IBG Workbench

Project Description

This project entails developing solutions for anaylsis of Mass Spectrometry data. This includes analysis tools such as SpectralMatch and HDXRates but also a set of C libraries which gives IO and data structure support to developers. Most of the current code is written in C but we do have some functionality written in Java which correlates to our IBG Desktop project.

Download the Current Release of the IBG Workbench C libraries PGP Signature SHA1sum MD5sum

IBG Workbench API Documentation

Development

There are several projects underway including:

IBG Workbench C libraries

• This project, code named MSIOP, is the core set of objects and IO routines to build Mass Spectrometry tools upon. We are currently producing shared libraries so that developers will have a basic set of utilities to build upon when developing complex mass spectrometry analysis tools. The motivation behind this is a lack of development libraries needed to quickly build up analysis tools for hypothesis driven experiments in Mass Spectrometry. (NSF REU Funded)
• All of our functions and objects are developed in C but we intend to leverage Swig to autogenerate wrappers so that our libraries will be accessible from Python, Perl, Ruby, Java and more. Please contact Kevin Drew, kdrew[at]cti.depaul.edu for more information.
• Download the Current Release of the IBG Workbench C libraries PGP Signature SHA1sum MD5sum (download includes Spectral Match and HDXRates)

Spectral Match

• Based on the core functionality of the C libraries, this tool finds a peptide fragment in a given known sequence that matches a given spectrum. The implementation was built upon the libraries of MSIOP. Details of this algorithm can be found in Kevin Drew's Master's thesis.
• Download the Current Release of the IBG Workbench SpectralMatch

HDXRates

• Also based on the core functionality of the C libraries, this tool analyzes MS data from an Hydrogen Deueterium Exchange experiment to compute deuterium content of a peptide. Details of this algorithm can be found in Kevin Drew's Master's thesis.
• Download the Current Release of the IBG Workbench HDXRates

IBG Desktop

• This is a desktop tool that is a vertical application handling all of the needs of a proteomic research. It contains analysis tools and acts as an interfact to data management tools and grid and web based analysis tools. IBG Desktop

Simple Cosine Similarity Spectral Comparison

• Simple Cosine Similarity Spectral Comparison compares mass spectra using cosine similarity. It was developed during the spring of 2005 and is currently complete. It was built upon the MSIOP framework.

k-Mutation Spectral Alignment

• Compares Mass Spectra using a more complex Spectral Alignment algorithm that will find similarity even with k-mutations or modifications

Mass Spec Data Management

• A tool that utilizes Argonne Researcher Ed Frank's Kah project to manage Mass Spec data and to facilitate running analys routines on them.

High Throughput Molecular Screening Library Assistant

• MALDI-TOF for high throughput signal transduction inhibitor screening. High throughput screening utilizing mass spectrometry, which allows using the change in mass of peptide probes as a screening assay with a tremendous ability to multiplex and increase throughput. If an assay follows a chemical change in some organic molecule, its mass shift can be detected along with dozens of other organic molecules in a single pass. The mass pattern of the test sample will be compared to controls, and databases, tandem mass spectrometry, or both will be utilized to determine what kind of chemical modifications were made.
• Extracts from cells treated with individual compounds from a library of small molecules for multiple signal transduction pathways in a single experiment will be assayed. Software will be utilized to recognize changes in the relative abundance f different mass species so that any small molecules that affect one or more signaling pathways can be flagged for further analysis. 10,000 compound libraries have been shown to be able to be screened by this assay. The initial work will involve screening tyrosine kinase inhibitors and will target relevant signaling pathways, such as cell proliferation, apoptosis, differentiation, stress, metabolism, etc. These high throughput screening assays may help researchers investigate cancer and other diseases.
• This work is funded in part by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant R01 HG3864. Information on the Molecular Libraries Roadmap Initiative can be obtained from http://nihroadmap.nih.gov/molecularlibraries/
• Documentation pages and work area

New projects are listed on the ProjectList page. Anyone who is interested in any of these projects, please contact one of the Project Members.

Development versions of our software can be checked out of subversion on http://histone.cti.depaul.edu/svn/ .

Statistics: Approx. Lines of Code as of 7-7-05:

List	Tests	dta_IO	peptideObject	spectrumObject	spectralMatch	HDXRates	Total
316	1261	99	1567	3445	4699	1410	12797

Project Members

• Dave Angulo PI
• Kevin Drew (kdrew [at] cti.depaul.edu)
• Eric Puryear
• Paiboon Siwamutita
• Jennifer Van Puymbrouck
• Rob Vogelbacher
• Dominic Battre
• Alex Schilling

Links

IBGWorkbench (subversion)

Bug Reports (bugzilla)

ProjectTasks

-- DaveAngulo - 15 Mar 2006
-- KevinDrew - 20 Jan 2005

• Hard at Work: