Version Compatibility

Reference examples tested with: MSnbase 2.28+, pandas 2.2+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Mass Spectrometry Data Import

"Load my mass spec data into Python" → Parse mzML/mzXML raw files or MaxQuant proteinGroups.txt into data structures for programmatic access and downstream analysis.

• Python: pyopenms.MzMLFile().load() for raw spectra, pandas.read_csv() for search engine outputs
• R: MSnbase::readMSData() for raw, read.delim() for MaxQuant/Proteome Discoverer

Loading mzML/mzXML Files with pyOpenMS

Goal: Parse raw mass spectrometry data files into memory for programmatic access.

Approach: Load mzML/mzXML into an MSExperiment object, then iterate spectra by MS level to access peaks and precursor info.

from pyopenms import MSExperiment, MzMLFile, MzXMLFile

exp = MSExperiment()
MzMLFile().load('sample.mzML', exp)

for spectrum in exp:
    if spectrum.getMSLevel() == 1:
        mz, intensity = spectrum.get_peaks()
    elif spectrum.getMSLevel() == 2:
        precursor = spectrum.getPrecursors()[0]
        precursor_mz = precursor.getMZ()

Loading MaxQuant Output

Goal: Import MaxQuant proteinGroups.txt with contaminant and decoy filtering.

Approach: Read the TSV file, remove reverse hits, contaminants, and site-only identifications, then extract intensity columns.