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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


MERS CoV spillover at the camel human interface

PMCID: 5777824
PMID: 29336306
DOI: 10.7554/eLife.31257.038

[…] on models are available in BEAST v2 () but not in BEAST v1 (). We use the more computationally intensive MultiTypeTree module () over approximate methods also available in BEAST v2, such as BASTA (), MASCOT (), and PhyDyn (). Structured coalescent model implemented in the MultiTypeTree module () estimates four parameters: rate of coalescence in human viruses, rate of coalescence in camel viruses, […]


The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle

Sci Rep
PMCID: 5120318
PMID: 27876851
DOI: 10.1038/srep37536

[…] S spectra were acquired using the TOP15 method following the equipment manufacturer’s instructions. All analyses were run in duplicates, including treatment samples and controls. ProteinPilot (v4.5), Mascot (v2.4), MaxQuant (v1.3.0.5), and Sequest (v1.3) software were used to identify peptides and proteins in each sample (see software references in ). In all cases, a tolerance in the mass measurem […]


Urbilaterian origin of paralogous GnRH and corazonin neuropeptide signalling pathways

Sci Rep
PMCID: 4923880
PMID: 27350121
DOI: 10.1038/srep28788
call_split See protocol

[…] m coupled to a Synapt G2 HDMS mass spectrometer (Waters Corporation, Milford, MA, USA) and MassLynx v4.1 SCN 908 software (Waters Corporation, Milford, MA, USA). All MS/MS samples were analyzed using Mascot (Matrix Science, London, UK; version 2.5.0) and Scaffold (version Scaffold_4.2.1, Proteome Software Inc., Portland, OR) was used to validate MS/MS based peptide and protein identifications. [Fo […]


Identifying Kinase Substrates via a Heavy ATP Kinase Assay and Quantitative Mass Spectrometry

Sci Rep
PMCID: 4921819
PMID: 27346722
DOI: 10.1038/srep28107

[…] tive data were searched with mass tolerances of ±20 ppm and 0.045 Da on the precursor and fragment ions (HCD only), respectively. Results were filtered to include peptide spectrum matches (PSMs) with Mascot ion scores of ≥17, Sequest HT cross-correlation factor (Xcorr) scores of ≥1.7 and medium and high peptide confidence. Lower peptide thresholds and medium peptide confidence settings were chosen […]


Data in support of the identification of neuronal and astrocyte proteins interacting with extracellularly applied oligomeric and fibrillar α synuclein assemblies by mass spectrometry

PMCID: 4773484
PMID: 26958642
DOI: 10.1016/j.dib.2016.02.018

[…] NanoLC-MS/MS raw data were processed automatically using the Scaffold software (version 3.6.4) and the SwissProt_18112011 database with both the Mascot (Version: 2.3.02) and the X! Tandem (Version CYCLONE 2010.12.01.1) search engine, a specific trypsin digestion with up to 2 missed cleavages, a tolerance of 0.5 Da for fragment monoisotopic m […]


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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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