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MSCAN specifications


Unique identifier OMICS_09260
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Wyeth Wasserman

Publications for MSCAN

MSCAN citations


A reverse vaccinology approach to the identification and characterization of Ctenocephalides felis candidate protective antigens for the control of cat flea infestations

PMCID: 5774092
PMID: 29347954
DOI: 10.1186/s13071-018-2618-x

[…] acid in acetonitrile). ESI ionization was done using a Fused-silica PicoTip Emitter ID 10 μm (New Objective, Woburn, MA, USA) interface. Peptides were detected in survey scans from 400 to 1600 amu (1 μscan), followed by three data dependent MS/MS scans (Top 3), using an isolation width of 2 mass-to-charge ratio units, normalized collision energy of 35%, and dynamic exclusion applied during 30 s pe […]


Impaired hypoxic tolerance in APP23 mice: a dysregulation of neuroprotective globin levels

PMCID: 5518225
PMID: 28391636
DOI: 10.1002/1873-3468.12651

[…] served globin expression patterns.Binding sequences for REST, also known as Neuron‐Restrictive Silencer Factor, have been identified before in the regulatory region of Ngb, using both rVista 2.0 and MSCAN . To the best of our knowledge, we are the first to identify a recognition sequence in the regulatory region of Cygb as well. REST expression is induced during normal brain aging and its activat […]


A New Algorithm for Identifying Cis Regulatory Modules Based on Hidden Markov Model

Biomed Res Int
PMCID: 5405574
PMID: 28497059
DOI: 10.1155/2017/6274513

[…] tegory employ statistical approaches to score clusters of motif sites in windows of a predefined given size and to identify the statistically significant site clusters as candidate CRMs. For example, MSCAN [] uses p values to score clusters of motif sites in each window region. MotEvo [] uses a Bayesian approach to calculate the posterior probabilities of all given motifs in each aligned window. S […]


Quantitative proteomics reveals Piccolo as a candidate serological correlate of recovery from Guillain Barré syndrome

PMCID: 5342688
PMID: 27776345
DOI: 10.18632/oncotarget.12789

[…] the polydimethylcyclosiloxane ions (protonated (Si(CH3)2O))6; m/z 445.120025) were used for internal recalibration of the mass spectra. Peptides were detected in survey scans from 400 to 1600 amu (1 μscan) using an isolation width of 2 u (in mass-to-charge ratio units), normalized collision energy of 40% for HCD fragmentation, and dynamic exclusion applied during periods of 30 seconds. Precursors […]


Molecular Mechanism for Cellular Response to β Escin and Its Therapeutic Implications

PLoS One
PMCID: 5058498
PMID: 27727329
DOI: 10.1371/journal.pone.0164365

[…] fication and relative quantitation of all detectable proteins present in the samples.[] Proteins were identified with Mascot and differentially expressed proteins were assessed using the Diffprot and MScan software tools with estimation of statistical significance []. A minimum number of two peptides with a false-discovery rate <1% were used for confident identification of a protein in the iTRAQ e […]


Variants in the SCN5A Promoter Associated With Various Arrhythmia Phenotypes

PMCID: 5079027
PMID: 27625342
DOI: 10.1161/JAHA.116.003644

[…] xperiment, and its activity level served as the baseline. Potential muscle‐specific transcriptional regulatory modules in CNS28 were predicted using the M‐SCAN algorithm ( To study the affinities of a human heart protein for the transcription factors that were predicted to bind to sequences within CNS28, an electrophoretic mobility shift assay was performe […]


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MSCAN institution(s)
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, B.C., Canada; Stockholm Bioinformatics Center and Department of Numerical Analysis and Computer Science, KTH, Stockholm, Sweden

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