Quantitative strategies relying on stable isotope labeling and isotope dilution mass spectrometry have proven to be a very robust alternative to the well established gel-based techniques for the study of the dynamic proteome. Postdigestion 18O labeling is becoming very popular mainly due to the simplicity of the enzyme-catalyzed exchange reaction, the peptide handling and storage procedures, and the flexibility and versatility introduced by decoupling protein digestion from peptide labeling. Despite recent progresses, peptide quantification by postdigestion 18O labeling still involves several computational problems. In this work we analyzed the behavior of large collections of peptides when they were subjected to postdigestion labeling and concluded that this process can be explained by a universal kinetic model. On the basis of this observation, we developed an advanced quantification algorithm for this kind of labeling. Our method fits the entire isotopic envelope to parameters related with the kinetic exchange model, allowing at the same time an accurate calculation of the relative proportion of peptides in the original samples and of the specific labeling efficiency of each one of the peptides. We demonstrated that the new method eliminates artifacts produced by incomplete oxygen exchange in subsets of peptides that have a relatively low labeling efficiency and that may be considered indicative of false protein ratio deviations. Finally using a rigorous statistical analysis based on the calculation of error rates associated with false expression changes, we showed the validity of the method in the practice by detecting significant expression changes, produced by the activation of a model preparation of T cells, with only 5 microg of protein in three proteins among a pool of more than 100. By allowing a full control over potential artifacts, our method may improve automation of the procedures for relative protein quantification using this labeling strategy.
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http://dx.doi.org/10.1074/mcp.T600029-MCP200 | DOI Listing |
iScience
December 2024
Department of Molecular Environmental Biotechnology, Helmholtz-Centre for Environmental Research - UFZ, 04318 Leipzig, Saxony, Germany.
Protein-based stable isotope probing (protein-SIP) can link microbial taxa to substrate assimilation. Traditionally, protein-SIP requires a sample-specific metagenome-derived database for samples with unknown composition. Here, we describe GroEL-prototyping-based stable isotope probing (GroEL-SIP), that uses GroEL as a taxonomic marker protein to identify bacterial taxa (GroEL-proteotyping) coupled to SIP directly linking identified taxa to substrate consumption.
View Article and Find Full Text PDFChem Res Toxicol
December 2024
Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.
The algal macrolide goniodomin A (GDA) undergoes ring-cleavage under unusually mild, alkaline conditions to form mixtures of stereoisomers of seco acids GDA-sa and iso-GDA-sa. In the primary fragmentation pathway, opening of the macrolide ring occurs by displacement of the carboxyl group by a base-catalyzed attack of the C32 hemiketal hydroxy group on C31, yielding an oxirane-carboxylic acid, named goniodomic acid. The oxirane ring is unstable, undergoing solvolytic opening to form mainly GDA-sa.
View Article and Find Full Text PDFEnviron Sci Technol
December 2024
Department Environmental Analytical Chemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany.
Wastewater ozonation is commonly employed to enhance the subsequent biodegradation of effluent organic matter (EfOM) and contaminants of concern. However, there is evidence suggesting the formation of recalcitrant ozonation products (OPs) from EfOM. To investigate the biodegradability of OPs we conducted batch biodegradation experiments using wastewater effluent ozonated with mass-labeled (O) ozone.
View Article and Find Full Text PDFFree Radic Biol Med
December 2024
Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark. Electronic address:
Angew Chem Int Ed Engl
November 2024
School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
Activating the lattice oxygen can significantly improve the kinetics of oxygen evolution reaction (OER), however, it often results in reduced stability due to the bulk structure degradation. Here, we develop a spinel FeCoCrO with active lattice oxygen by high-throughput methods, achieving high OER activity and stability, superior to the benchmark IrO. The oxide exhibits an ultralow overpotential (190 mV at 10 mA cm) with outstanding stability for over 170 h at 100 mA cm.
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