ArticleJournal of proteome research2008
Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.
Article in Journal of proteome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 45 citations in OpenAlex.
- A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS.Scientific data · 2023Article
- Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis inMicroorganisms · 2022Article
- Quantitative Mass Spectrometry by SILAC in Haloferax volcanii.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A wide-ranging Pseudomonas aeruginosa PeptideAtlas build: A useful proteomic resource for a versatile pathogen.Journal of proteomics · 2021Article
- The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics.Nature communications · 2020Article
- Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea.RNA biology · 2018Article
- Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses.Environmental microbiology · 2018Article
- The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.Journal of proteome research · 2017Article
- Article
- Development of New Modular Genetic Tools for Engineering the Halophilic Archaeon Halobacterium salinarum.PloS one · 2015Article
- A Candida albicans PeptideAtlas.Journal of proteomics · 2014Article
- Effects of intracellular Mn on the radiation resistance of the halophilic archaeon Halobacterium salinarum.Extremophiles : life under extreme conditions · 2013Article
- The state of the human proteome in 2012 as viewed through PeptideAtlas.Journal of proteome research · 2013Article
- A role for programmed cell death in the microbial loop.PloS one · 2013Article
- A probabilistic framework for peptide and protein quantification from data-dependent and data-independent LC-MS proteomics experiments.Omics : a journal of integrative biology · 2012Article
- The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon.BMC genomics · 2012Article
- Extreme challenges and advances in archaeal proteomics.Current opinion in microbiology · 2012Review
- Statistical methods for quantitative mass spectrometry proteomic experiments with labeling.BMC bioinformatics · 2012Review
- Relative quantification: characterization of bias, variability and fold changes in mass spectrometry data from iTRAQ-labeled peptides.Journal of proteome research · 2011Article
- Generating and navigating proteome maps using mass spectrometry.Nature reviews. Molecular cell biology · 2010Review
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
Abstract
The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.
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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.