Exporting Crosslink-Spectrum-Matches to xiFDR

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

    Installed pyXLMS version: 1.5.3

from pyXLMS import parser
from pyXLMS import exporter

All exporting functionality is available via the exporter submodule. We also import the parser submodule to read crosslink-spectrum-matches and crosslinks.

parser_result = parser.read(
    "../../data/ms_annika/XLpeplib_Beveridge_QEx-HFX_DSS_R1_CSMs.txt",
    engine="MS Annika",
    crosslinker="DSS",
)
csms = parser_result["crosslink-spectrum-matches"]

    Reading MS Annika CSMs...: 100%|█████████████████████████████████████████████████████████████████████████████████| 826/826 [00:00<00:00, 6353.79it/s]

We read crosslink-spectrum-matches using the generic parser  from a single MS Annika .txt file. For easier access we also assign our crosslink-spectrum-matches to the variable csms.

_df = exporter.to_xifdr(csms, filename=None)

The function exporter.to_xifdr() exports a list of crosslink-spectrum-matches to xiFDR  format for external validation. The tool xiFDR is accessible via the link rappsilberlab.org/software/xifdr . The to_xifdr() function requires that alpha_proteins, beta_proteins, alpha_proteins_peptide_positions, beta_proteins_peptide_positions, alpha_decoy, beta_decoy, charge and score fields are set for all crosslink-spectrum-matches. You can read more about the to_xifdr() function and all its parameters here: docs.