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LuciPHOr specifications


Unique identifier OMICS_06809
Name LuciPHOr
Alternative name LuciPHOr2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes


No version available


  • person_outline Alexey Nesvizhskii <>
  • person_outline Hyungwon Choi <>

Publications for LuciPHOr

LuciPHOr citations


Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines

PMCID: 5747350
PMID: 29226804
DOI: 10.1016/j.cels.2017.11.002

[…] as a variable modification was added. a 0.01 iprophet-peptide fdr cutoff was used to control for false identifications. for each annotated spectra a false localization score was calculated using luciphor2 () and annotations with a false localization rate (flr) of lower than 0.01 are annotated as localized phosphopeptides (localized modification is depicted in protein name, see ). […]


Inference and quantification of peptidoforms in large sample cohorts by SWATH MS

PMCID: 5593115
PMID: 28604659
DOI: 10.1038/nbt.3908

[…] was smaller., we further used the results of the dia-umpire analysis to benchmark the site-localization component of ipf against established methods for spectrum-centric site-localization (, ). luciphor, is a recently developed algorithm for site localization. in addition to site-localization it also estimates the false localization rate (flr). using a version of ipf reduced to the second, […]


Phosphoprotein network analysis of white adipose tissues unveils deregulated pathways in response to high fat diet

PMCID: 4867603
PMID: 27180971
DOI: 10.1038/srep25844

[…] the trans-proteomic pipeline (tpp) with the default option -opdaewt –drev –ppm., to perform semi-quantitation by spectral counting at individual phosphorylation sites, site localization algorithm luciphor was applied to the results with the following options: high mass accuracy option for model fitting; tpp peptideprophet probability 0.95 for feature learning in the positive set; ms2 […]


Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling

PMCID: 4790442
PMID: 26539879
DOI: 10.1021/acs.analchem.5b04123

[…] of search engines, which can improve correct localization by as much as 25.7% compared to using mascot alone., using mass accuracy and peak intensities, nesvizhskii and co-workers introduced luciphor to improve site localization and false localization rate (flr) estimation. this tool estimates flr based on a target-decoy framework, in which artificial phosphorylation is used to generate […]


Integrating phosphoproteomics in systems biology

PMCID: 4204398
PMID: 25349677
DOI: 10.1016/j.csbj.2014.07.003

[…] in different regions is different across each spectrum, and developed phosphors, which extends the a-score method by taking this into account ., more recently, nesvizhskii and colleagues developed luciphor, which uses mass accuracy (m/z) and peak intensities for phosphosite localization scoring . luciphor is based on the principle that the distribution of peak intensity and m/z for random […]

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LuciPHOr institution(s)
Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
LuciPHOr funding source(s)
Supported by Singapore MOE [grant R-608-000-088-112] and NIH [R01-GM-094231].

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