OpenPepXL

OpenPepXL identifies protein–protein cross-linked peptides from cross-linking mass spectrometry (XL-MS) data to improve detection of cross-linked residue pairs for structural and interaction studies, supporting uncleavable labeled and label-free cross-linkers but not cleavable cross-linkers.

Key Features:

• Full quadratic search-space exploration: Searches the entire quadratic search space without heuristic reductions for exhaustive cross-link identification.
• Cross-linker support: Tailored for uncleavable labeled and label-free cross-linkers and does not support cleavable cross-linkers.
• Efficient data structures and parallelization: Leverages efficient data structures and built-in parallelization to achieve low memory footprint and fast runtimes.
• Implementation and integration: Implemented in C++ as part of the OpenMS suite.
• Standardized output: Supports the MzIdentML 1.2 format for XL-MS identification results.
• Increased sensitivity: Identifies from 7% to over 50% more unique residue pairs (URPs) at 5% FDR compared to other tools.
• Improved structural validation: Reports from 7% to over 40% more structurally validated URPs and at least 12% more validated URPs on synthetic peptide datasets versus other tools.

Scientific Applications:

• Cross-link identification in XL-MS datasets: Detection of cross-linked peptides and residue pairs in XL-MS experiments.
• Protein–protein interaction mapping: Mapping interaction sites and residue contacts between proteins.
• Structural model validation: Validating high-resolution structural models using cross-link-derived distance constraints.
• Benchmarking and method evaluation: Objective validation and benchmarking of cross-link identification using synthetic peptide datasets.

Methodology:

Searches the full quadratic search space without heuristic reductions; uses efficient data structures and built-in parallelization to minimize runtime and memory; implemented in C++ within the OpenMS suite; outputs results in MzIdentML 1.2 and is tailored for uncleavable labeled and label-free cross-linkers.