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Welcome to the lucXor wiki!
The LucXor is a Java Application developed by Alexey Nesvizhskii Lab to enable site localization for generic post-translational modifications (PTMs) using tandem mass spectrometry data.
LucXor introduces a novel scoring approach that utilizes both peak intensity and mass accuracy to aid the computation of an objective score for phosphosite determination and dynamically adapts to characteristic peak properties in different types of instrumentation and fragmentation methods. It computes the scores for phosphosite permutations and associated FLR estimates for the best scoring prediction at the peptide level. It also reports site-level scores for multi-phosphorylated peptides, with an acknowledgment that it is difficult to rigorously estimate the FLR in such cases.
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Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI. LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol Cell Proteomics. 2013;12(11):3409‐3419. doi:10.1074/mcp.M113.028928
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Damian Fermin, Dmitry Avtonomov, Hyungwon Choi, Alexey I. Nesvizhskii, LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data, Bioinformatics, Volume 31, Issue 7, 1 April 2015, Pages 1141–1143, https://doi.org/10.1093/bioinformatics/btu788