BrukerTimsFile#

class pyopenms.BrukerTimsFile(*args, **kwargs)#

Bases: object

Reader for Bruker TimsTOF .d directories via opentims.

Supports DDA-PASEF, DIA-PASEF, and raw frame-level 4D access. Ion mobility data is stored in VSSC (1/K0) units using IM_PEAK format for MS1 and DIA MS2, and scalar drift times for DDA MS2.

This class is only available when OpenMS is built with WITH_OPENTIMS=ON (the default). The Bruker SDK (timsdata.dll / libtimsdata.so) is not bundled with pyOpenMS; supply it via the OPENMS_BRUKER_SDK_PATH environment variable or Config.bruker_sdk_path.

Use hasattr(pyopenms, "BrukerTimsFile") to feature-detect at runtime.

__init__(self) → None#

Attributes

`endProgress`	Ends the progress display
`getLogType`	Returns the type of progress log being used
`load`	Overloaded function.
`nextProgress`	Increment progress by 1 (according to range begin-end)
`readDIAMetadata`	Overloaded function.
`setLogType`	Sets the progress log that should be used.
`setProgress`	Sets the current progress
`startProgress`

class Config(*args, **kwargs)#

Bases: object

Processing and export configuration for BrukerTimsFile.load() and readDIAMetadata()

class CentroidAlgo(*values)#

Bases: Enum

GREEDY2D = 1#

HILL_BASED = 2#

OFF = 0#

class ExportMode(*values)#

Bases: Enum

AUTO = 0#

FRAME = 2#

SPECTRUM = 1#

class PressureCompensation(*values)#

Bases: Enum

GLOBAL = 1#

NONE = 0#

PER_FRAME = 2#

class TimsCalibrationStrategy(*values)#

Bases: Enum

AUTO = 0#

BRUKER_SDK = 1#

LINEAR = 3#

RATIONAL = 2#

property bruker_sdk_path#: Path to Bruker SDK library (empty = discover from OPENMS_BRUKER_SDK_PATH env var)

property calibrate#: Enable m/z recalibration (off by default; may fail on some datasets)

property calibration_tolerance#: m/z recalibration tolerance in Da (0 = default 0.1 Da)

property dia_ms2_centroid#: DIA MS2 2D peak picking: Gaussian smoothing + local maxima detection

property dia_ms2_min_support#: DIA MS2 denoising: minimum occupied neighbors in 3x3 (m/z x IM) grid

property dia_ms2_n_neighbors#: DIA MS2 frame aggregation: number of adjacent frames on each side (0 = disabled)

property export_mode#: AUTO detects DDA vs DIA; SPECTRUM forces per-precursor; FRAME returns raw 4D frames

property load_ms1#: Load MS1 spectra. Disable for MS2-only workflows.

property ms1_centroid_im_pct#: MS1 IM-centroiding ion mobility tolerance in percent (0 = disabled, suggested: 3.0)

property ms1_centroid_max_peaks#: Upper bound on centroided peaks per MS1 spectrum

property ms1_centroid_mz_ppm#: MS1 IM-centroiding m/z tolerance in ppm (0 = disabled, suggested: 5.0)

property ms1_max_rt_distance_sec#: Cap RT distance (s) between neighbor MS1 frame and center frame during aggregation (0 = no cap)

property ms1_min_support#: MS1 denoising after aggregation: min occupied 3x3 neighbors (0 = disabled)

property ms1_n_neighbors#: MS1 frame aggregation: adjacent MS1 frames on each side (0 = disabled)

property ms2_centroid_algo#: MS2 centroiding algorithm for DIA-PASEF and DDA-PASEF

property pressure_compensation#: Pressure compensation strategy (only effective with BRUKER_SDK calibration)

property tims_calibration_strategy#: Strategy for converting TIMS scan indices to 1/K0 values

class DIAStreamingMetadata(*args, **kwargs)#

Bases: object

Metadata describing DIA SWATH layout for streaming consumers

property boundaries#: One SwathMap per DIA window (MS2 only)

property nr_ms1_spectra#: Number of MS1 frames

property nr_ms2_spectra#: Per-window spectrum counts (parallel to boundaries)

endProgress#: Ends the progress display

getLogType#: Returns the type of progress log being used

load#

Overloaded function.

load(self, path: str) -> pyopenms._pyopenms_experiment.MSExperiment

Load a .d directory into a new MSExperiment using default configuration

load(self, path: str, config: pyopenms._pyopenms_format.BrukerTimsFile.Config) -> pyopenms._pyopenms_experiment.MSExperiment

Load a .d directory into a new MSExperiment with explicit configuration

nextProgress#: Increment progress by 1 (according to range begin-end)

readDIAMetadata#

Overloaded function.

readDIAMetadata(self, path: str) -> tuple

Read DIA SWATH boundaries and spectrum counts (no peak data). Returns (DIAStreamingMetadata, ExperimentalSettings).

readDIAMetadata(self, path: str, config: pyopenms._pyopenms_format.BrukerTimsFile.Config) -> tuple

Read DIA SWATH boundaries and spectrum counts with explicit configuration. Returns (DIAStreamingMetadata, ExperimentalSettings).

setLogType#: Sets the progress log that should be used. The default type is NONE!

setProgress#: Sets the current progress

startProgress#