MASCOT protocols

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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



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

Additional information

Publication for Marginal Approximation of the Structured COalescenT

MASCOT in pipelines

PMCID: 5804310
PMID: 29412357
DOI: 10.1590/0074-02760170340

[…] 4800 proteomics analyzer)., bioinformatics - peptide sequences (protein identity) were determined by matching protein databases with the acquired fragmentation pattern using the software program mascot (matrix science), and all ms/ms spectra were searched against the entire ncbinr protein database or a modified ncbinr database created to search “fragilis” recognised proteins, assuming use […]

PMCID: 5823890
PMID: 29472725
DOI: 10.1038/s41467-018-03142-x

[…] massive (accessions msv000081912 and msv000081913) and proteomexchange (accessions pxd008657 and pxd008658). deposited search results (.dat and.mzidentml) were generated using the latest version of mascot (2.6)., phylogeny of the aa15 lpmo family as a whole was carried out as follows. the lpmo protein sequences identified in the transcriptome of thermobia were searched via blastp against ncbi […]

PMCID: 5841299
PMID: 29515152
DOI: 10.1038/s41598-018-22540-1

[…] as 25 °c and 37 °c sabhs, respectively), and subjected to lc-ms/ms analysis. the set of 14,962 predicted proteins of py. insidiosum, theoretically digested with trypsin, was used as an in-house mascot library for lc-ms/ms search. any peptide identified by lc-ms/ms in at least two replicates was recruited for protein validation, resulting in a pool of 120,265 peptides. a total of 4,445 […]

PMCID: 5854367
PMID: 29258832
DOI: 10.1016/j.ijpara.2017.09.007

[…] in the final sporozoite proteome list., in order to rank the identified proteins by their abundance in the sample, an exponentially modified protein abundance index (empai) was calculated using mascot (matrix science) (). empai is the exponential form of protein abundance index (pai) minus 1 (empai = 10pai − 1) and is proportional to protein content in a protein mixture (). pai […]

PMCID: 5862453
PMID: 29561852
DOI: 10.1371/journal.pone.0193739

[…] ms/ms parameters used in the acquisition of peptides were detailed in supplementary material ., the raw data from ms/ms were converted using the msconvert software, version 3.0.6398 [] into mgf a mascot generic file. we merged the output files with the two technical replicates. the mgf file and the predicted database were used in mascot (matrix science, london, uk; available at: […]

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MASCOT in publications

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, […]

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 […]

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 […]

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 […]

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 […]

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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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