Normalization of Aligned LC-MS Data

12 Jan 2009 | Tools | Contributor(s): Ann Christine Catlin, George Howlett

Normalization attempts to quantitatively filter overall peak intensity variations due to experiment errors such as systematic variable injection volumes loaded onto LC-MS.

http://ccehub.org/resources/normal

OMIC Data Formats: Notes for the Modeling Research Group

20 Feb 2009 | Notes | Contributor(s): Ann Christine Catlin

Each OMIC analysis laboratory has one or more analysis workflows that begin with instrument-generated datasets, where the format of the instrument dataset made available to modeling researchers for …

http://ccehub.org/resources/222

Global Proteomics Sample Preparation Protocol

13 Feb 2009 | Notes | Contributor(s): Catherine Riley

The urea-based trypsin digestion sample preparation protocol is used for the plasma samples acquired through the Cancer Care Engineering Colorectal Cancer OMIC Study. Prepared samples are analyzed …

http://ccehub.org/resources/207

LECO GC-TOF Instrument Setup: Metabolomics for Cancer Care Engineering

13 Feb 2009 | Notes | Contributor(s): Daniel Raftery

This document describes the setup for the LECO GC-TOF mass spectrometry instrument in preparation for metabolomics GCxGC-MS analysis of serum samples processed from patient whole blood at the IUSCC …

http://ccehub.org/resources/205

Sample Preparation : Metabolomics Analysis for Cancer Care Engineering

13 Feb 2009 | Notes | Contributor(s): Daniel Raftery, Ann Christine Catlin

This document describes the preparation of serum samples in the Raftery Laboratory for metabolomics GCxCG-MS analysis using the LECO GC-TOF mass spectrometer.Serum samples are processed from patient …

http://ccehub.org/resources/203

Klaunig Oxidative Stress Analysis Laboratory

07 Feb 2009 | Series | Contributor(s): James E. Klaunig, Ph.D., Xinzhu Pu

Studies in the laboratory of James Klaunig concentrate on understanding the mechanism by which chemicals induce cancer and the means to prevent or retard this process. Recent investigations have …

http://ccehub.org/resources/201

Global Proteomics Analysis Laboratory

07 Feb 2009 | Series | Contributor(s): Ann Christine Catlin

The proteomic and metabolomic laboratory at Purdue University's Bindley Bioscience Center performs global proteomics analysis for the CCE project. The facility uses proteomic and metabolomic tools to …

http://ccehub.org/resources/199

Spectrum Deconvolution of LC-MS Data

05 Sep 2008 | Tools | Contributor(s): Ann Christine Catlin, George Howlett

Spectral deconvolution differentiates analyte signals from contaminants or instrumental noise, and reduces data dimensionality to benefit downstream statistical analysis.

http://ccehub.org/resources/xmass

GCxGC-MS Data Classification and Alignment

11 Jun 2008 | Tools | Contributor(s): Dabao Zhang, Min Zhang, Jason Catlin

Align and classify GCxGC-MS data

http://ccehub.org/resources/GC2MSClass

Statistical Modeling of OMIC Data

30 Oct 2008 | Teaching Materials | Contributor(s): Min Zhang

This presentation describes the statistical modeling work of Professor Min Zhang. A discussion of statistical methods for identifying biomarkers is presented first, including Classical methods and …

http://ccehub.org/resources/141

Example Computations for Ion Detection

14 Oct 2008 | Teaching Materials | Contributor(s): Zhenwen Zhao

The excel spreadsheet describes the lipidomics analysis process for negative and positive ion detection applied to five samples.

http://ccehub.org/resources/113

Sample Preparation Protocol: Lipidomics for Cancer Care Engineering

14 Oct 2008 | Notes | Contributor(s): Zhenwen Zhao

This document describes the preparation of the plasma sample for lipidomics analysis using the API-4000 mass spectrometer. The plasma was processed from the patient whole blood at the IUSCC clinic …

http://ccehub.org/resources/118

API-4000 Instrument Setup : Lipidomics for Cancer Care Engineering

14 Oct 2008 | Notes | Contributor(s): Zhenwen Zhao

This document describes the setup for the API-4000 mass spectrometry instrument in preparation for lipidomics analysis of the plasma processed from the patient whole blood.

http://ccehub.org/resources/117

Xu Lipidomics Analysis Laboratory

14 Oct 2008 | Series | Contributor(s): Yan Xu, Zhenwen Zhao

The lipidomic approach in the laboratory of Yan Xu deals with understanding, at the molecular level, the mechanism of development of ovarian, breast, prostate, and other malignancies. These include …

http://ccehub.org/resources/112

Visual Analytics for GCxGC-MS Data

13 Oct 2008 | Series | Contributor(s): David S. Ebert, Ross Maciejewski

Visual Analytics for OMIC Data A critical issue for the CCE project is how to rapidly evaluate and validate model predictions. An interactive, integrated, visual and statistical analysis …

http://ccehub.org/resources/105

Integrative Mathematical Models

13 Oct 2008 | Series

Statistical, Population-based and Agent-based Modeling Data from the four OMIC analyses will be transferred to the statistical modelers for integration and analysis. Integrative statistical modeling …

http://ccehub.org/resources/104

Biological Data Analysis Laboratories

13 Oct 2008 | Series

The Biological Data Analysis Laboratories at IUSCC and Purdue University Processed samples will undergo lipidomic, oxidative stress, and SNP analysis at the IU Simon Cancer Center and global …

http://ccehub.org/resources/103

CCE Retreat 2008 Part II

28 Aug 2008 | Online Presentations | Contributor(s): Julie S. Nagel

Cancer Care Engineering Retreat Video Part II. (one hour) The following presentations are included in the video: Gabi Chiorean, MD, Indiana University School of Medicine, Hematology/Oncology. …

http://ccehub.org/resources/35

Cancer Care Engineering : A Collaborative Transformational Project

19 Jun 2008 | Online Presentations | Contributor(s): Joseph F Pekny, Marietta L. Harrison

The Cancer Care Engineering (CCE) project focuses on applying system engineering principles to the cancer problem. The initial focus is on colon cancer. The project has two main goals: to identify …

http://ccehub.org/resources/18