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Number of citations per year for the bioinformatics software tool MSBlender
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MSBlender specifications

Information


Unique identifier OMICS_19891
Name MSBlender
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
gcc, GNU Scientific Library, matplotlib
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Edward Marcotte
  • person_outline Alexey Nesvizhskii
  • person_outline Hyungwon Choi
  • person_outline Taejoon Kwon

Additional information


http://www.marcottelab.org/index.php/MSblender

Publication for MSBlender

MSBlender citations

 (6)
library_books

Microvesicles from brain extract—treated mesenchymal stem cells improve neurological functions in a rat model of ischemic stroke

2016
Sci Rep
PMCID: 5016792
PMID: 27609711
DOI: 10.1038/srep33038

[…] A, lipids, and other molecules, our primary focus was on identifying candidate MV proteins that participate in brain tissue regeneration. The extract-treated MSC-MV proteomes were characterised using MSblender, an algorithm that integrates results from multiple peptide search algorithms via multivariate modelling and can identify substantially more peptides and proteins than a single search algori […]

library_books

Network Based Protein Biomarker Discovery Platforms

2016
PMCID: 4838525
PMID: 27103885
DOI: 10.5808/GI.2016.14.1.2

[…] es the integration of Paragon and Mascot () [] by assigning the peptides with higher scores from the two search engines to the MS/MS spectra, which can leads to unreliable false positive rates. Also, MSblender integrates the search scores from the search engines into a probability score for every possible PSM and then estimates FDRs for the PSMs in a reliable manner []. This method identifies more […]

library_books

Proteome wide dataset supporting the study of ancient metazoan macromolecular complexes

2015
PMCID: 4738005
PMID: 26870755
DOI: 10.1016/j.dib.2015.11.062

[…] quantitation mass spectra were searched using 3 search engines: Tide, INSPECT and MSGFDB each employing a different search methodology, and the spectral counts were integrated probabilistically using MSblender . We found we were able to increase the total peptide-spectral matches and proteins identified by 20–60% depending on the sample compared to using Sequest alone, with a false discovery rate […]

library_books

Scientific workflow optimization for improved peptide and protein identification

2015
BMC Bioinformatics
PMCID: 4558836
PMID: 26335531
DOI: 10.1186/s12859-015-0714-x

[…] MS3 or a combination of these. Several groups have also published efforts in combining multiple algorithms for peptide-spectrum matching, for instance the framework developed by Searle et al. [], the MSblender software from Kwon et al. [] or the FDRAnalysis algorithm of Wedge et al. []. Recently, in de Bruin et al. [] and Mohammed et al. [] we have shown how some of these algorithms can be integra […]

library_books

Universal database search tool for proteomics

2014
Nat Commun
PMCID: 5036525
PMID: 25358478
DOI: 10.1038/ncomms6277

[…] ], ProteoSuite [], IDPicker [], SearchGUI [], Scaffold [], ProteoSAFe, Skyline [], and Percolator [, ]. Peptide identification tools that combine the results of multiple database search tools such as MSblender [], Peptide-Shaker [], and PepArML [] also currently support MS-GF+. MS-GF+ is freely available at http://proteomics.ucsd.edu. […]

library_books

Protein to mRNA Ratios Are Conserved between Pseudomonas aeruginosa Strains

2014
J Proteome Res
PMCID: 4012837
PMID: 24742327
DOI: 10.1021/pr4011684

[…] d the same search parameters as described previously except that MS-GFDB was newly added for the current study (with the settings –t 300 ppm –c13 1 –nnet 0 –n 2). Then, we combined these results with MSblender and considered peptide−spectrum matches with an estimated FDR less than 0.01. Subsequently, we calculated APEX scores, with weighted spectral counts per protein (using a FDR < 0.01 estimated […]


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MSBlender institution(s)
Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA; Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Center for Genomics and Systems Biology, Department of Biology, New York University, NY, USA; Department of Pathology and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
MSBlender funding source(s)
Supported grants from the NIH, NSF, the Welch (F1515) & Packard Foundations, and NIH grants R01- GM094231 and R01-CA126239.

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