def _get_dda_scan_param(self, mz, intensity, isolation_width, mz_tol,
rt_tol, collision_energy):
dda_scan_params = ScanParameters()
dda_scan_params.set(ScanParameters.MS_LEVEL, 2)
# create precursor object, assume it's all singly charged
precursor_charge = +1 if (self.environment.mass_spec.ionisation_mode
== POSITIVE) else -1
precursor = Precursor(precursor_mz=mz,
precursor_intensity=intensity,
precursor_charge=precursor_charge,
precursor_scan_id=self.last_ms1_scan.scan_id)
dda_scan_params.set(ScanParameters.PRECURSOR_MZ, precursor)
# set the full-width isolation width, in Da
dda_scan_params.set(ScanParameters.ISOLATION_WIDTH, isolation_width)
# define dynamic exclusion parameters
dda_scan_params.set(ScanParameters.DYNAMIC_EXCLUSION_MZ_TOL, mz_tol)
dda_scan_params.set(ScanParameters.DYNAMIC_EXCLUSION_RT_TOL, rt_tol)
# define other fragmentation parameters
dda_scan_params.set(ScanParameters.COLLISION_ENERGY, collision_energy)
dda_scan_params.set(ScanParameters.POLARITY,
self.environment.mass_spec.ionisation_mode)
dda_scan_params.set(ScanParameters.FIRST_MASS,
DEFAULT_MSN_SCAN_WINDOW[0])
dda_scan_params.set(ScanParameters.LAST_MASS,
DEFAULT_MSN_SCAN_WINDOW[1])
return dda_scan_params
def _process_scan(self, scan, queue_size):
# if there's a previous ms1 scan to process
new_tasks = []
if self.last_ms1_scan is not None:
rt = self.last_ms1_scan.rt
# then get the last ms1 scan, select bin walls and create scan locations
mzs = self.last_ms1_scan.mzs
default_range = [
DEFAULT_MS1_SCAN_WINDOW
] # TODO: this should maybe come from somewhere else?
locations = DiaWindows(mzs, default_range, self.dia_design,
self.window_type, self.kaufmann_design,
self.extra_bins, self.num_windows).locations
logger.debug('Window locations {}'.format(locations))
for i in range(
len(locations)
): # define isolation window around the selected precursor ions
isolation_windows = locations[i]
dda_scan_params = ScanParameters()
dda_scan_params.set(ScanParameters.MS_LEVEL, 2)
dda_scan_params.set(ScanParameters.ISOLATION_WINDOWS,
isolation_windows)
new_tasks.append(dda_scan_params
) # push this dda scan to the mass spec queue
# set this ms1 scan as has been processed
self.last_ms1_scan = None
return new_tasks
def __init__(self,
mass_spec,
N,
scan_param_changepoints,
isolation_window,
mz_tol,
rt_tol,
min_ms1_intensity,
n_purity_scans=None,
purity_shift=None,
purity_threshold=0):
super().__init__(mass_spec)
self.last_ms1_scan = None
self.N = np.array(N)
if scan_param_changepoints is not None:
self.scan_param_changepoints = np.array([0] +
scan_param_changepoints)
else:
self.scan_param_changepoints = np.array([0])
self.isolation_window = np.array(
isolation_window
) # the isolation window (in Dalton) to select a precursor ion
self.mz_tol = np.array(
mz_tol
) # the m/z window (ppm) to prevent the same precursor ion to be fragmented again
self.rt_tol = np.array(
rt_tol
) # the rt window to prevent the same precursor ion to be fragmented again
self.min_ms1_intensity = min_ms1_intensity # minimum ms1 intensity to fragment
self.n_purity_scans = n_purity_scans
self.purity_shift = purity_shift
self.purity_threshold = purity_threshold
# make sure the input are all correct
assert len(self.N) == len(self.scan_param_changepoints) == len(
self.isolation_window) == len(self.mz_tol) == len(self.rt_tol)
if self.purity_threshold != 0:
assert all(self.n_purity_scans < np.array(self.N))
mass_spec.reset()
current_N, current_rt_tol, idx = self._get_current_N_DEW()
mass_spec.current_N = current_N
mass_spec.current_DEW = current_rt_tol
default_scan = ScanParameters()
default_scan.set(ScanParameters.MS_LEVEL, 1)
default_scan.set(ScanParameters.ISOLATION_WINDOWS,
[[DEFAULT_MS1_SCAN_WINDOW]])
mass_spec.set_repeating_scan(default_scan)
# register new event handlers under this controller
mass_spec.register(IndependentMassSpectrometer.MS_SCAN_ARRIVED,
