Software:TPP-MaRiMba
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| - | '''TPP-MaRiMba: MRM-aware SpectraST Pipeline''' | + | '''TPP-MaRiMba: Branch of TPP containing MaRiMba, a tool for the creation of customized MRM lists from spectral libraries''' |
| - | ==Description== | + | 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. |
| - | MaRiMba is used to automate the creation of explicitly defined transition lists required for multiple reaction monitoring (MRM) experiments. MaRiMba creates MRM transition lists from pre-existing or custom 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 corresponding transitions for isotopically heavy peptides, for which the precursor and product ions are adjusted according to user specifications. MaRiMba outputs the final MRM list to a text file ready for upload to a mass spectrometer. | + | |
| - | ==Current Version== | + | ==Getting the Software== |
| - | 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. | + | ===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== | + | ===Requirments=== |
| - | Windows XP, Service Pack 2 or above. For instrument-to-mzXML conversion, you will need the corresponding vendor software on the same system. See [[Formats:mzXML]] for more information. | + | * Windows XP, Service Pack 2 or above |
| + | * ActivePerl, version 5.8 or above | ||
| - | ==Downloading the software== | + | 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). | The software will be available for public download from this site after publication of the manuscript (currently under review). | ||
| - | ==Troubleshooting== | + | ===Installing the software=== |
| + | # Download and install ActivePerl, version 5.8 or above (http://www.activestate.com/activeperl/) | ||
| + | # 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 [http://www.peptideatlas.org/speclib/ PeptideAtlas] | ||
Revision as of 00:17, 3 March 2009
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
- Download and install ActivePerl, version 5.8 or above (http://www.activestate.com/activeperl/)
- 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
