Open source mass spectrometry file format interoperability

Open-source mass spectrometry file format interoperability

Summary

Enable conversion and interoperability between proprietary Bruker .baf/.d mass spectrometry imaging formats and open standards (mzML) using pyBaf2Sql or ProteoWizard MSConvert. This skill bridges vendor lock-in and prepares raw instrument data for downstream processing in MSIGen and other open-source platforms.

When to use

When working with Bruker .d/.baf mass spectrometry imaging data and needing to feed it into MSIGen or other open-source MSI processing pipelines. Specifically, when your input is raw Bruker binary data and your analysis goal requires conversion to a portable, open format (mzML) or direct programmatic access via Python.

When NOT to use

• Input is already in an open format such as mzML, mzXML, or netCDF — conversion is unnecessary and introduces potential data loss.
• Data is from a non-Bruker vendor (e.g., Thermo, Waters, SCIEX) — pyBaf2Sql and this workflow are Bruker-specific.
• The Bruker .d folder is corrupted or missing the .baf file — conversion will fail or produce incomplete spectra.

Inputs

• Bruker .d folder (directory containing proprietary mass spectrometry imaging data)
• Bruker .baf binary file (raw binary spectra data within .d folder)
• Ion mobility mass spectrometry data (optional, if acquired in TIMS mode)

Outputs

• mzML file (standardized, portable XML-based mass spectrometry data format)
• NumPy array or Pandas DataFrame with m/z and intensity columns (from pyBaf2Sql)
• Metadata-enriched data structure readable by MSIGen msigen() function

How to apply

Install either pyBaf2Sql (via pip install git+https://github.com/gtluu/pyBaf2Sql with Python >=3.9 and <=3.11) or ProteoWizard MSConvert GUI for format conversion. For pyBaf2Sql: load the Bruker .d folder into a BafData object, iterate through spectra frames, and extract m/z and intensity arrays as NumPy arrays or DataFrames. For MSConvert: open the GUI, select Bruker .d/.baf input file(s), set output format to 'mzML', specify an output directory, and execute conversion. Verify that the output file (converted .mzML or pyBaf2Sql-processed data) contains expected mass spectrometry metadata (m/z values, intensity arrays, and ion mobility if applicable) before passing the file path to MSIGen's msigen() function with the example_file parameter.

Related tools

• pyBaf2Sql (Programmatic Python wrapper for Bruker Baf2Sql data access library; extracts m/z, intensity, and metadata from .baf files into NumPy arrays or Pandas DataFrames.) — https://github.com/gtluu/pyBaf2Sql
• ProteoWizard MSConvert (GUI-based vendor-neutral mass spectrometry data converter; converts Bruker .d/.baf to mzML format.) — https://proteowizard.sourceforge.io/download.html
• MSIGen (Downstream consumer tool; accepts converted .mzML or pyBaf2Sql-processed data via msigen() function for mass spectrometry imaging visualization.) — https://github.com/LabLaskin/MSIGen
• Python (Runtime environment; required version >=3.9 and <=3.11 for pyBaf2Sql and MSIGen compatibility.)
• Anaconda/Miniconda (Virtual environment manager; recommended for isolating pyBaf2Sql and MSIGen dependencies.) — https://www.anaconda.com/download

Examples

pip install git+https://github.com/gtluu/pyBaf2Sql && python -c "from pyBaf2Sql.init_baf2sql import init_baf2sql_api; from pyBaf2Sql.classes import BafData; dll = init_baf2sql_api(); data = BafData(bruker_d_folder_name='sample.d', baf2sql=dll); print(f'Loaded {data.analysis[\"Spectra\"].shape[0]} spectra')"

Evaluation signals

• Converted .mzML file is readable by MSIGen without errors; verify using MSIGen's msigen().get_image_data(verbose=True) and check for successful NumPy array (pixels.npy) and metadata JSON output.
• Mass spectrometry metadata is present and consistent: m/z arrays match expected mass ranges for the experiment, intensity values are non-negative, and metadata JSON contains expected fields (scan count, polarity, mass analyzer type).
• pyBaf2Sql extraction produces non-empty Pandas DataFrames for each spectrum frame with m/z and intensity columns; verify no NaN or infinite values introduced during conversion.
• Ion mobility values (if TIMS-acquired data) are preserved and fall within expected ranges; check metadata for 'mobility' or 'CCS' columns.
• File size and spectrum count of converted data match or are proportional to the original Bruker .d folder; unexpectedly small output files may indicate truncated or failed conversion.

Limitations

• pyBaf2Sql requires Python 3.9–3.11; later Python versions (≥3.12) are not supported and will cause installation or runtime failures.
• Bruker .d data must be in .baf format; older or alternative Bruker formats (.ms, .ser) are not supported by pyBaf2Sql.
• ProteoWizard MSConvert is a GUI tool and requires manual file selection and parameter specification; it is less suitable for batch processing than pyBaf2Sql but is easier for single-file conversion.
• No changelog was available in the source materials; version compatibility and breaking changes between pyBaf2Sql and MSIGen versions are not documented.
• Ion mobility data preservation depends on the instrument acquisition mode (TIMS vs. non-TIMS); standard mzML conversion may not fully capture all Bruker-proprietary ion mobility metadata.

Evidence

• [readme] If you are planning on using Bruker .d data in the .baf format, you will also need to install pyBaf2Sql from GitHub: "If you are planning on using Bruker .d data in the .baf format, you will also need to install pyBaf2Sql from GitHub"
• [other] Install pyBaf2Sql from GitHub as a prerequisite dependency before feeding data into MSIGen conversion.: "Install pyBaf2Sql from GitHub as a prerequisite dependency before feeding data into MSIGen conversion."
• [methods] Using an environment with python version >=3.9 and <=3.11: "Using an environment with python version >=3.9 and <=3.11"
• [other] If using MSConvert, open the MSConvert GUI, select Bruker .d/.baf input file(s) via 'Add Files', set output format to 'mzML', specify output directory, and click 'Start' to convert.: "If using MSConvert, open the MSConvert GUI, select Bruker .d/.baf input file(s) via 'Add Files', set output format to 'mzML', specify output directory, and click 'Start' to convert."
• [other] Verify converted .mzML file or pyBaf2Sql-processed data is readable and contains expected mass spectrometry metadata (m/z, intensity, mobility if applicable).: "Verify converted .mzML file or pyBaf2Sql-processed data is readable and contains expected mass spectrometry metadata (m/z, intensity, mobility if applicable)."
• [other] Pass the prepared file path to MSIGen's msigen() function with example_file parameter pointing to the converted .mzML or processed .baf data: "Pass the prepared file path to MSIGen's msigen() function with example_file parameter pointing to the converted .mzML or processed .baf data"
• [readme] Get all spectra from a BAF file as a list of pd.DataFrames with columns for m/z and intensity in centroid mode.: "Get all spectra from a BAF file as a list of pd.DataFrames with columns for m/z and intensity in centroid mode."