OpenPepXL: An open-source tool for sensitive identification of cross-linked peptides in XL-MS.

OpenPepXL: An open-source tool for sensitive identification of cross-linked peptides in XL-MS.
Mol Cell Proteomics. 2020 Oct 16;:
Authors: Netz E, Dijkstra TMH, Sachsenberg T, Zimmermann L, Walzer M, Monecke T, Ficner R, Dybkov O, Urlaub H, Kohlbacher O
Abstract
Cross-linking mass spectrometry (XL-MS) has been recognized as an effective source of information about protein structures and interactions. In contrast to regular peptide identification, XL-MS has to deal with a quadratic search space, where peptides from every protein could potentially be cross-linked to any other protein. To cope with this search space, most tools apply different heuristics for search space reduction. We introduce a new open-source XL-MS database search algorithm, OpenPepXL, which offers increased sensitivity compared to other tools. OpenPepXL searches the full search space of an XL-MS experiment without using heuristics to reduce it. Due to efficient data structures and built-in parallelization OpenPepXL achieves excellent runtimes and can also be deployed on large compute clusters and cloud services while maintaining a slim memory footprint. We compared OpenPepXL to several other commonly used tools for identification of non-cleavable labeled and label-free cross-linkers on a diverse set of XL-MS experiments. In our first comparison, we used a dataset from a fraction of a cell lysate with a protein database of 128 targets and 128 decoys. At 5% FDR, OpenP...

Source: Molecular and Cellular Proteomics : MCP - October 16, 2020 Category: Molecular Biology Authors: Netz E, Dijkstra TMH, Sachsenberg T, Zimmermann L, Walzer M, Monecke T, Ficner R, Dybkov O, Urlaub H, Kohlbacher O Tags: Mol Cell Proteomics Source Type: research