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ModLS specifications


Unique identifier OMICS_20949
Name ModLS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline David Trudgian

Publication for ModLS

ModLS citations


A positive feedback loop between Gli1 and tyrosine kinase Hck amplifies shh signaling activities in medulloblastoma

PMCID: 4670963
PMID: 26619401
DOI: 10.1038/oncsis.2015.38

[…] algorithm (OMSSA) search engines against the mouse protein database from Uniprot, 23 Gli1 peptides were identified, which covers 26.3% of the Gli1 protein. Phosphorylation sites were localized using ModLS PTM Localization and confirmed by manual interpretation. […]


Comprehensive identification of arginine methylation in primary T cells reveals regulatory roles in cell signalling

Nat Commun
PMCID: 4396391
PMID: 25849564
DOI: 10.1038/ncomms7758

[…] ginine, heavy dimethylarginine were set as variable modifications. Precursor mass tolerance was 20 p.p.m., fragment mass tolerance was 0.1 Da. Localization of arginine methylation was performed using ModLS. A maximum of three mis-cleavages were allowed for tryptic specificity, two mis-cleavages were allowed for chymotrypsin and GluC. FDR was set to 5% at the peptide level and results filtered for […]


Mapping the Phosphoproteome of Influenza A and B Viruses by Mass Spectrometry

PLoS Pathog
PMCID: 3493474
PMID: 23144613
DOI: 10.1371/journal.ppat.1002993

[…] es may not always assign phosphorylation at the site that is most probable given the spectral evidence, since their emphasis is on peptide identification rather than phosphorylation localisation. The ModLS algorithm re-assigns phosphorylation sites when the search-engine reported assignment is a poorer fit to the spectral evidence than an alternative localisation. PTMScores are calculated as previ […]


A Method for Large scale Identification of Protein Arginine Methylation*

PMCID: 3494207
PMID: 22865923
DOI: 10.1074/mcp.M112.020743

[…] of a methylSILAC pair to corroborate each methylated peptide increases confidence and enables even low scoring peptides to be considered (). Modification localization scoring was performed using the ModLS algorithm (unpublished) which extends the PTMScore method to incorporate automatic specificity expansion. For each variable modification chosen for the database search all amino acid specificiti […]


Labile disulfide bonds are common at the leucocyte cell surface

Open Biol
PMCID: 3352085
PMID: 22645650
DOI: 10.1098/rsob.110010

[…] e estimates of the relative protein abundance between reduced and control samples. Localization of chemical modifications, when more than one Cys was present in a peptide, was determined by running a ModLS localization algorithm within the CPFP [].Protein identifications were exported from the CPFP and uploaded to ProteinCenter (v. 3.7.10003, Proxeon) for filtering, comparison, annotation, classif […]


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ModLS institution(s)
Proteomics Core, Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA; Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
ModLS funding source(s)
Supported by ERC FP7 grant (project 233240), Cancer Prevention Research Institute of Texas award RP120613, UT Southwestern Medical Center at Dallas.

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