Function process_spectrum 

pub fn process_spectrum(
    tof: &[i32],
    mz: &[f64],
    intensity: &[f64],
    config: &SpectrumProcessingConfig,
) -> (Vec<f32>, Vec<f32>)

Process a single spectrum: flatten, optionally deisotope, filter top N peaks.

Arguments

• tof - TOF indices
• mz - m/z values
• intensity - intensity values
• config - processing configuration

Returns

Tuple of (processed_mass, processed_intensity) as f32 vectors for Sage compatibility. Note: m/z values are converted to neutral mass by subtracting the proton mass, matching Sage’s Peak representation which stores neutral mass.