Xilmass

Xilmass identifies cross-linked peptides from chemical cross-linking coupled with mass spectrometry (MS) data to map protein–protein interactions and support structural analyses such as cryo-electron microscopy (cryo-EM).

Key Features:

• Explicit encoding of cross-linking sites: Represents cross-linked peptide entries in the search database with explicit encoding of cross-linking sites to enable precise identification of linked residues.
• Adapted scoring function: Employs an Andromeda-derived scoring function adapted to evaluate theoretical tandem mass spectrometry (MS/MS) spectra including peaks from all possible fragment ions of a cross-linked peptide pair.
• Distinct and predicted site identification: Identifies both distinct and predicted cross-linked sites in analyzed datasets.

Scientific Applications:

• Protein–protein interaction mapping: Maps protein–protein interactions, including weak and transient contacts, to inform studies of cellular mechanisms.
• Complement to structural determination: Provides cross-linking evidence to complement structural determination methods such as cryo-electron microscopy (cryo-EM).

Methodology:

Represents cross-linked peptides with explicit encoding in the search database; uses an Andromeda-derived scoring function to evaluate theoretical MS/MS spectra including all possible fragment ions; and was evaluated against Kojak and pLink using a calmodulin-plectin complex dataset and three additional published datasets.