Software:TPP-MaRiMba

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TPP-MaRiMba: Branch of TPP containing MaRiMba, a tool for the creation of customized MRM lists from spectral libraries

MaRiMba is a software tool for the automated creation of explicitly defined transition lists required for multiple reaction monitoring (MRM) experiments. MaRiMba creates MRM transition lists from downloaded or custom-built spectral libraries, restricts output to specified proteins or peptides of interest, and filters MRM lists based on user-defined precursor peptide and product ion properties. MaRiMba can also create MRM lists containing isotopically heavy transitions for use with isotopic labeling strategies such as SILAC. MaRiMba outputs the final MRM list to a text file convenient for upload to a mass spectrometer.

Contents

Getting the Software

Current Version

The current version of TPP-MaRiMba is 4.1.0. This number reflects the main TPP version number, from which TPP-MaRiMba is branched. TPP-MaRiMba is slated for public release in early 2009, after which MaRiMba will merged with the main TPP release.

Requirments

  • Windows XP, Service Pack 2 or above
  • ActivePerl, version 5.8 or above

For instrument-to-mzXML conversion, a non-MaRiMba-related component of the TPP, you will also need the corresponding vendor software on the same system. See Formats:mzXML for more information.

Downloading the software

The software will be available for public download from this site after publication of the manuscript (currently under review).

Installing the software

  1. Download and install ActivePerl, version 5.8 or above (http://www.activestate.com/activeperl/)
  2. Download and run the TPP-MaRiMba installer, following the directions for default installation

Resources

  • To receive email announcements regarding the TPP, sign up for the SPC Tools Announcement Group at spctools-announce.googlegroups.com
  • To post a question or comment regarding TPP and/or MaRiMba, use the SPC Tools Discussion Group at spctools-discuss.googlegroups.com
  • Public spectral libraries are available for download at PeptideAtlas
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