Working with metabolomics results#

MODOS supports mzTab 2.0-M files to represent mass spectrometry results from metabolomics.

These files can be added to an existing MODO and some metadata can be extracted automatically.

Including a file#

mztab files can be embedded like any other file into the digital object:

python

from modos.api import MODO
import modos_schema.datamodel as model

# Load modo (see above)
modo = MODO(path = "data/ex")

# Generate a data element
data = model.DataEntity(id="metabo_MS1", name= "Metabo MS1", description = "Some mass spectrometry results", data_format="mzTab", data_path = "metabo_ms1.mztab")

# Add element to modo
modo.add_element(element = data, source_file="path/to/source.mztab")

cli

modos add --source-file path/to/source.mztab data/ex data

Extracting metadata#

Once the mzTab file is included, some of its metadata can be extracted to enrich the MODOS metadata:

python

from modos.api import MODO

# Load modo (see above)
modo = MODO(path = "data/ex")
modo.enrich_metadata()

cli

modos enrich data/ex

This will check all files in the modos for metadata to be extracted. After running it, samples described in the mzTab files should be visible in the MODOS metadata, and can be viewed e.g. by running modos show –zarr.

Opening mzTab files#

pyteomics ofter an intuitive API to work with mzTab files, however it only works with local files. If the MODO is local, the mzTab can be opened directly with pyteomics. Otherwise, it must be downloaded first:

from modos.api import MODO
from pyteomics.mztab import MzTab

# if the modo is local
mz = MzTab('data/ex/metabo_ms1.mztab')

# if remote

modo = MODO('s3://example/modo')
with open("local.mztab", "w") as mz_handle:
  for line in modo.storage.open("metabo_ms1.mztab"):
      mz_handle.write(line)

mz = MzTab("local.mztab")