Mass spectrometry data matrix construction

mass-spectrometry-data-matrix-construction

Summary

Parse mass spectrometry intensities and m/z values from binary imzML files and organize them into a feature matrix where m/z values form columns (variables) and spatial coordinates form rows (observations), then encapsulate into an AnnData object for downstream metabolomic analysis.

When to use

You have raw spatial metabolomics imzML files (paired with .ibd binary data files) that need to be loaded into a unified AnnData format for integration with spatial transcriptomics data or for cross-modal spatial pattern identification in single or multiple sample datasets.

When NOT to use

• Input is already in CSV or tabular format (use read_sm_csv_as_anndata instead)
• Data lacks spatial coordinates or spot identifiers
• Binary data file (.ibd) is missing or corrupted

Inputs

• imzML file (spatial metabolomics metadata file)
• ibd file (ion binary data file, paired with imzML)

Outputs

• AnnData object with intensity matrix in .X, m/z values in .var, spatial coordinates in .obs

How to apply

Use spatialmeta.pp.read_sm_imzml_as_anndata to simultaneously parse the imzML XML metadata and accompanying .ibd (ion binary data) file. Extract mass spectrometry intensities and their corresponding m/z values from the binary format, organizing intensities into a feature matrix with observations indexed by spatial coordinates (x, y positions) and variables indexed by m/z ratios. Construct an AnnData object with the intensity matrix in the .X slot, m/z values stored in .var (variable metadata), spatial coordinates and spot identifiers in .obs (observation metadata), ensuring consistent indexing and data types. This structured format enables subsequent alignment to a unified resolution with spatial transcriptomics data and cross-modal pattern discovery.

Related tools

• spatialMETA (Provides read_sm_imzml_as_anndata preprocessing function for loading and parsing imzML files into AnnData objects) — https://github.com/WanluLiuLab/SpatialMETA

Examples

from spatialmeta.pp import read_sm_imzml_as_anndata; adata_sm = read_sm_imzml_as_anndata('sample.imzML')

Evaluation signals

• AnnData .X matrix has shape (n_spots, n_mz_features) with non-negative intensity values
• .var index contains unique m/z values sorted in ascending order
• .obs index contains spatial coordinates (x, y) and spot identifiers with no missing values
• Data types are consistent: intensities as float/int, m/z as float, coordinates as numeric
• No NaN or infinite values in intensity matrix; m/z values fall within expected mass range (e.g., 50–2000 m/z for typical spatial metabolomics)

Limitations

• Requires both imzML and .ibd files to be present and correctly paired; missing or corrupted binary data will cause parsing failure
• Performance depends on file size; very large imzML datasets may require substantial memory for full matrix construction
• m/z alignment across samples requires subsequent use of get_mz_reference or manual harmonization to handle mass shift or calibration drift

Evidence

• [other] Load the imzML file and its accompanying ibd (ion binary data) file using the read_sm_imzml_as_anndata function from spatialMETA preprocessing module.: "Load the imzML file and its accompanying ibd (ion binary data) file using the read_sm_imzml_as_anndata function from spatialMETA preprocessing module"
• [other] Parse mass spectrometry intensities and m/z values from the binary format, organizing them into a feature matrix with m/z as columns (variables) and spatial coordinates as rows (observations).: "Parse mass spectrometry intensities and m/z values from the binary format, organizing them into a feature matrix with m/z as columns (variables) and spatial coordinates as rows (observations)"
• [other] Construct an AnnData object with the intensity matrix in the .X slot, m/z values stored in .var, spatial coordinates and spot identifiers in .obs, and return the formatted object for downstream metabolomic analysis.: "Construct an AnnData object with the intensity matrix in the .X slot, m/z values stored in .var, spatial coordinates and spot identifiers in .obs, and return the formatted object for downstream"
• [readme] spatialMETA is a method for integrating spatial multi-omics data. SMOI aligns ST and SM to a unified resolution: "spatialMETA is a method for integrating spatial multi-omics data. SMOI aligns ST and SM to a unified resolution"
• [other] spatialmeta.pp.read_sm_imzml_as_anndata: "spatialmeta.pp.read_sm_imzml_as_anndata"