self.handle_scan)
mass_spec.register(
IndependentMassSpectrometer.ACQUISITION_STREAM_OPENING,
self.handle_acquisition_open)
mass_spec.register(
IndependentMassSpectrometer.ACQUISITION_STREAM_CLOSING,
self.handle_acquisition_closing)
def __init__(self,
mass_spec,
dia_design,
window_type,
kaufmann_design,
extra_bins,
num_windows=None):
super().__init__(mass_spec)
self.last_ms1_scan = None
self.dia_design = dia_design
self.window_type = window_type
self.kaufmann_design = kaufmann_design
self.extra_bins = extra_bins
self.num_windows = num_windows
mass_spec.reset()
default_scan = ScanParameters()
default_scan.set(ScanParameters.MS_LEVEL, 1)
default_scan.set(ScanParameters.ISOLATION_WINDOWS,
[[DEFAULT_MS1_SCAN_WINDOW]])
mass_spec.set_repeating_scan(default_scan)
mass_spec.register(IndependentMassSpectrometer.MS_SCAN_ARRIVED,
self.handle_scan)
mass_spec.register(
IndependentMassSpectrometer.ACQUISITION_STREAM_OPENING,
self.handle_acquisition_open)
mass_spec.register(
IndependentMassSpectrometer.ACQUISITION_STREAM_CLOSING,
self.handle_acquisition_closing)
def __init__(self, mass_spec, N, isolation_window, mz_tol, rt_tol,
min_ms1_intensity):
super().__init__(mass_spec)
self.last_ms1_scan = None
self.N = N
self.isolation_window = isolation_window # the isolation window (in Dalton) to select a precursor ion
self.mz_tol = mz_tol # the m/z window (ppm) to prevent the same precursor ion to be fragmented again
self.rt_tol = rt_tol # the rt window to prevent the same precursor ion to be fragmented again
self.min_ms1_intensity = min_ms1_intensity # minimum ms1 intensity to fragment
mass_spec.reset()
mass_spec.current_N = N
mass_spec.current_DEW = rt_tol
default_scan = ScanParameters()
default_scan.set(ScanParameters.MS_LEVEL, 1)
default_scan.set(ScanParameters.ISOLATION_WINDOWS,
[[DEFAULT_MS1_SCAN_WINDOW]])
mass_spec.set_repeating_scan(default_scan)
# register new event handlers under this controller
mass_spec.register(IndependentMassSpectrometer.MS_SCAN_ARRIVED,
self.handle_scan)
mass_spec.register(
IndependentMassSpectrometer.ACQUISITION_STREAM_OPENING,
self.handle_acquisition_open)
mass_spec.register(
IndependentMassSpectrometer.ACQUISITION_STREAM_CLOSING,
self.handle_acquisition_closing)
def __init__(self,
mass_spec,
isolation_window,
mz_tol,
min_ms1_intensity,
min_roi_intensity,
min_roi_length,
score_method,
N=None,
rt_tol=math.inf,
score_params=None):
super().__init__(mass_spec)
self.last_ms1_scan = None
self.N = N
self.isolation_window = isolation_window # the isolation window (in Dalton) to select a precursor ion
self.mz_tol = mz_tol # the m/z window (ppm) to prevent the same precursor ion to be fragmented again
self.rt_tol = rt_tol # the rt window to prevent the same precursor ion to be fragmented again
self.min_ms1_intensity = min_ms1_intensity # minimum ms1 intensity to fragment
# ROI stuff
self.min_roi_intensity = min_roi_intensity
self.mz_units = 'Da'
self.min_roi_length = min_roi_length
# Score stuff
self.score_params = score_params
self.score_method = score_method
# Create ROI
self.live_roi = []
self.dead_roi = []
self.junk_roi = []
self.live_roi_fragmented = []
self.live_roi_last_rt = [] # last fragmentation time of ROI
mass_spec.reset()
mass_spec.current_N = N
mass_spec.current_DEW = rt_tol
mass_spec.use_exclusion_list = False
default_scan = ScanParameters()
default_scan.set(ScanParameters.MS_LEVEL, 1)
default_scan.set(ScanParameters.ISOLATION_WINDOWS,
[[DEFAULT_MS1_SCAN_WINDOW]])
mass_spec.set_repeating_scan(default_scan)
# register new event handlers under this controller
mass_spec.register(IndependentMassSpectrometer.MS_SCAN_ARRIVED,
self.handle_scan)
mass_spec.register(
IndependentMassSpectrometer.ACQUISITION_STREAM_OPENING,
self.handle_acquisition_open)
mass_spec.register(
IndependentMassSpectrometer.ACQUISITION_STREAM_CLOSING,
