Reading mzIdentML Result Files

from pyXLMS import __version__
 
print(f"Installed pyXLMS version: {__version__}")

    Installed pyXLMS version: 1.5.1

from pyXLMS import parser
from pyXLMS import transform

All functionality to parse crosslink-spectrum-matches (CSMs) from mzIdentML  result files is available via the parser submodule. We also import the transform submodule to show some summary statistics of the read files.

Reading mzIdentML Result Files via parser.read()

parser_result = parser.read(
    "../../data/ms_annika/XLpeplib_Beveridge_QEx-HFX_DSS_R1.mzid",
    engine="mzIdentML",
    crosslinker="DSS",
)

    C:\Users\micha.birklbauer\AppData\Local\Programs\Python\Python312\Lib\site-packages\pyXLMS\parser\parser_xldbse_mzid.py:142: UserWarning: Please be aware that mzIdentML parsing is currently an experimental feature!
    Please check the documentation for parser.read_mzid for more information!
      warnings.warn(
    100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1353/1353 [00:00<00:00, 104076.83it/s]

We can read any mzIdentML result file using the parser.read() method and setting engine="mzIdentML". The method also requires us to specify the used crosslinker, in this case DSS was used (crosslinker="DSS"). You can read the documentation for the parser.read() method here: docs.

for k, v in parser_result.items():
    print(f"{k}: {type(v) if isinstance(v, list) else v}")

    data_type: parser_result
    completeness: partial
    search_engine: mzIdentML
    crosslink-spectrum-matches: <class 'list'>
    crosslinks: None

The parser.read() method returns a dictionary with a set of specified keys and their values. We refer to this dictionary as a parser_result object. All parser.read* methods return such a parser_result object, you can read more about that here: docs, and here: data types specification.

As you can see from the parser_result the mzIdentML result file contained CSMs. We would be able to access those via parser_result["crosslink-spectrum-matches"].

_ = transform.summary(parser_result)

    Number of CSMs: 786.0
    Number of unique CSMs: 786.0
    Number of intra CSMs: 0.0
    Number of inter CSMs: 786.0
    Number of target-target CSMs: 0.0
    Number of target-decoy CSMs: 0.0
    Number of decoy-decoy CSMs: 0.0
    Minimum CSM score: nan
    Maximum CSM score: nan

With the transform.summary() method we can also print out some summary statistics about our read CSMs. You can read more about the method here: docs.

sample_csm = parser_result["crosslink-spectrum-matches"][0]
for k, v in sample_csm.items():
    print(f"{k}: {v}")

    data_type: crosslink-spectrum-match
    completeness: partial
    alpha_peptide: GQKNSR
    alpha_modifications: None
    alpha_peptide_crosslink_position: 3
    alpha_proteins: None
    alpha_proteins_crosslink_positions: None
    alpha_proteins_peptide_positions: None
    alpha_score: None
    alpha_decoy: None
    beta_peptide: GQKNSR
    beta_modifications: None
    beta_peptide_crosslink_position: 3
    beta_proteins: None
    beta_proteins_crosslink_positions: None
    beta_proteins_peptide_positions: None
    beta_score: None
    beta_decoy: None
    crosslink_type: inter
    score: None
    spectrum_file: C:\Users\P42587\Documents\GitHub\pdresult_reader\study_folder\XLpeplib_Beveridge_QEx-HFX_DSS_R1.mzML
    scan_nr: 1
    charge: None
    retention_time: None
    ion_mobility: None
    additional_information: None

Here is an example CSM, you can learn more about the specific attributes and their values here: docs, and here: data types specification.

type(parser_result["crosslinks"])

    NoneType

In this example parser_result["crosslinks"] is None because the mzIdentML format does not report any crosslinks. Therefore, no crosslinks can be displayed here.

Reading mzIdentML Result Files via parser.read_mzid()

parser_result = parser.read_mzid(
    "../../data/ms_annika/XLpeplib_Beveridge_QEx-HFX_DSS_R1.mzid"
)

    C:\Users\micha.birklbauer\AppData\Local\Programs\Python\Python312\Lib\site-packages\pyXLMS\parser\parser_xldbse_mzid.py:142: UserWarning: Please be aware that mzIdentML parsing is currently an experimental feature!
    Please check the documentation for parser.read_mzid for more information!
      warnings.warn(
    100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1353/1353 [00:00<00:00, 87245.65it/s]

We can also read any mzIdentML result file using the parser.read_mzid() method which allows a more nuanced control over reading mzIdentML result files - even though theoretically everything can be done with the parser.read() function as well. You can read the documentation for the parser.read_mzid() method here: docs.

_ = transform.summary(parser_result)

    Number of CSMs: 786.0
    Number of unique CSMs: 786.0
    Number of intra CSMs: 0.0
    Number of inter CSMs: 786.0
    Number of target-target CSMs: 0.0
    Number of target-decoy CSMs: 0.0
    Number of decoy-decoy CSMs: 0.0
    Minimum CSM score: nan
    Maximum CSM score: nan

There are several other parameters that can be set, you can read more about them here: docs.