ArticleMolecular & cellular proteomics : MCP2011
Quantitative tracking of isotope flows in proteomes of microbial communities.
Article in Molecular & cellular proteomics : MCP, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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.
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Who cites it
30 citing papers in PubMed, 81 citations in OpenAlex.
- Review
- Proteomic stable isotope probing with an upgraded Sipros algorithm for improved identification and quantification of isotopically labeled proteins.Microbiome · 2024Article
- Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes.Microbiome · 2023Article
- DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Flow-through stable isotope probing (Flow-SIP) minimizes cross-feeding in complex microbial communities.The ISME journal · 2021Article
- Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat.Applied and environmental microbiology · 2020Article
- Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities UsingFrontiers in microbiology · 2019Article
- Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Sipros Ensemble improves database searching and filtering for complex metaproteomics.Bioinformatics (Oxford, England) · 2018Article
- Identification of peptide-binding sites within BSA using rapid, laser-induced covalent cross-linking combined with high-performance mass spectrometry.Journal of molecular recognition : JMR · 2018Article
- Phylogenetically conserved resource partitioning in the coastal microbial loop.The ISME journal · 2017Article
- Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage.Frontiers in microbiology · 2016Article
- Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities.Frontiers in microbiology · 2016Article
- The activity of protein phosphatase 5 towards native clients is modulated by the middle- and C-terminal domains of Hsp90.Scientific reports · 2015Article
- Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota.Proteomics · 2015Review
- Proteomic tools to decipher microbial community structure and functioning.Environmental science and pollution research international · 2015Review
- Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Analytics for Metabolic Engineering.Frontiers in bioengineering and biotechnology · 2015Review
- Systems-based approaches to unravel multi-species microbial community functioning.Computational and structural biotechnology journal · 2015Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identifies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences between closely related protein sequences, and for detecting labeling patterns in low-abundance proteins or proteins derived from rare community members. The proteomic SIP method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, ∼50%, and ∼98%. The method was then used to monitor incorporation of (15)N into established and regrowing microbial biofilms. The results indicate organism-specific migration patterns from established communities into regrowing communities and provide insights into metabolism during biofilm formation. The proteomic SIP method can be extended to many systems to track fluxes of (13)C or (15)N in microbial communities.
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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.