Software:SuperHirn

From SPCTools

(Difference between revisions)
Jump to: navigation, search
Revision as of 06:30, 13 July 2007
Jtasman (Talk | contribs)
(creating SuperHirn page)
← Previous diff
Revision as of 06:37, 13 July 2007
Jtasman (Talk | contribs)

Next diff →
Line 1: Line 1:
 +==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== ==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
 + 
 + 
 +==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.

Personal tools