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MaRiMba specifications

Information


Unique identifier OMICS_19548
Name MaRiMba
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data A list of proteins or peptides.
Input format TXT
Output data A MRM transition list.
Output format TXT
Operating system Windows
Programming languages Perl
Computer skills Medium
Version 4.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Daniel Martin

Publication for MaRiMba

MaRiMba citations

 (3)
library_books

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

2014
Biochim Biophys Acta
PMCID: 3898926
PMID: 23467006
DOI: 10.1016/j.bbapap.2013.02.032

[…] ploys user-filtered transitions and takes the transition quantification values to infer protein-level abundance changes by comparing the protein quantification level among classes of samples.Finally, MaRiMba is a framework to automate the creation of explicitly defined SRM transition lists required for triple quadrupole mass spectrometers. MaRiMba creates transition lists from spectral libraries, […]

library_books

Targeted Quantitation of Proteins by Mass Spectrometry

2013
Biochemistry
PMCID: 3674507
PMID: 23517332
DOI: 10.1021/bi400110b

[…] ing target peptides exist, characteristic peptide fragmentations empirically found to provide a high signal intensity have been described. Several software tools, such as MRMaid, SRMAtlas, MRMer, and MaRiMba, for facilitating transition selection have been described. Because MRM assays are largely conducted with triple quadrupole instruments (see below), optimization has been directed to this type […]

library_books

Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research

2010
J Proteomics
PMCID: 2958306
PMID: 20615486
DOI: 10.1016/j.jprot.2010.06.008

[…] ntitative Analysis by MRM) , a desktop Java application to facilitate the selection of peptide and transitions. It consists of three applications: TIQAM-Digestor, TIQAM-PeptideAtlas and TIQAM-Viewer.-MaRiMba , a new component of the TPP since July 2009. It makes use of spectral libraries to create transition lists. Libraries of consensus spectra can be retrieved directly from PeptideAtlas, or can […]

Citations

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MaRiMba institution(s)
Institute for Systems Biology, Seattle, WA, USA; University of Wisconsin, WI, USA; UW Medicine at South Lake Union, Seattle, WA, USA; Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland; Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
MaRiMba funding source(s)
Supported by the NIH grants R21 CA126216 and P50 GM076547/Center for Systems Biology and in part with federal funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, under contract number N01-HV-28179.

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