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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

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

[…] nine 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 ). Phosphopepti […]


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

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

[…] LuciPHOr, 2 (1.2014Oct10-iprophet) was modified to support iProphet posterior probabilities, required for DIA-Umpire pseudo spectra identifications. Static, variable and target residue modifiability w […]


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

Sci Rep
PMCID: 4867603
PMID: 27180971
DOI: 10.1038/srep25844

[…] 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 tolerance […]


Computational phosphoproteomics: From identification to localization

PMCID: 4384807
PMID: 25475148
DOI: 10.1002/pmic.201400372

[…] c acid, which correlate with serine and threonine, respectively, in the general context of these criteria [,].In 2013, Fermin and colleagues achieved a milestone in the field where they presented the LuciPHOr algorithm [], the first algorithm to include a formal FLR estimation. Using a synthetic set of phosphopeptides [], allowing the calculation of the true FLR, they demonstrate similar or superi […]


Integrating phosphoproteomics in systems biology

Comput Struct Biotechnol J
PMCID: 4204398
PMID: 25349677
DOI: 10.1016/j.csbj.2014.07.003

[…] eaks 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 peaks […]


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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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