rustdf/sim/dda.rs
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use mscore::data::peptide::{PeptideIon, PeptideProductIonSeriesCollection};
use mscore::data::spectrum::{IndexedMzSpectrum, MsType, MzSpectrum};
use mscore::simulation::annotation::{
MzSpectrumAnnotated, TimsFrameAnnotated, TimsSpectrumAnnotated,
};
use mscore::timstof::frame::TimsFrame;
use mscore::timstof::quadrupole::{IonTransmission, TimsTransmissionDDA};
use mscore::timstof::spectrum::TimsSpectrum;
use std::collections::{BTreeMap, HashSet};
use std::path::Path;
use rayon::prelude::*;
use rayon::ThreadPoolBuilder;
use crate::sim::handle::TimsTofSyntheticsDataHandle;
use crate::sim::precursor::TimsTofSyntheticsPrecursorFrameBuilder;
pub struct TimsTofSyntheticsFrameBuilderDDA {
pub path: String,
pub precursor_frame_builder: TimsTofSyntheticsPrecursorFrameBuilder,
pub transmission_settings: TimsTransmissionDDA,
pub fragment_ions:
Option<BTreeMap<(u32, i8, i32), (PeptideProductIonSeriesCollection, Vec<MzSpectrum>)>>,
pub fragment_ions_annotated: Option<
BTreeMap<(u32, i8, i32), (PeptideProductIonSeriesCollection, Vec<MzSpectrumAnnotated>)>,
>,
}
impl TimsTofSyntheticsFrameBuilderDDA {
pub fn new(path: &Path, with_annotations: bool, num_threads: usize) -> Self {
let handle = TimsTofSyntheticsDataHandle::new(path).unwrap();
let fragment_ions = handle.read_fragment_ions().unwrap();
let transmission_settings = handle.get_transmission_dda();
let synthetics = TimsTofSyntheticsPrecursorFrameBuilder::new(path).unwrap();
match with_annotations {
true => {
let fragment_ions =
Some(TimsTofSyntheticsDataHandle::build_fragment_ions_annotated(
&synthetics.peptides,
&fragment_ions,
num_threads,
));
Self {
path: path.to_str().unwrap().to_string(),
precursor_frame_builder: synthetics,
transmission_settings,
fragment_ions: None,
fragment_ions_annotated: fragment_ions,
}
}
false => {
let fragment_ions = Some(TimsTofSyntheticsDataHandle::build_fragment_ions(
&synthetics.peptides,
&fragment_ions,
num_threads,
));
Self {
path: path.to_str().unwrap().to_string(),
precursor_frame_builder: synthetics,
transmission_settings,
fragment_ions,
fragment_ions_annotated: None,
}
}
}
}
/// Build a frame for DDA 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(
&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 {
// determine if the frame is a precursor frame
match self
.precursor_frame_builder
.precursor_frame_id_set
.contains(&frame_id)
{
true => self.build_ms1_frame(
frame_id,
mz_noise_precursor,
uniform,
precursor_noise_ppm,
right_drag,
),
false => self.build_ms2_frame(
frame_id,
fragmentation,
mz_noise_fragment,
uniform,
fragment_noise_ppm,
right_drag,
),
}
}
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 {
match self
.precursor_frame_builder
.precursor_frame_id_set
.contains(&frame_id)
{
true => self.build_ms1_frame_annotated(
frame_id,
mz_noise_precursor,
uniform,
precursor_noise_ppm,
right_drag,
),
false => self.build_ms2_frame_annotated(
frame_id,
fragmentation,
mz_noise_fragment,
uniform,
fragment_noise_ppm,
right_drag,
),
}
}
pub fn get_fragment_ion_ids(&self, precursor_frame_ids: Vec<u32>) -> Vec<u32> {
let mut peptide_ids: HashSet<u32> = HashSet::new();
// get all peptide ids for the precursor frame ids
for frame_id in precursor_frame_ids {
for (peptide_id, peptide) in self.precursor_frame_builder.peptides.iter() {
if peptide.frame_start <= frame_id && peptide.frame_end >= frame_id {
peptide_ids.insert(*peptide_id);
}
}
}
// get all ion ids for the peptide ids
let mut result: Vec<u32> = Vec::new();
for item in peptide_ids {
let ions = self.precursor_frame_builder.ions.get(&item).unwrap();
for ion in ions.iter() {