self.handle_acquisition_closing)
def __init__(self, mass_spec):
super().__init__(mass_spec)
default_scan = ScanParameters()
default_scan.set(ScanParameters.MS_LEVEL, 1)
default_scan.set(ScanParameters.ISOLATION_WINDOWS,
[[DEFAULT_MS1_SCAN_WINDOW]])
mass_spec.reset()
mass_spec.current_N = 0
mass_spec.current_DEW = 0
mass_spec.set_repeating_scan(default_scan)
mass_spec.register(IndependentMassSpectrometer.MS_SCAN_ARRIVED,
self.handle_scan)
mass_spec.register(
IndependentMassSpectrometer.ACQUISITION_STREAM_OPENING,
self.handle_acquisition_open)
mass_spec.register(
IndependentMassSpectrometer.ACQUISITION_STREAM_CLOSING,
self.handle_acquisition_closing)
def __init__(self,
mass_spec,
controller,
min_time,
max_time,
progress_bar=True,
out_dir=None,
out_file=None):
"""
Initialises a synchronous environment to run the mass spec and controller
:param mass_spec: An instance of Mass Spec object
:param controller: An instance of Controller object
:param min_time: start time
:param max_time: end time
:param progress_bar: True if a progress bar is to be shown
"""
self.scan_channel = []
self.task_channel = []
self.mass_spec = mass_spec
self.controller = controller
self.min_time = min_time
self.max_time = max_time
self.progress_bar = progress_bar
self.default_scan_params = ScanParameters()
self.default_scan_params.set(ScanParameters.MS_LEVEL, 1)
self.default_scan_params.set(ScanParameters.ISOLATION_WINDOWS,
[[DEFAULT_MS1_SCAN_WINDOW]])
self.default_scan_params.set(ScanParameters.ISOLATION_WIDTH,
DEFAULT_ISOLATION_WIDTH)
self.default_scan_params.set(ScanParameters.COLLISION_ENERGY,
DEFAULT_COLLISION_ENERGY)
self.default_scan_params.set(ScanParameters.POLARITY,
self.mass_spec.ionisation_mode)
self.default_scan_params.set(ScanParameters.FIRST_MASS,
DEFAULT_MS1_SCAN_WINDOW[0])
self.default_scan_params.set(ScanParameters.LAST_MASS,
DEFAULT_MS1_SCAN_WINDOW[1])
self.out_dir = out_dir
self.out_file = out_file
def run(self, schedule_file, progress_bar=True):
self.schedule = pd.read_csv(schedule_file)
for idx, row in self.schedule.iterrows():
target_mass = row.targetMass
target_time = row.targetTime
if np.isnan(target_mass):
ms_level = 1
isolation_windows = [[(0, 1000)]]
precursor = None
else:
ms_level = 2
mz_lower = target_mass - self.isolation_window
mz_upper = target_mass + self.isolation_window
isolation_windows = [[(mz_lower, mz_upper)]]
precursor_charge = +1 if (self.mass_spec.ionisation_mode
== POSITIVE) else -1
scan_id = 0
precursor = Precursor(precursor_mz=target_mass,
precursor_intensity=0,
precursor_charge=precursor_charge,
precursor_scan_id=scan_id)
dda_scan_params = ScanParameters()
dda_scan_params.set(ScanParameters.MS_LEVEL, ms_level)
dda_scan_params.set(ScanParameters.ISOLATION_WINDOWS,
isolation_windows)
dda_scan_params.set(ScanParameters.TIME, target_time)
if precursor:
dda_scan_params.set(ScanParameters.PRECURSOR, precursor)
self.mass_spec.add_task(
dda_scan_params) # push this scan to the mass spec queue
if progress_bar:
with tqdm(total=target_time, initial=0) as pbar:
self.mass_spec.run(self.schedule, pbar=pbar)
else:
self.mass_spec.run(self.schedule)
def _update_parameters(self, scan):
# if there's a previous ms1 scan to process
if self.last_ms1_scan is not None:
self.current_roi_mzs = [roi.get_mean_mz() for roi in self.live_roi]
self.current_roi_intensities = [
roi.get_max_intensity() for roi in self.live_roi
]
rt = self.last_ms1_scan.rt
# loop over points in decreasing score
scores = self.get_scores(self.score_method, self.score_params)
idx = np.argsort(scores)[::-1]
for i in idx:
mz = self.current_roi_mzs[i]
intensity = self.current_roi_intensities[i]
# stopping criteria is done based on the scores
if scores[i] <= 0:
self.logger.debug(
'Time %f Top-%d ions have been selected' %
(self.mass_spec.time, self.N))
break
