CharmeRT

CharmeRT is a workflow that allows for deeper insights into tandem mass spectra by enabling the identification and validation of chimeric spectra using retention time prediction.

About

We have extended the database search engine MS Amanda by adding a chimeric spectra identification method and implemented Elutator, a new tool to validate the identified spectra using machine learning based on the principles of Percolator and an algorithm for retention time prediction.
The CharmeRT workflow is currently available as installation for Proteome Discoverer 1.4 and 2.1, a standalone version and a version for PD 2.2 is currently in progress. Please note that chimeric spectra identification requires MS1 information, .mgf files are not sufficient.

Installation of CharmeRT for Proteome Discoverer 1.4 or 2.1

The Proteome Discoverer nodes of MS Amanda 2.0 and Elutator can be used with Thermo Scientific Proteome Discoverer v. 1.4 or 2.1. To install CharmeRT, please perform the following steps:

  1. Please download the latest version here:
  2. See the PD Nodes google group for information on latest changes.
  3. Run "CharmeRT.exe".
  4. Restart Proteome Discoverer
  5. MS Amanda 2.0 and Elutator should now be successfully installed and appear as nodes in PD.
  6. The model file for Elutator can be downloaded here

To run the CharmeRT workflow please use the provided CharmeRT template (Processing Template in 2.1) that has been added through installation.

Additional Tools

Elutator RT Trainer

You can create your own RT model that is optimized for your in-house instruments; please prepare raw files for different organisms at the same instrument settings. To install the Elutator RT Trainer please perform the following steps:

  1. Please download the latest version here:
  2. See the PD Nodes google group for information on latest changes.
  3. Run "ElutatorRTTrainer.exe".
  4. The Elutator RT Trainer is now successfully installed on your computer.

Multi-confident PSMs-fix Node

We also supply a Proteome Discoverer node to filter hits where two or more confident PSMs have been reported for a single spectrum and no second search has been applied. To install the "Multi-confident PSMs-fix" node, please perform the following steps:

  1. Please download the latest version here:
  2. See the PD Nodes google group for information on latest changes.
  3. Run "MultiConfidentPSMsFix_PDX.X.exe".
  4. The Multi-confident PSMs-fix node is now successfully installed on your computer.

Contact

This research project is a collaboration of the Protein Chemistry Group at IMP and the Bioinformatics Research Group at FH Upper Austria, Hagenberg Campus.
For any further questions, bug reports, ideas,... please contact Viktoria Dorfer, Sergey Maltsev, Stephan Winkler, or Karl Mechtler or post your comment in the PD Nodes Google Group.

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