result.push(ion.ion_id);
}
}
result
}
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> {
let thread_pool = ThreadPoolBuilder::new()
.num_threads(num_threads)
.build()
.unwrap();
let mut tims_frames: Vec<TimsFrame> = Vec::new();
thread_pool.install(|| {
tims_frames = frame_ids
.par_iter()
.map(|frame_id| {
self.build_frame(
*frame_id,
fragmentation,
mz_noise_precursor,
uniform,
precursor_noise_ppm,
mz_noise_fragment,
fragment_noise_ppm,
right_drag,
)
})
.collect();
});
tims_frames.sort_by(|a, b| a.frame_id.cmp(&b.frame_id));
tims_frames
}
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> {
let thread_pool = ThreadPoolBuilder::new()
.num_threads(num_threads)
.build()
.unwrap();
let mut tims_frames: Vec<TimsFrameAnnotated> = Vec::new();
thread_pool.install(|| {
tims_frames = frame_ids
.par_iter()
.map(|frame_id| {
self.build_frame_annotated(
*frame_id,
fragmentation,
mz_noise_precursor,
uniform,
precursor_noise_ppm,
mz_noise_fragment,
fragment_noise_ppm,
right_drag,
)
})
.collect();
});
tims_frames.sort_by(|a, b| a.frame_id.cmp(&b.frame_id));
tims_frames
}
fn build_ms1_frame(
&self,
frame_id: u32,
mz_noise_precursor: bool,
uniform: bool,
precursor_ppm: f64,
right_drag: bool,
) -> TimsFrame {
let mut tims_frame = self.precursor_frame_builder.build_precursor_frame(
frame_id,
mz_noise_precursor,
uniform,
precursor_ppm,
right_drag,
);
let intensities_rounded = tims_frame
.ims_frame
.intensity
.iter()
.map(|x| x.round())
.collect::<Vec<_>>();
tims_frame.ims_frame.intensity = intensities_rounded;
tims_frame
}
fn build_ms1_frame_annotated(
&self,
frame_id: u32,
mz_noise_precursor: bool,
uniform: bool,
precursor_ppm: f64,
right_drag: bool,
) -> TimsFrameAnnotated {
let mut tims_frame = self
.precursor_frame_builder
.build_precursor_frame_annotated(
frame_id,
mz_noise_precursor,
uniform,
precursor_ppm,
right_drag,
);
let intensities_rounded = tims_frame
.intensity
.iter()
.map(|x| x.round())
.collect::<Vec<_>>();
tims_frame.intensity = intensities_rounded;
tims_frame
}
fn build_ms2_frame(
&self,
frame_id: u32,
fragmentation: bool,
mz_noise_fragment: bool,
uniform: bool,
fragment_ppm: f64,
right_drag: bool,
) -> TimsFrame {
match fragmentation {
false => {
let mut frame = self.transmission_settings.transmit_tims_frame(
&self.build_ms1_frame(
frame_id,
mz_noise_fragment,
uniform,
fragment_ppm,
right_drag,
),
None,
);
let intensities_rounded = frame
.ims_frame
.intensity
.iter()
.map(|x| x.round())
.collect::<Vec<_>>();
frame.ims_frame.intensity = intensities_rounded;
frame.ms_type = MsType::FragmentDia;
frame
}
true => {
let mut frame = self.build_fragment_frame(
frame_id,
&self.fragment_ions.as_ref().unwrap(),
mz_noise_fragment,
uniform,
fragment_ppm,
None,
None,
None,
Some(right_drag),
);
let intensities_rounded = frame
.ims_frame
.intensity
.iter()
.map(|x| x.round())
.collect::<Vec<_>>();
frame.ims_frame.intensity = intensities_rounded;
frame
}
}
}
fn build_ms2_frame_annotated(
&self,
frame_id: u32,
fragmentation: bool,
mz_noise_fragment: bool,
uniform: bool,
fragment_ppm: f64,
right_drag: bool,
) -> TimsFrameAnnotated {
match fragmentation {
false => {
let mut frame = self.transmission_settings.transmit_tims_frame_annotated(
&self.build_ms1_frame_annotated(
frame_id,
mz_noise_fragment,
uniform,
fragment_ppm,
right_drag,
),
None,
);
let intensities_rounded = frame
.intensity
.iter()
.map(|x| x.round())
.collect::<Vec<_>>();
frame.intensity = intensities_rounded;
frame.ms_type = MsType::FragmentDia;
frame
}
true => {
let mut frame = self.build_fragment_frame_annotated(
frame_id,
&self.fragment_ions_annotated.as_ref().unwrap(),
mz_noise_fragment,
uniform,
