have the same length as rt; element i corresponds to rt[i]." mz: type: "list" optional: true nullable: true doc: "Optional observed m/z at each retention time, aligned with rt; enables mass-error traces. Null when the producer does not report a per-point m/z." is_decoy: type: bool optional: true nullable: true doc: "Decoy flag for the precursor when the producer reports one; null when the trace is not classified." additional_scores: type: "list" optional: true doc: "Trace-level scores reported by the producer. Feature-by-trace score tables (several candidate features sharing one trace) are outside this view." # Metadata cv_params: type: "list" optional: true doc: "Controlled-vocabulary parameters for trace-specific metadata. Settings that are constant for a run (m/z tolerance, extraction-window width, smoothing method) belong in run/provenance metadata, not repeated on every row."