Tools

Visualize
Overview
Visualize is a workstation based tool that allows the user to visualize and analyze proteomics data in the .ez2 format produced by ViPDAC (Virtual Proteomics Data Analysis Cluster), the MAPW (MCW Automated Proteomics Workflow) or the Epitomize program. In addition to being able to view the protein, peptide and spectral data, the user can carry out analysis of modifications, cleavage sites, amino acids. Protein lists can be annotated using included databases (GO, KEGG, serum, membrane and mitochondrial proteins) as well as using user generated lists. Results from multiple .ez2 files can be combined both between experiments and for the same experiment from searches using different parameters or algorithms. Visualize can also compare results from multiple files and quantitate using either spectral counting or SILAC using the SPeCtRA method. Results can be exported in a number of different formats including a journal report format.

  • visualize_144_setup.exe This .exe file contains the Visualize instsller program.
  • visualize_144.exe This program can be run without installation and does not require any administrator privileges.
  • visualize_data.zip This .zip file contains the same supplementary databases as the pro setup file. These files should be placed in the same folder as the Visualize Program.
  • visualize.pdf PDF file containing help for Visualize • sample_data.ez2 Sample data to explore the functions of Visualize with.
  • Microsoft Visual C++ 2008 SP1 Redistributable Package (x86) Some users may need to install this package if they receive missing .dll file errors when trying to run Visualize.

Epitomize
Overview
The Epitomize application is part of a suite of programs that help to automate and simplify the process of analyzing proteomics experiments. It takes proteomics search results from Sequest, Mascot, X!Tandem, or OMSSA and calculates peptide probabilities. The results are filtered and formatted for output in the .ez2 or other formats.

Epitomize is provided as a Perl source code file:

ZoomQuant
Overview
The ZoomQuant application is part of a suite of programs that help to automate and simplify the process of analyzing experiments using 18O labeling of peptides.

PepID
Overview
The PepID web tool uses a peptide composition vector database to map peptide sequences to proteins.

DeNovoID
Overview
The DeNovoID web tool uses a peptide composition vector database to map peptide sequences and sequence and mass tags derived from De novo peptide sequencing to proteins.

ProMost
Overview
The Promost web tool calculates the predicted pI and molecular mass for proteins with and without post-translational modifications. It displays the data both as a table and an a graphical representation of the migration of the proteins in 2 dimensional gel electrophoresis.

ViPDAC
Overview
ViPDAC uses Amazon Web Services to analyze proteomics data. To use ViPDAC you first sign up for access to Amazon’s Web Services, then you can log in to the Amazon console which is used to start up a personal copy of the ViPDAC server. This starts ViPDAC running on one of Amazon’s servers from where you can now access the ViPDAC web interface. At this point normal proteomics analysis procedures take over – you can pick an existing set of parameters or configure a new analysis (cleavage enzyme, modifications, protein database to search, etc) and select your data file (spectra in .mgf format) and then submit the job. ViPDAC will then upload the data file to the your area on Amazon’s S3 storage and run the analysis using the EC2 nodes available in your cluster. Once the analysis is complete ViPDAC will compile the results and save them back onto S3 where they can be stored or downloaded to the desktop for further analysis. At this point you can continue to do more analyses or simply turn the cluster off until you need it again. One of the benefits of the dynamic nature of the cloud is that if you want the analysis to go faster you can add more nodes to your cluster at any time.