fragment_ppm,
None,
None,
None,
Some(right_drag),
);
let intensities_rounded = frame
.intensity
.iter()
.map(|x| x.round())
.collect::<Vec<_>>();
frame.intensity = intensities_rounded;
frame
}
}
}
/// Build a fragment frame
///
/// # Arguments
///
/// * `frame_id` - The frame id
/// * `mz_min` - The minimum m/z value in fragment spectrum
/// * `mz_max` - The maximum m/z value in fragment spectrum
/// * `intensity_min` - The minimum intensity value in fragment spectrum
///
/// # Returns
///
/// A TimsFrame
///
fn build_fragment_frame(
&self,
frame_id: u32,
fragment_ions: &BTreeMap<
(u32, i8, i32),
(PeptideProductIonSeriesCollection, Vec<MzSpectrum>),
>,
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>,
) -> TimsFrame {
// check frame id
let ms_type = match self
.precursor_frame_builder
.precursor_frame_id_set
.contains(&frame_id)
{
false => MsType::FragmentDda,
true => MsType::Unknown,
};
let mut tims_spectra: Vec<TimsSpectrum> = Vec::new();
// Frame might not have any peptides
if !self
.precursor_frame_builder
.frame_to_abundances
.contains_key(&frame_id)
{
return TimsFrame::new(
frame_id as i32,
ms_type.clone(),
*self
.precursor_frame_builder
.frame_to_rt
.get(&frame_id)
.unwrap() as f64,
vec![],
vec![],
vec![],
vec![],
vec![],
);
}
// Get the peptide ids and abundances for the frame, should now save to unwrap since we checked if the frame is in the map
let (peptide_ids, frame_abundances) = self
.precursor_frame_builder
.frame_to_abundances
.get(&frame_id)
.unwrap();
// Go over all peptides in the frame with their respective abundances
for (peptide_id, frame_abundance) in peptide_ids.iter().zip(frame_abundances.iter()) {
// jump to next peptide if the peptide_id is not in the peptide_to_ions map
if !self
.precursor_frame_builder
.peptide_to_ions
.contains_key(&peptide_id)
{
continue;
}
// get all the ions for the peptide
let (ion_abundances, scan_occurrences, scan_abundances, charges, spectra) = self
.precursor_frame_builder
.peptide_to_ions
.get(&peptide_id)
.unwrap();
for (index, ion_abundance) in ion_abundances.iter().enumerate() {
// occurrence and abundance of the ion in the scan
let all_scan_occurrence = scan_occurrences.get(index).unwrap();
let all_scan_abundance = scan_abundances.get(index).unwrap();
// get precursor spectrum for the ion
let spectrum = spectra.get(index).unwrap();
// go over occurrence and abundance of the ion in the scan
for (scan, scan_abundance) in
all_scan_occurrence.iter().zip(all_scan_abundance.iter())
{
// first, check if precursor is transmitted
if !self.transmission_settings.any_transmitted(
frame_id as i32,
*scan as i32,
&spectrum.mz,
None,
) {
continue;
}
// calculate abundance factor
let total_events = self
.precursor_frame_builder
.peptide_to_events
.get(&peptide_id)
.unwrap();
let fraction_events =
frame_abundance * scan_abundance * ion_abundance * total_events;
// get PASEF settings for the given frame
let maybe_pasef_meta = self.transmission_settings.pasef_meta.get(&(frame_id as i32));
let collision_energy: f64 = match maybe_pasef_meta {
Some(pasef_meta) => {
pasef_meta
.iter()
.find(|scan_meta| scan_meta.scan_start <= *scan as i32 && scan_meta.scan_end >= *scan as i32)
.map(|s| s.collision_energy)
.unwrap_or(0.0)
},
None => 0.0
};
let collision_energy_quantized = (collision_energy * 1e1).round() as i32;
// get charge state for the ion
let charge_state = charges.get(index).unwrap();
// extract fragment ions for the peptide, charge state and collision energy
let maybe_value = fragment_ions.get(&(
*peptide_id,
*charge_state,
collision_energy_quantized,
));
// jump to next peptide if the fragment_ions is None (can this happen?)
