Software:SuperHirn
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| + | ==Description== | ||
| + | '''SuperHirn''' is a novel tool to quantitatively analyze multi dimensional LC-MS data in a label-free approach and was developed by the group of Prof. Ruedi Aebersold at the Institute of Molecular Systems Biology (ETHZ, Switzerland). The software is programmed in C++ and is compatible with Unix platforms (tested on Linux and OSX). LC-MS data are preprocessed by a MS1 feature extraction routine and the different LC-MS runs are then combined by a multi dimensional LC-MS alignment into a general repository called ''MasterMap''. ''SuperHirn'' then offers several modules for post data analysis of the ''MasterMap'': | ||
| + | * LC-MS similarity analysis: Binary similarity analysis of LC-MS runs (intensity reproducibility, feature overlap) | ||
| + | * Feature intensity normalization: global MS1 feature intensity normalization across LC-MS runs | ||
| + | * Unsupervised feature profiling: Kmeans cluster analysis of MS1 features | ||
| + | * Targeted peptide/protein profiling: Correlate peptide/protein profile vs. a given target profile | ||
| + | * MS1 feature annotation: Annotation of MS1 features in the ''MasterMap'' (inclusion list etc.) | ||
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| ==Getting the software== | ==Getting the software== | ||
| - | Coming soon... | + | Download ''SuperHirn'' Source Code: [http://prottools.ethz.ch/muellelu/web/SuperHirn.php go to download page] |
| - | ==In a nutshell== | ||
| - | Coming soon... | ||
| - | ==More info== | + | Supporting material to this software: |
| - | Coming soon... | + | * To access the benchmark Latin Square profiling data from the SuperHirn technical manuscript (Mueller et al.), follow [http://prottools.ethz.ch/muellelu/web/Latin_Square_Data.php this link]. |
| + | * For more details about ''SuperHirn'', please read the corresponding publication (Mueller et al.) or download the [http://tools.proteomecenter.org/doc/superhirn_user_manual.pdf ''SuperHirn'' User Manual]. | ||
| + | * For an example data set of ''SuperHirn'', please download from this link: [http://prottools.ethz.ch/muellelu/web/SuperHirn/example_data_set.zip Example Test Set]. | ||
| + | * For additional readings for experimental wetlab procedures in combination with ''SuperHirn'' data processing: [http://tools.proteomecenter.org/doc/experimental_tips.pdf Experimental Tips]. | ||
| ==Reference== | ==Reference== | ||
| - | Coming soon... | + | Mueller, LN, Rinner, O, Schmidt, A, Letarte, S, Bodenmiller, B, Brusniak, MY, Vitek, O, Aebersold, R and Muller, M, ''SuperHirn'' - a novel tool for high resolution LC-MS based peptide/protein profiling, Proteomics, accepted for publication |
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| + | |||
| + | ==Avaliablity== | ||
| + | The software is now free available to the community. | ||
Revision as of 06:37, 13 July 2007
Contents |
Description
SuperHirn is a novel tool to quantitatively analyze multi dimensional LC-MS data in a label-free approach and was developed by the group of Prof. Ruedi Aebersold at the Institute of Molecular Systems Biology (ETHZ, Switzerland). The software is programmed in C++ and is compatible with Unix platforms (tested on Linux and OSX). LC-MS data are preprocessed by a MS1 feature extraction routine and the different LC-MS runs are then combined by a multi dimensional LC-MS alignment into a general repository called MasterMap. SuperHirn then offers several modules for post data analysis of the MasterMap:
- LC-MS similarity analysis: Binary similarity analysis of LC-MS runs (intensity reproducibility, feature overlap)
- Feature intensity normalization: global MS1 feature intensity normalization across LC-MS runs
- Unsupervised feature profiling: Kmeans cluster analysis of MS1 features
- Targeted peptide/protein profiling: Correlate peptide/protein profile vs. a given target profile
- MS1 feature annotation: Annotation of MS1 features in the MasterMap (inclusion list etc.)
Getting the software
Download SuperHirn Source Code: go to download page
Supporting material to this software:
- To access the benchmark Latin Square profiling data from the SuperHirn technical manuscript (Mueller et al.), follow this link.
- For more details about SuperHirn, please read the corresponding publication (Mueller et al.) or download the SuperHirn User Manual.
- For an example data set of SuperHirn, please download from this link: Example Test Set.
- For additional readings for experimental wetlab procedures in combination with SuperHirn data processing: Experimental Tips.
Reference
Mueller, LN, Rinner, O, Schmidt, A, Letarte, S, Bodenmiller, B, Brusniak, MY, Vitek, O, Aebersold, R and Muller, M, SuperHirn - a novel tool for high resolution LC-MS based peptide/protein profiling, Proteomics, accepted for publication
Avaliablity
The software is now free available to the community.
