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Principal Component Analysis of Proteome Dynamics in Iron-starved Mycobacterium Tuberculosis

Principal Component Analysis of Proteome Dynamics in Iron-starved Mycobacterium Tuberculosis 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 spec- trometry. We previously reported assessing protein dynamics in iron-starved Mycobacterium tuberculosis, re- vealing 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 func- tional 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 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Proteomics & Bioinformatics Unpaywall

Principal Component Analysis of Proteome Dynamics in Iron-starved Mycobacterium Tuberculosis

Rao, Prahlad K.; Li, Qingbo
Journal of Proteomics & Bioinformatics – Jan 10, 2009
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Unpaywall
ISSN
0974-276X
DOI
10.4172/jpb.1000058
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Abstract

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 spec- trometry. We previously reported assessing protein dynamics in iron-starved Mycobacterium tuberculosis, re- vealing 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 func- tional 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

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Journal of Proteomics & Bioinformatics – Unpaywall

Published: Jan 10, 2009

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