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chevron_left Metabolite identification Quality control Metabolite quantification Peak detection Spectral visualization chevron_right

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SIMAT specifications


Unique identifier OMICS_09685
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.0
Stability Stable
grid, BiocGenerics, ggplot2, RUnit, R(>=3.0.0), reshape2, mzR, Rcpp(>=0.11.3)
Maintained Yes


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  • person_outline R. Nezami Ranjbar

Publication for SIMAT

SIMAT citations


Freely suspended perforated polymer nanomembranes for protein separations

Sci Rep
PMCID: 5849607
PMID: 29535317
DOI: 10.1038/s41598-018-22200-4

[…] above. to counteract aggregation and settling, tio2-np were treated in an ultrasonication bath for 30 minutes prior to use., silicon wafers with one polished side and 50.8 mm (2 inch) diameter (simat) were immersed in concentrated (96%) sulfuric acid for at least 15 minutes for cleaning and then thoroughly rinsed with distilled water prior to spin coating. all spin coating steps were done […]


Silicanin 1 is a conserved diatom membrane protein involved in silica biomineralization

BMC Biol
PMCID: 5525289
PMID: 28738898
DOI: 10.1186/s12915-017-0400-8

[…] acid solutions in vitro [–]. a recent proteomics analysis revealed several novel biosilica-associated proteins with unknown functions in the diatom thalassiosira pseudonana []. one of these, simat7, differs markedly from silaffins, cingulins, and silacidins regarding amino acid composition and predicted secondary structure. in the present work, we have investigated the function of simat7 […]


Dynamic responses to silicon in Thalasiossira pseudonana Identification, characterisation and classification of signature genes and their corresponding protein motifs

Sci Rep
PMCID: 5501833
PMID: 28687794
DOI: 10.1038/s41598-017-04921-0

[…] new gene families with putative roles in si metabolism and frustule synthesis were identified, including 15 transmembrane proteins with common domain structure that included the frustule protein simat7. this study provides a high-resolution gene expression map of the dynamic responses to si availability, and lays the foundation for detailed functional studies of si-related processes., two […]


Developing a Hierarchical Model for the Spatial Analysis of PM10 Pollution Extremes in the Mexico City Metropolitan Area

PMCID: 5551172
PMID: 28684720
DOI: 10.3390/ijerph14070734

[…] network established by the comision ambiental metropolitana of mexico city to monitor compliance with ambient air quality standards; this network is part of the sistema de monitoreo atmosférico (simat), a program responsible for ongoing measurements of the main air pollutants in mexico city., we constructed a gev model of the pm10 maxima in the mexico city metropolitan area, using […]


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] and 13c-enriched. metaboqc [] is a quality control approach that evaluates alignment and suggests optimal parameters for feature detection based on discrepancies between replicate samples, and simat [] allows the selection of the optimal set of fragments and retention time windows for target analytes in gc–single ion monitoring–ms-based analysis., metabolomics datasets are usually […]


Establishing super resolution imaging for proteins in diatom biosilica

Sci Rep
PMCID: 5101815
PMID: 27827427
DOI: 10.1038/srep36824

[…] that occurs with the help of self-assembled biosilica forming templates. over the past decade, biochemical studies have identified several organic components (i.e. silaffins, cingulins, silacidins, simat proteins, long-chain polyamines, chitin) that are tightly associated with the diatom silica and believed to be involved in formation of the species-specific silica nano- and micropatterns. live […]

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SIMAT institution(s)
Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, USA; Department of Oncology, Georgetown University, Washington DC, USA

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