MS Annika

MS Annika identifies cross-linked peptides in mass spectrometry spectra to enable analysis of protein structures and interactions using cleavable and non-cleavable crosslinkers.

Key Features:

• Versatility with Crosslinkers: Supports cleavable crosslinkers to reduce search space for proteome-wide studies and handles non-cleavable crosslinks using an algorithm based on sparse matrix multiplication.
• Advanced Search Algorithms: Implements a scoring function for peptides identified across multiple MS stages (MS2-MS3) and enables proteome-wide searches with non-cleavable crosslinks.
• Robust FDR Control: Estimates false discovery rates using a target-decoy approach to provide realistic FDR estimates without arbitrary score cutoffs.
• Performance and Efficiency: Optimized for fast, parallelized processing for large-scale proteome-wide studies and reported to detect more true unique cross-links than XlinkX and MaXLinker in comparative evaluations.
• Visualization Capabilities: Maps identified cross-links onto protein 3D structures to support structural analysis of proteins and complexes.

Scientific Applications:

• Protein-protein interaction mapping: Identification of protein-protein interactions and generation of structural insights into proteins and complexes.
• Discovery of novel interactions: Applied to uncover previously unknown interactions, for example within the Box C/D complex in C. elegans nuclei samples.
• Crosslinking mass spectrometry workflows: Support for both cleavable and non-cleavable crosslinks enables application across diverse XL-MS experimental approaches.

Methodology:

Built upon MS Amanda; uses a sparse matrix multiplication algorithm for non-cleavable crosslinks; applies a scoring function for peptides identified across MS2–MS3 stages; employs a target-decoy approach for FDR estimation; and includes optimizations for fast, parallelized processing.