if maybe_value.is_none() {
continue;
}
// for each fragment ion series, create a spectrum and add it to the tims_spectra
for fragment_ion_series in maybe_value.unwrap().1.iter() {
let scaled_spec = fragment_ion_series.clone() * fraction_events as f64;
let right_drag = right_drag.unwrap_or(false);
let mz_spectrum = if mz_noise_fragment {
match uniform {
true => scaled_spec.add_mz_noise_uniform(fragment_ppm, right_drag),
false => scaled_spec.add_mz_noise_normal(fragment_ppm),
}
} else {
scaled_spec
};
tims_spectra.push(TimsSpectrum::new(
frame_id as i32,
*scan as i32,
*self
.precursor_frame_builder
.frame_to_rt
.get(&frame_id)
.unwrap() as f64,
*self
.precursor_frame_builder
.scan_to_mobility
.get(&scan)
.unwrap() as f64,
ms_type.clone(),
IndexedMzSpectrum::new(
vec![0; mz_spectrum.mz.len()],
mz_spectrum.mz,
mz_spectrum.intensity,
)
.filter_ranged(100.0, 1700.0, 1.0, 1e9),
));
}
}
}
}
if tims_spectra.is_empty() {
return TimsFrame::new(
frame_id as i32,
ms_type.clone(),
*self
.precursor_frame_builder
.frame_to_rt
.get(&frame_id)
.unwrap() as f64,
vec![],
vec![],
vec![],
vec![],
vec![],
);
}
let tims_frame = TimsFrame::from_tims_spectra(tims_spectra);
tims_frame.filter_ranged(
mz_min.unwrap_or(100.0),
mz_max.unwrap_or(1700.0),
0,
1000,
0.0,
10.0,
intensity_min.unwrap_or(1.0),
1e9,
)
}
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 {
let ms_type = match self
.precursor_frame_builder
.precursor_frame_id_set
.contains(&frame_id)
{
false => MsType::FragmentDia,
true => MsType::Unknown,
};
let mut tims_spectra: Vec<TimsSpectrumAnnotated> = Vec::new();
if !self
.precursor_frame_builder
.frame_to_abundances
.contains_key(&frame_id)
{
return TimsFrameAnnotated::new(
frame_id as i32,
*self
.precursor_frame_builder
.frame_to_rt
.get(&frame_id)
.unwrap() as f64,
ms_type.clone(),
vec![],
vec![],
vec![],
vec![],
vec![],
vec![],
);
}
let (peptide_ids, frame_abundances) = self
.precursor_frame_builder
.frame_to_abundances
.get(&frame_id)
.unwrap();
for (peptide_id, frame_abundance) in peptide_ids.iter().zip(frame_abundances.iter()) {
if !self
.precursor_frame_builder
.peptide_to_ions
.contains_key(&peptide_id)
{
continue;
}
let (ion_abundances, scan_occurrences, scan_abundances, charges, _) = self
.precursor_frame_builder
.peptide_to_ions
.get(&peptide_id)
.unwrap();
for (index, ion_abundance) in ion_abundances.iter().enumerate() {
let all_scan_occurrence = scan_occurrences.get(index).unwrap();
let all_scan_abundance = scan_abundances.get(index).unwrap();
let peptide = self
.precursor_frame_builder
.peptides
.get(peptide_id)
.unwrap();
let ion = PeptideIon::new(
peptide.sequence.sequence.clone(),
charges[index] as i32,
*ion_abundance as f64,
Some(*peptide_id as i32),
);
