Struct TimsTofSyntheticsFrameBuilderDIA 

pub struct TimsTofSyntheticsFrameBuilderDIA {
    pub path: String,
    pub precursor_frame_builder: TimsTofSyntheticsPrecursorFrameBuilder,
    pub transmission_settings: TimsTransmissionDIA,
    pub fragmentation_settings: TimsTofCollisionEnergyDIA,
    pub fragment_ions: Option<BTreeMap<(u32, i8, i32), (PeptideProductIonSeriesCollection, Vec<MzSpectrum>)>>,
    pub fragment_ions_annotated: Option<BTreeMap<(u32, i8, i32), (PeptideProductIonSeriesCollection, Vec<MzSpectrumAnnotated>)>>,
    pub isotope_config: IsotopeTransmissionConfig,
    pub fragment_ions_with_transmission: Option<BTreeMap<(u32, i8, i32), FragmentIonsWithComplementary>>,
    pub capabilities: InstrumentCapabilities,
}

Fields

path: String

precursor_frame_builder: TimsTofSyntheticsPrecursorFrameBuilder

transmission_settings: TimsTransmissionDIA

fragmentation_settings: TimsTofCollisionEnergyDIA

fragment_ions: Option<BTreeMap<(u32, i8, i32), (PeptideProductIonSeriesCollection, Vec<MzSpectrum>)>>

fragment_ions_annotated: Option<BTreeMap<(u32, i8, i32), (PeptideProductIonSeriesCollection, Vec<MzSpectrumAnnotated>)>>

isotope_config: IsotopeTransmissionConfig

Configuration for quad-selection dependent isotope transmission (already gated by the instrument capabilities at construction — P5e).

fragment_ions_with_transmission: Option<BTreeMap<(u32, i8, i32), FragmentIonsWithComplementary>>

Fragment ions with complementary data for transmission-dependent calculations

capabilities: InstrumentCapabilities

Physical instrument capabilities (P5e). Default = Bruker timsTOF.

Implementations

impl TimsTofSyntheticsFrameBuilderDIA

pub fn new( path: &Path, with_annotations: bool, num_threads: usize, ) -> Result<Self>

pub fn new_with_config( path: &Path, with_annotations: bool, num_threads: usize, isotope_config: IsotopeTransmissionConfig, ) -> Result<Self>

pub fn new_with_config_and_source( path: &Path, with_annotations: bool, num_threads: usize, isotope_config: IsotopeTransmissionConfig, source: &DistributionSource, ) -> Result<Self>

As [new_with_config], but the precursor builder’s occurrence/abundance distributions come from source (P4: Columns default, or the projector).

pub fn build_frame( &self, frame_id: u32, fragmentation: bool, mz_noise_precursor: bool, uniform: bool, precursor_noise_ppm: f64, mz_noise_fragment: bool, fragment_noise_ppm: f64, right_drag: bool, ) -> TimsFrame

Build a frame for DIA synthetic experiment

Arguments

• frame_id - The frame id
• fragmentation - A boolean indicating if fragmentation is enabled, if false, the frame has same mz distribution as the precursor frame but will be quadrupole filtered

Returns

A TimsFrame

pub fn build_frame_annotated( &self, frame_id: u32, fragmentation: bool, mz_noise_precursor: bool, uniform: bool, precursor_noise_ppm: f64, mz_noise_fragment: bool, fragment_noise_ppm: f64, right_drag: bool, ) -> TimsFrameAnnotated

pub fn get_fragment_ion_ids(&self, precursor_frame_ids: Vec<u32>) -> Vec<u32>

pub fn build_frames( &self, frame_ids: Vec<u32>, fragmentation: bool, mz_noise_precursor: bool, uniform: bool, precursor_noise_ppm: f64, mz_noise_fragment: bool, fragment_noise_ppm: f64, right_drag: bool, num_threads: usize, ) -> Vec<TimsFrame>

pub fn build_frames_annotated( &self, frame_ids: Vec<u32>, fragmentation: bool, mz_noise_precursor: bool, uniform: bool, precursor_noise_ppm: f64, mz_noise_fragment: bool, fragment_noise_ppm: f64, right_drag: bool, num_threads: usize, ) -> Vec<TimsFrameAnnotated>

pub fn render_fragment_scan( &self, frame_id: u32, window: &WindowTransmission, nce: f64, data_mode: DataMode, ) -> RenderedEvent

Render a fragment (MS2) frame as a vendor-neutral RenderedEvent::Scan for a non-IMS instrument (P6e): collapse ONE isolation window’s fragment signal into the single MS2 spectrum an Astral/Orbitrap records.

Astral has no ion-mobility axis, so (a) each precursor ion is gated into the window ONCE via WindowTransmission::any_transmitted on its isotope envelope (an m/z window, NOT a scan range), and (b) every transmitted ion contributes its fragment series at the FULL mobility marginal frame_abundance × ion_abundance × total_events (scan factor folded to 1.0) — the same marginal contract as the MS1 render (TimsTofSyntheticsPrecursorFrameBuilder::precursor_scan_marginal_spectrum), NOT the Bruker per-scan scan_abundance sum. The isotope-transmission mode is None (Astral capabilities gate it off), so the shared [fragment_series_spectrum] kernel does the per-series scaling. nce is the window’s normalized collision energy: both the CE key the stored fragments were predicted at AND the applied CE (the keying is unit-agnostic). A precursor whose fragments are not stored near nce is SKIPPED (predicted at a different window’s CE) — compatibility is enforced once at registration (P6d), so the render core never panics on a per-precursor miss. Returns an empty-spectrum MS2 Scan when nothing is transmitted / no fragments exist — the writer must still consume and clear that template slot (zero residual).

Fragments ONLY: precursor-survival signal is intentionally not modelled here (it is stochastic, which would break this deterministic render), and an Astral run that configures precursor_survival_* is rejected at config load rather than silently dropping it.

pub fn build_fragment_frame_annotated( &self, frame_id: u32, fragment_ions: &BTreeMap<(u32, i8, i32), (PeptideProductIonSeriesCollection, Vec<MzSpectrumAnnotated>)>, mz_noise_fragment: bool, uniform: bool, fragment_ppm: f64, mz_min: Option<f64>, mz_max: Option<f64>, intensity_min: Option<f64>, right_drag: Option<bool>, ) -> TimsFrameAnnotated

pub fn get_ion_transmission_matrix( &self, peptide_id: u32, charge: i8, include_precursor_frames: bool, ) -> Vec<Vec<f32>>

pub fn count_number_transmissions( &self, peptide_id: u32, charge: i8, ) -> (usize, usize)

pub fn count_number_transmissions_parallel( &self, peptide_ids: Vec<u32>, charge: Vec<i8>, num_threads: usize, ) -> Vec<(usize, usize)>

Trait Implementations

impl TimsTofCollisionEnergy for TimsTofSyntheticsFrameBuilderDIA

fn get_collision_energy(&self, frame_id: i32, scan_id: i32) -> f64