Struct ProteinConfig 

pub struct ProteinConfig {
    pub rt_window: f64,
    pub im_window: f64,
    pub mass_z_window: f64,
    pub fdr: f64,
    pub optimize_thresholds: bool,
    pub max_feature_isotopes_gate: f64,
    pub ml_rescore: bool,
}

Fields

rt_window: f64

A peptide counts as “observed” if its winning feature match has |rt_diff| within this window (minutes). Applied equally to targets and decoys, so the decoy-estimated hit rate stays calibrated.

im_window: f64

Additional ion-mobility consistency window (1/K0). When the data has IM, an observed peptide must also have |im_diff| within this window. IM is orthogonal to RT, so this cuts random coincidences sharply — the main reason ion mobility boosts MS1 depth. Ignored on non-IM data.

mass_z_window: f64

Recalibrated-mass window in sigma units. An observed peptide must match within this many sigma of the per-run mass error. Tight mass is the dominant background suppressor (ms1searchpy’s mass recalibration).

fdr: f64

Target protein FDR the threshold optimization maximizes proteins at.

optimize_thresholds: bool

Optimize the RT/mass thresholds to maximize proteins at fdr (ms1searchpy’s worker grid scan). When true, rt_window/mass_z_window are upper bounds for the scan; when false they are used as fixed cutoffs.

max_feature_isotopes_gate: f64

Minimum feature shape quality (n_isotopes) for a peptide to count as observed. Real peptides sit on well-formed features; random matches scatter onto junk features, so this gate drops the random-match background asymmetrically. The scan tries [0, this] — 0 disables it. Inert when the input has no shape descriptors (feat_quality == 0 everywhere).

ml_rescore: bool

Rescore proteins with a cross-validated Fisher LDA over protein-level features (binomial score, log#peptides, coverage, RT/mass consistency, mean peptide discriminant). Deterministic (closed-form, 3-fold CV by accession hash) so it does not reintroduce ms1searchpy-style ML variance.

Trait Implementations

impl Clone for ProteinConfig

fn clone(&self) -> Self

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for ProteinConfig

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for ProteinConfig

fn default() -> Self

Returns the “default value” for a type.

impl<'de> Deserialize<'de> for ProteinConfig

where ProteinConfig: Default,

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.