// TODO: make this configurable
let spectrum = ion.calculate_isotopic_spectrum_annotated(1e-3, 1e-8, 200, 1e-4);
for (scan, scan_abundance) in
all_scan_occurrence.iter().zip(all_scan_abundance.iter())
{
if !self.transmission_settings.any_transmitted(
frame_id as i32,
*scan as i32,
&spectrum.mz,
None,
) {
continue;
}
let total_events = self
.precursor_frame_builder
.peptide_to_events
.get(&peptide_id)
.unwrap();
let fraction_events =
frame_abundance * scan_abundance * ion_abundance * total_events;
// get PASEF settings for the given frame
let maybe_pasef_meta = self.transmission_settings.pasef_meta.get(&(frame_id as i32));
let collision_energy: f64 = match maybe_pasef_meta {
Some(pasef_meta) => {
pasef_meta
.iter()
.find(|scan_meta| scan_meta.scan_start <= *scan as i32 && scan_meta.scan_end >= *scan as i32)
.map(|s| s.collision_energy)
.unwrap_or(0.0)
},
None => 0.0
};
let collision_energy_quantized = (collision_energy * 1e1).round() as i32;
let charge_state = charges.get(index).unwrap();
let maybe_value = fragment_ions.get(&(
*peptide_id,
*charge_state,
collision_energy_quantized,
));
if maybe_value.is_none() {
continue;
}
for fragment_ion_series in maybe_value.unwrap().1.iter() {
let scaled_spec = fragment_ion_series.clone() * fraction_events as f64;
let right_drag = right_drag.unwrap_or(false);
let mz_spectrum = if mz_noise_fragment {
match uniform {
true => scaled_spec.add_mz_noise_uniform(fragment_ppm, right_drag),
false => scaled_spec.add_mz_noise_normal(fragment_ppm),
}
} else {
scaled_spec
};
tims_spectra.push(TimsSpectrumAnnotated::new(
frame_id as i32,
*scan,
*self
.precursor_frame_builder
.frame_to_rt
.get(&frame_id)
.unwrap() as f64,
*self
.precursor_frame_builder
.scan_to_mobility
.get(&scan)
.unwrap() as f64,
ms_type.clone(),
vec![0; mz_spectrum.mz.len()],
mz_spectrum,
));
}
}
}
}
if tims_spectra.is_empty() {
return TimsFrameAnnotated::new(
frame_id as i32,
*self
.precursor_frame_builder
.frame_to_rt
.get(&frame_id)
.unwrap() as f64,
ms_type.clone(),
vec![],
vec![],
vec![],
vec![],
vec![],
vec![],
);
}
let tims_frame = TimsFrameAnnotated::from_tims_spectra_annotated(tims_spectra);
tims_frame.filter_ranged(
mz_min.unwrap_or(100.0),
mz_max.unwrap_or(1700.0),
0.0,
10.0,
0,
1000,
intensity_min.unwrap_or(1.0),
1e9,
)
}
pub fn get_collision_energy(&self, frame_id: i32, scan_id: i32) -> f64 {
self.transmission_settings.get_collision_energy(frame_id, scan_id).unwrap_or(0.0)
}
pub fn get_collision_energies(&self, frame_ids: Vec<i32>, scan_ids: Vec<i32>) -> Vec<f64> {
let mut collision_energies: Vec<f64> = Vec::new();
for frame_id in frame_ids {
for scan_id in &scan_ids {
collision_energies.push(self.get_collision_energy(frame_id, *scan_id));
}
}
collision_energies
}
}