CRG - Software

 

COMPASS

COMPASS is the Coon OMSSA (Open Mass Spectrometry Search Algorithm) Proteomic Analysis Software Suite.

Updated Release v1.3

COMPASS has been heavily upgraded from the original publication version. Complete source code and current binaries are located here:


Publication Version 1.0

It includes the following components:

  • Database Maker
  • DTA Generator
  • OMSSA Navigator
  • FDR Optimizer
  • TagQuant
  • Protein Herder
  • ProteinTagQuant

System Requirements:


Supporting Files:

Install COMPASS (Microsoft ClickOnce deployment)

Download COMPASS (in case installer does not work)

Download COMPASS source code (Microsoft Visual Studio 2010)

When using this software in a publication, please cite:
Wenger CD, Phanstiel DH, Lee MV, Bailey DJ, Coon JJ. COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA, Proteomics, 2011; 11(6): 1064–74


 

Elution Profiler

ElutionProfiler is a target peptide detection algorithm for Parallel Reaction Monitoring data collected on a high resolution and high mass accuracy instrument (Q Exactive). See the ReadMe file for more information.

System Requirements:


Sample Input File:

Download Elution Profiler

Download Elution Profiler source code (Microsoft Visual Studio 2010)

When using this software in a publication, please cite:
Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics, Mol Cell Proteomics, 2012; mcp.O112.020131.


 

Theoretical PRM and TPRM Parser

Theoretical PRM is a script for performing theoretical calculations of how specific a selected ion monitoring or reaction monitoring experiment is for a given target peptide based on a confounding "peptidome" and various user-selected isolation and mass analysis parameters. TPRM Parser is a script which organizes and recasts the Theoretical PRM output files in a more usable format. See the ReadMe file for more information.

System Requirements:


Sample Input Files:

Install Theoretical PRM and TPRM Parser

Download Theoretical PRM and TPRM Parser source code (Microsoft Visual Studio 2010)

When using this software in a publication, please cite:
Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics, Mol Cell Proteomics, 2012; mcp.O112.020131.


 

Intellinsity

This software package is a tool for visualization and analysis of liquid chromatography/tandem mass spectrometry sampling events.

System Requirements:


Installation Instructions:


Download entire Intellinsity software package

When using this software in a publication, please cite:
Xia Q, Good DM, Wenger CD, Coon JJ. Intellinsity: a tool for visualization and analysis of liquid chromatography/tandem mass spectrometry sampling events, Rapid Communications in Mass Spectrometry, 2010; 24(21): 3217–8


 

FluorAid

FluorAid is an application written in C#, designed to seamlessly combine data sets generated from a tandem mass spectrometer and intrinsic fluorescence excitation and detection device. The program requires three input files: an intrinsic fluorescence data file (LABVIEW), a database search output file filtered to a 1% false discovery rate (OMSSA), and a mass spectrometer output file (Thermo Scientific). Intrinsic fluorescence data files are read by the program and are graphically displayed as fluorescence signal versus time. OMSSA-searched output files are used to populate a list box with every tryptophan-containing peptide identified at a 1% false discovery rate. When the user selects a peptide a table displays information about the selected peptide generated from the uploaded OMSSA output including its amino acid sequence, observed mass, charge state, E-Value, spectrum number, and retention time. Simultaneously, an extracted ion chromatogram for the selected peptide precursor m/z generated from the corresponding mass spectrometer RAW file is overlaid on the same graph used to display the fluorescence chromatogram. Graphs are normalized and fit into a 10-minute retention time window centered on the retention time of the selected peptide. The user can visually compare fluorescence peaks with peaks from extracted ion chromatograms to help determine which fluorescence peaks, if any, correspond to the selected peptide. To assist the user with the comparison, a user-defined retention time offset can be used for data alignment. Peak integration and background correction tools have been built into the program to allow user integration of fluorescence peaks for use in quantitative comparisons.

System Requirements:


To Run:

  • Step 1: Extract all files from FluorAid.rar into a single folder
  • Step 2: Double-click the FluorAid.exe file to run the program
  • For operation instructions, see the ReadMe.txt file

Download FluorAid

Download FluorAid source code (Microsoft Visual Studio 2010)

When using this software in a publication, please cite:
Russell JD, Hilger RT, Ladror DT, Tervo MA, Scalf M, Shortreed MR, Coon JJ, Smith LM. Parallel Detection of Intrinsic Fluorescence from Peptides and Proteins for Quantification during Mass Spectrometric Analysis, Analytical Chemistry, 2011; 83(6): 2187–93


 

Morpheus

Morpheus is a database search algorithm designed from the ground up for high-resolution tandem mass spectra. We have discovered that for high-resolution MS/MS, simple spectrum preprocessing and scoring performs superior to more complex algorithms originally developed for low-resolution MS/MS, such as Sequest, Mascot, and OMSSA. Morpheus is also very fast—up to nearly 5 times faster than OMSSA for large human datasets. It is written in C# and is available open source under the permissive MIT License.

Now available at
http://morpheus-ms.sourceforge.net/

For supporting data, please visit http://www.chem.wisc.edu/~coon/Downloads/Morpheus.

When using this software in a publication, please cite:
Wenger CD, Coon JJ. A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra, Journal of Proteome Research, 2013; 12(3): 1377-86