ReviewProteomics2007
Protein abundance ratios for global studies of prokaryotes.
Review in Proteomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
13 citing papers in PubMed.
- What are We Learning and What Can We Learn from the Human Oral Microbiome Project?Current oral health reports · 2016Article
- Effective correction of experimental errors in quantitative proteomics using stable isotope labeling by amino acids in cell culture (SILAC).Journal of proteomics · 2012Article
- Cellular and bacterial profiles associated with oral epithelium-microbiota interactions.Periodontology 2000 · 2010Review
- The transcription unit architecture of the Escherichia coli genome.Nature biotechnology · 2009Article
- Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.BMC microbiology · 2009Article
- Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis.BMC microbiology · 2009Article
- The oligopeptide transport system is essential for the development of natural competence in Streptococcus thermophilus strain LMD-9.Journal of bacteriology · 2009Article
- Proteomics of Porphyromonas gingivalis within a model oral microbial community.BMC microbiology · 2009Article
- Tools for interpreting large-scale protein profiling in microbiology.Journal of dental research · 2008Review
- Science, marketing and wishful thinking in quantitative proteomics.Proteomics · 2008Article
- Comprehensive proteomics of Methylobacterium extorquens AM1 metabolism under single carbon and nonmethylotrophic conditions.Proteomics · 2008Article
- Proteomic identification of novel proteins associated with Lewy bodies.Frontiers in bioscience : a journal and virtual library · 2008Article
- Quantitative proteomics of intracellular Porphyromonas gingivalis.Proteomics · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
The use of multidimensional capillary HPLC combined with MS/MS has allowed high qualitative and quantitative proteome coverage of prokaryotic organisms. The determination of protein abundance change between two or more conditions has matured to the point that false discovery rates can be very low and for smaller proteomes coverage is sufficiently high to explicitly consider false negative error. Selected aspects of using these methods for global protein abundance assessments are reviewed. These include instrumental issues that influence the reliability of abundance ratios; a comparison of sources of nonlinearity, errors, and data compression in proteomics and spotted cDNA arrays; strengths and weaknesses of spectral counting versus stable isotope metabolic labeling; and a survey of microbiological applications of global abundance analysis at the protein level. Proteomic results for two organisms that have been studied extensively using these methods are reviewed in greater detail. Spectral counting and metabolic labeling data are compared and the utility of proteomics for global gene regulation studies are discussed for the methanogenic Archaeon Methanococcus maripaludis. The oral pathogen Porphyromonas gingivalis is discussed as an example of an organism where a large percentage of the proteome differs in relative abundance between the intracellular and extracellular phenotype.
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What OpenQuestion holds
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.