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isobar specifications

Information


Unique identifier OMICS_02491
Name isobar
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.28
Stability Stable
Requirements
R(>=2.10.0), limma, methods, stats, plyr, RColorBrewer, gplots, Biobase, ggplot2, biomaRt, MASS, DBI, Hmisc, XML, gridExtra, MSnbase, boot, distr, OrgMassSpecR, RJSONIO
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Florian P. Breitwieser <>

Publications for isobar

isobar in publications

 (8)
PMCID: 5836375
PMID: 29208752
DOI: 10.1074/mcp.RA117.000186

[…] and tf are retention times of the earliest and the latest psm for a given peptide. we consider the larger of as and a0f as an estimate of peptide area for the top3 algorithm., the r software package isobar () was used to calculate protein ratios. isobar is publically available under the lgpl license from the cemm web site (http://bioinformatics.cemm.oeaw.ac.at) and through bioconductor […]

PMCID: 5799768
PMID: 28925403
DOI: 10.1038/onc.2017.341

[…] against a reversed database to assess the protein group false discovery rate (fdr). peptide and protein group identifications were <0.1 and <1% fdr, respectively. the r software package isobar was used to calculate protein ratios and assess their significance. protein ratios were calculated based on unique peptides. proteins were denoted as significantly regulated when their ratio […]

PMCID: 5236063
PMID: 27916275
DOI: 10.1016/j.cell.2016.11.010

[…] 3.5, respectively (p value < 10-3). the validated proteins retrieved by the two search engines were merged, any spectral conflicts discarded and grouped according to shared peptides. using the isobar software (), quantitation of the relative fold change of each protein after drug treatment (f) was calculated by determining the ratios of tmt reporter ion intensities. the tmt reporter ion […]

PMCID: 5516859
PMID: 28725479
DOI: 10.1038/npjsba.2016.27

[…] and 0.1% at the peptide level as detailed in bennett et al. protein-level quantitation for total cellular proteome and peptide-level quantification for phosphoproteome data were performed using isobar r package, and robust z score were calculated. protein (for total cellular proteome) or peptide (for phosphoproteome) with an absolute z score⩾2.5 and p value⩽0.05 were considered […]

PMCID: 4580311
PMID: 26400155
DOI: 10.1186/s12915-015-0186-5

[…] the sum of the peptide scores. protein identification requires the match of at least two independent peptides with a score of >25., for quantitative analysis of the proteomics data, the software isobar version 1.7.5 was used []. mascot identification and quantification data were normalized using isobar's default normalization method, which corrects for differences in reporter channel median […]


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isobar institution(s)
CeMM, Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
isobar funding source(s)
Supported by an Austrian Science Fund (FWF) grant No P 24321-B21.

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