# updated fragmented list and times
if self.live_roi_fragmented[i]:
continue
self.live_roi_fragmented[i] = True
self.live_roi_last_rt[
i] = rt # TODO: May want to update this to use the time of the MS2 scan
# send a new ms2 scan parameter to the mass spec
dda_scan_params = ScanParameters()
dda_scan_params.set(ScanParameters.MS_LEVEL, 2)
# create precursor object, assume it's all singly charged
precursor_charge = +1 if (self.mass_spec.ionisation_mode
== POSITIVE) else -1
precursor = Precursor(
precursor_mz=mz,
precursor_intensity=intensity,
precursor_charge=precursor_charge,
precursor_scan_id=self.last_ms1_scan.scan_id)
mz_lower = mz - self.isolation_window # Da
mz_upper = mz + self.isolation_window # Da
isolation_windows = [[(mz_lower, mz_upper)]]
dda_scan_params.set(ScanParameters.ISOLATION_WINDOWS,
isolation_windows)
dda_scan_params.set(ScanParameters.PRECURSOR, precursor)
# save dynamic exclusion parameters too
dda_scan_params.set(ScanParameters.DYNAMIC_EXCLUSION_MZ_TOL,
self.mz_tol)
dda_scan_params.set(ScanParameters.DYNAMIC_EXCLUSION_RT_TOL,
self.rt_tol)
# push this dda scan parameter to the mass spec queue
self.mass_spec.add_task(dda_scan_params)
for param in self.mass_spec.get_task_queue():
precursor = param.get(ScanParameters.PRECURSOR)
if precursor is not None:
self.logger.debug('- %s' % str(precursor))
# set this ms1 scan as has been processed
self.last_ms1_scan = None
def _update_parameters(self, scan):
# if there's a previous ms1 scan to process
if self.last_ms1_scan is not None:
mzs = self.last_ms1_scan.mzs
intensities = self.last_ms1_scan.intensities
rt = self.last_ms1_scan.rt
# set up current scan parameters
current_N, current_rt_tol, idx = self._get_current_N_DEW()
current_isolation_window = self.isolation_window[idx]
current_mz_tol = self.mz_tol[idx]
# calculate purities
purities = []
for mz_idx in range(len(self.last_ms1_scan.mzs)):
nearby_mzs_idx = np.where(
abs(self.last_ms1_scan.mzs - self.last_ms1_scan.mzs[mz_idx]
) < current_isolation_window)
if len(nearby_mzs_idx[0]) == 1:
purities.append(1)
else:
total_intensity = sum(
self.last_ms1_scan.intensities[nearby_mzs_idx])
purities.append(self.last_ms1_scan.intensities[mz_idx] /
total_intensity)
# loop over points in decreasing intensity
fragmented_count = 0
idx = np.argsort(intensities)[::-1]
for i in idx:
mz = mzs[i]
intensity = intensities[i]
purity = purities[i]
# stopping criteria is after we've fragmented N ions or we found ion < min_intensity
if fragmented_count >= current_N:
self.logger.debug(
'Time %f Top-%d ions have been selected' %
(self.mass_spec.time, current_N))
break
if intensity < self.min_ms1_intensity:
self.logger.debug(
'Time %f Minimum intensity threshold %f reached at %f, %d'
% (self.mass_spec.time, self.min_ms1_intensity,
intensity, fragmented_count))
break
# skip ion in the dynamic exclusion list of the mass spec
if self.mass_spec.is_excluded(mz, rt):
continue
if purity < self.purity_threshold:
purity_shift_amounts = [
self.purity_shift * (i - (self.n_purity_scans - 1) / 2)
for i in range(self.n_purity_scans)
]
for purity_idx in range(self.n_purity_scans):
# send a new ms2 scan parameter to the mass spec
dda_scan_params = ScanParameters()
dda_scan_params.set(ScanParameters.MS_LEVEL, 2)
dda_scan_params.set(ScanParameters.N, current_N)
# create precursor object, assume it's all singly charged
precursor_charge = +1 if (
self.mass_spec.ionisation_mode == POSITIVE) else -1
precursor = Precursor(
precursor_mz=mz,
precursor_intensity=intensity,
precursor_charge=precursor_charge,
precursor_scan_id=self.last_ms1_scan.scan_id)
mz_lower = mz + purity_shift_amounts[
purity_idx] - current_isolation_window # Da
mz_upper = mz + purity_shift_amounts[
purity_idx] + current_isolation_window # Da
isolation_windows = [[(mz_lower, mz_upper)]]
dda_scan_params.set(ScanParameters.ISOLATION_WINDOWS,
