Bruker mass spectrum data import

bruker-mass-spectrum-data-import

Summary

Load and initialize Bruker Solarix FT-ICR mass spectrometry raw data (.d format) into CoreMS data structures, preparing transient or magnitude-mode spectra for subsequent noise thresholding, peak picking, and molecular formula assignment.

When to use

You have received a Bruker Solarix FT-ICR raw data directory (.d format, containing CompassXtract output or native ser/fid transients) and need to import it into a Python-based analysis workflow for FT-MS signal processing, calibration, or molecular formula search. This skill is the mandatory first step when working with Bruker instrument output.

When NOT to use

• Input is already a centroid mass list (CSV, Excel, or mzML) — use a generic mass list importer instead.
• Input is from a different vendor (Thermo, Spectroswiss, MagLab) — use vendor-specific readers.
• The .d directory is corrupted or missing mandatory calibration metadata — validate file integrity first.

Inputs

• Bruker Solarix .d directory (containing ser, fid, or CompassXtract output files)
• MSParameters object with field-strength calibration constants

Outputs

• CoreMS MassSpectrum object with m/z, intensity, and metadata
• Transient or magnitude-mode frequency-domain spectrum ready for noise and peak processing

How to apply

Use CoreMS ReadBrukerSolarix to load the .d directory into a CoreMS mass spectrum object. Initialize MSParameters with field-strength-specific settings (e.g., 12 T or 15 T magnetic field calibration constants). Set noise thresholding method (relative_abundance, log, or signal_noise) and peak prominence thresholds (e.g., peak_min_prominence_percent = 1, noise_threshold_min_relative_abundance = 1) according to instrument resolution and expected dynamic range. The importer automatically handles FT magnitude-mode conversion and transient metadata extraction. Verify that m/z range, resolving power, and baseline noise floor are consistent with acquisition parameters before proceeding to peak picking.

Related tools

• CoreMS (Provides ReadBrukerSolarix importer and MassSpectrum data structure for Bruker .d file parsing and FT-ICR metadata extraction) — https://github.com/EMSL-Computing/CoreMS
• Bruker Solarix (Source instrument and data acquisition platform generating .d directories with ser/fid transient or CompassXtract processed spectra)

Examples

from corems.transient.input.brukerSolarix import ReadBrukerSolarix; ms = ReadBrukerSolarix('path/to/sample.d'); print(ms.number_of_peaks, ms.resolving_power_calculator())

Evaluation signals

• MassSpectrum object is non-null and contains non-zero intensity array with matching m/z length.
• Metadata fields (scan_number, rt, polarity, resolving_power, field_strength) are populated and consistent with acquisition header.
• m/z range and mass resolution match Bruker instrument specifications (e.g., 50–1000 m/z at >100k resolving power for 12 T).
• Intensity baseline and dynamic range are appropriate for FT magnitude mode (no truncation or overflow).
• No exceptions or file-read errors are raised; ReadBrukerSolarix completes without timeout.

Limitations

• Only FT magnitude mode is supported; phase-corrected time-domain data requires external preprocessing.
• CompassXtract output may lose transient metadata; ser/fid native import is more reliable for advanced signal processing.
• Bruker proprietary binary formats are reverse-engineered; future CompassXtract versions may cause read failures.
• Import performance degrades for very large transients (>1 GB); streaming mode not yet available.

Evidence

• [other] Load the recalibrated FT-ICR mass spectrum data file (Bruker .d format) using CoreMS ReadBrukerSolarix.: "Load the recalibrated FT-ICR mass spectrum data file (Bruker .d format) using CoreMS ReadBrukerSolarix."
• [other] Import and process transient data is step 1 in FT-MS workflow.: "1. Import and process transient data"
• [readme] CoreMS supports direct access for almost all vendors' data formats.: "CoreMS supports direct access for almost all vendors' data formats"
• [readme] Bruker Solarix transients, ser and fid (FT magnitude mode only) are supported input formats.: "Bruker Solarix transients, ser and fid (FT magnitude mode only)"
• [other] Initialize mass spectrum parameters for a 12 T field-strength instrument, setting noise thresholding method.: "Initialize mass spectrum parameters for a 12 T field-strength instrument, setting noise thresholding method (e.g., relative_abundance or log) and peak prominence thresholds."