CRG - Software

COMPASS • Intellinsity • FluorAid
 

COMPASS

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

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


 

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


Copyright 2012 - The Joshua J. Coon Research Group