isolation_windows)
dda_scan_params.set(ScanParameters.PRECURSOR,
precursor)
# save dynamic exclusion parameters too
dda_scan_params.set(
ScanParameters.DYNAMIC_EXCLUSION_MZ_TOL,
current_mz_tol)
dda_scan_params.set(
ScanParameters.DYNAMIC_EXCLUSION_RT_TOL,
current_rt_tol)
# push this dda scan parameter to the mass spec queue
self.mass_spec.add_task(dda_scan_params)
fragmented_count += 1
# need to work out what we want to do here
else:
# send a new ms2 scan parameter to the mass spec
dda_scan_params = ScanParameters()
dda_scan_params.set(ScanParameters.MS_LEVEL, 2)
dda_scan_params.set(ScanParameters.N, current_N)
# create precursor object, assume it's all singly charged
precursor_charge = +1 if (self.mass_spec.ionisation_mode
== POSITIVE) else -1
precursor = Precursor(
precursor_mz=mz,
precursor_intensity=intensity,
precursor_charge=precursor_charge,
precursor_scan_id=self.last_ms1_scan.scan_id)
mz_lower = mz - current_isolation_window # Da
mz_upper = mz + current_isolation_window # Da
isolation_windows = [[(mz_lower, mz_upper)]]
dda_scan_params.set(ScanParameters.ISOLATION_WINDOWS,
isolation_windows)
dda_scan_params.set(ScanParameters.PRECURSOR, precursor)
# save dynamic exclusion parameters too
dda_scan_params.set(
ScanParameters.DYNAMIC_EXCLUSION_MZ_TOL,
current_mz_tol)
dda_scan_params.set(
ScanParameters.DYNAMIC_EXCLUSION_RT_TOL,
current_rt_tol)
# push this dda scan parameter to the mass spec queue
self.mass_spec.add_task(dda_scan_params)
fragmented_count += 1
for param in self.mass_spec.get_task_queue():
precursor = param.get(ScanParameters.PRECURSOR)
if precursor is not None:
self.logger.debug('- %s' % str(precursor))
# set this ms1 scan as has been processed
self.last_ms1_scan = None
def _update_parameters(self, scan):
# if there's a previous ms1 scan to process
if self.last_ms1_scan is not None:
mzs = self.last_ms1_scan.mzs
intensities = self.last_ms1_scan.intensities
rt = self.last_ms1_scan.rt
# loop over points in decreasing intensity
fragmented_count = 0
idx = np.argsort(intensities)[::-1]
for i in idx:
mz = mzs[i]
intensity = intensities[i]
# stopping criteria is after we've fragmented N ions or we found ion < min_intensity
if fragmented_count >= self.N:
self.logger.debug(
'Time %f Top-%d ions have been selected' %
(self.mass_spec.time, self.N))
break
if intensity < self.min_ms1_intensity:
self.logger.debug(
'Time %f Minimum intensity threshold %f reached at %f, %d'
% (self.mass_spec.time, self.min_ms1_intensity,
intensity, fragmented_count))
break
# skip ion in the dynamic exclusion list of the mass spec
if self.mass_spec.is_excluded(mz, rt):
continue
# send a new ms2 scan parameter to the mass spec
dda_scan_params = ScanParameters()
dda_scan_params.set(ScanParameters.MS_LEVEL, 2)
# create precursor object, assume it's all singly charged
precursor_charge = +1 if (self.mass_spec.ionisation_mode
== POSITIVE) else -1
precursor = Precursor(
precursor_mz=mz,
precursor_intensity=intensity,
precursor_charge=precursor_charge,
precursor_scan_id=self.last_ms1_scan.scan_id)
mz_lower = mz - self.isolation_window # Da
mz_upper = mz + self.isolation_window # Da
isolation_windows = [[(mz_lower, mz_upper)]]
dda_scan_params.set(ScanParameters.ISOLATION_WINDOWS,
isolation_windows)
dda_scan_params.set(ScanParameters.PRECURSOR, precursor)
# save dynamic exclusion parameters too
dda_scan_params.set(ScanParameters.DYNAMIC_EXCLUSION_MZ_TOL,
self.mz_tol)
dda_scan_params.set(ScanParameters.DYNAMIC_EXCLUSION_RT_TOL,
self.rt_tol)
# push this dda scan parameter to the mass spec queue
self.mass_spec.add_task(dda_scan_params)
fragmented_count += 1
for param in self.mass_spec.get_task_queue():
precursor = param.get(ScanParameters.PRECURSOR)
if precursor is not None:
self.logger.debug('- %s' % str(precursor))
# set this ms1 scan as has been processed
self.last_ms1_scan = None