ArticleJournal of proteomics & bioinformatics2009
Principal Component Analysis of Proteome Dynamics in Iron-starved Mycobacterium Tuberculosis.
Article in Journal of proteomics & bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed.
- Quantitative Proteomics in Translational Absorption, Distribution, Metabolism, and Excretion and Precision Medicine.Pharmacological reviews · 2022Review
- Assessment of Protein Profiles of RNAlater Stored and Fresh PBMC Cells Using Different Protein Extraction Buffers.The protein journal · 2020Article
- Article
- Application of mass spectrometry to elucidate the pathophysiology of Encephalitozoon cuniculi infection in rabbits.PloS one · 2017Article
- Article
- Comparative Proteomic Analyses of Avirulent, Virulent, and Clinical Strains of Mycobacterium tuberculosis Identify Strain-specific Patterns.The Journal of biological chemistry · 2016Article
- Article
- Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies.Inflammatory bowel diseases · 2015Article
- Alteration of actin dependent signaling pathways associated with membrane microdomains in hyperlipidemia.Proteome science · 2015Article
- Multifactorial comparative proteomic study of cytochrome P450 2E1 function in chronic alcohol administration.PloS one · 2014Article
- Mouse genetics and proteomic analyses demonstrate a critical role for complement in a model of DHRD/ML, an inherited macular degeneration.Human molecular genetics · 2014Article
- A comparative protein function analysis databaseof different Leishmania strains.Bioinformation · 2011Article
- Iron-sparing response of Mycobacterium avium subsp. paratuberculosis is strain dependent.BMC microbiology · 2010Article
- Tuberculosis: global approaches to a global disease.Current opinion in biotechnology · 2010Review
- Assigning significance in label-free quantitative proteomics to include single-peptide-hit proteins with low replicates.International journal of proteomics · 2010Article
- Systems biology approaches to understanding mycobacterial survival mechanisms.Drug discovery today. Disease mechanisms · 2010Article
- A systems biology approach to study the phagosomal proteome modulated by mycobacterial infections.International journal of clinical and experimental medicine · 2009Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.