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MASCOT specifications


Unique identifier OMICS_29483
Alternative name Marginal Approximation of the Structured COalescenT
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes




No version available


  • person_outline Nicola Muller <>
  • person_outline Tanja Stadler <>

Additional information

Publication for Marginal Approximation of the Structured COalescenT

MASCOT citations


MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] for the ltq and 106 ions for a full ftms scan. intact peptides were detected in the orbitrap velos at 60,000 resolution at m/z 400., for protein identification, raw ms data files were converted into mascot generic format (.mgf) files and searched against the human swissprot protein database (v. 2013.01) using the two search engines mascot (v2.3.02, matrixscience, london, uk) and phenyx (v2.6, […]


Smooth muscle like Ca2+ regulation of actin–myosin interaction in adult jellyfish striated muscle

PMCID: 5958069
PMID: 29773804
DOI: 10.1038/s41598-018-24817-x

[…] native actomyosin fraction prepared from the striated myoepithelium of adult moon jelly. eight major protein bands were identified by in-gel protease digestion, followed by mass spectrometry and a mascot search of the aurelia transcriptome database constructed by fuchs et al. (data set ‘db454_aaur_rc_final_contigs’ was downloaded from […]


Possible role of the Nipah virus V protein in the regulation of the interferon beta induction by interacting with UBX domain containing protein1

PMCID: 5955904
PMID: 29769705
DOI: 10.1038/s41598-018-25815-9

[…] were extracted with 5% (v/v) formic acid and acetonitrile, and analyzed with nanoscale liquid chromatography electrospray tandem mass spectrometry. the detected peptides were analyzed with the mascot search engine., escherichia coli strain bl21 was transformed with the vector expressing gst-tagged ubxn1, and the expression of the recombinant protein was induced with 1 mm isopropyl […]


Plasma proteins associated with circulating carotenoids in Nepalese school aged children☆

PMCID: 5937903
PMID: 29605494
DOI: 10.1016/

[…] by strong cation exchange (scx) chromatography and analyzed on a ltq orbitrap velos mass spectrometer (thermo scientific). ms/ms spectra were searched against the refseq 40 database using mascot (matrix science) through proteome discoverer software (version 1.3, thermo scientific) to quantify proteins with respect to the within-itraq medians of log2 transformed and normalized reporter […]


Liquid Biopsy of Vitreous Reveals an Abundant Vesicle Population Consistent With the Size and Morphology of Exosomes

PMCID: 5954840
PMID: 29774170
DOI: 10.1167/tvst.7.3.6

[…] in data-dependent mode, with the orbitrap operating at 60,000 and 17,500 fwhm for ms and ms/ms, respectively., the 15 most abundant ions were selected for ms/ms. data were searched using the mascot search engine with the swissprot human (forward and reverse appended with common contaminant proteins) database set to carbamidomethyl (c) fixed modification. variable modification parameters […]


Characterisation of proteins in excretory/secretory products collected from salmon lice, Lepeophtheirus salmonis

PMCID: 5948691
PMID: 29751843
DOI: 10.1186/s13071-018-2885-6

[…] μl/min-1 max) stainless steel nebuliser (agilent, ca95051, united states) and esi. parameters for tandem ms analysis were based on those described previously []., deconvoluted ms/ms data in .mgf (mascot generic format) format were imported into proteinscape™ v3.1 (bruker daltonics) proteomics data analysis software for downstream mining of a custom l. salmonis database. this custom database […]

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MASCOT institution(s)
ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
MASCOT funding source(s)
Supported in part by the Swiss National Science foundation (SNF; grant number CR32I3_166258); by the ETH Zürich Postdoctoral Fellowship Program and the Marie Curie Actions for People COFUND Program, and by the European Research Council under the Seventh Framework Programme of the European Commission (PhyPD: grant agreement number 335529).

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