Document Detail


Principal Component Analysis of Proteome Dynamics in Iron-starved Mycobacterium Tuberculosis.
MedLine Citation:
PMID:  19436767     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
The goal of this study is to use principal component analysis (PCA) for multivariate analysis of proteome dynamics based on both protein abundance and turnover information generated by high-resolution mass spectrometry. We previously reported assessing protein dynamics in iron-starved Mycobacterium tuberculosis, revealing interesting interconnection among the cellular processes involving protein synthesis, degradation, and secretion (Anal. Chem. 80, 6860-9). In this study, we use target-decoy database search approach to select peptides for quantitation at a false discovery rate of 4.2%. We further use PCA to reduce the data dimensions for simpler interpretation. The PCA results indicate that the protein turnover and relative abundance properties are approximately orthogonal in the data space defined by the first three principal components. We show the potential of the Hotelling's T2 (T2) value as a quantifiable index for comparing changes between protein functional categories. The T2 value represents the gross change of a protein in both abundance and turnover. Close examination of the antigen 85 complex demonstrates that T2 correctly predicts the coordinated changes of the antigen 85 complex proteins. The multi-dimensional protein dynamics data further reveal the secretion of the antigen 85 complex. Overall, this study demonstrates PCA as an effective means to facilitate interpretation of the multivariate proteome dynamics dataset which otherwise would remain a significant challenge using traditional methods.
Authors:
Prahlad K Rao; Qingbo Li
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Publication Detail:
Type:  JOURNAL ARTICLE    
Journal Detail:
Title:  Journal of proteomics & bioinformatics     Volume:  2     ISSN:  0974-276X     ISO Abbreviation:  -     Publication Date:  2009 Jan 
Date Detail:
Created Date:  2009-5-13     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101479045     Medline TA:  J Proteomics Bioinform     Country:  -    
Other Details:
Languages:  ENG     Pagination:  19-31     Citation Subset:  -    
Affiliation:
Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60607, USA.
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MeSH Terms
Descriptor/Qualifier:
Grant Support
ID/Acronym/Agency:
R03 AI073469-01A1//NIAID NIH HHS

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