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We describe a mass spectrometry method, QuantMode, which improves accuracy of isobaric tag-based quantification by alleviating the pervasive problem of precursor interference, simultaneous isolation and fragmentation of impurities, through gas-phase purification. QuantMode analysis of a yeast sample 'contaminated' with interfering human peptides showed substantially improved quantitative accuracy compared to a standard scan, with a small loss of spectral identifications. This technique enables large-scale, multiplexed quantitative proteomics using isobaric tagging.
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http://dx.doi.org/10.1038/nmeth.1716 | DOI Listing |
Biotechnol Adv
August 2025
Institute of Sustainable Processes, Dr. Mergelina, s/n, 47011 Valladolid, Spain; Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Dr. Mergelina, s/n, 47011 Valladolid, Spain. Electronic address:
Gasification has emerged as a promising platform to cope with recalcitrant organic waste within the framework of biomass-based biorefineries, producing syngas that can be fermented into valuable bioproducts. Despite its potential, syngas fermentation is based predominantly on pure cultures, which faces significant challenges, including the limited portfolio of generated compounds (primarily acetate and ethanol) and their low productivity. To address these bottlenecks, the potential of microbial consortia as effective platforms for syngas conversion has been evaluated.
View Article and Find Full Text PDFBiomacromolecules
September 2025
Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, International Innovation Center for Forest Chemicals and Materials, College of Chemical Engineering, Nanjing Forestry University, Longpan Road 159, Nanjing 210037, China.
Chitin/protein nanofibrils are extracted from decalcified crab shells using 100 mM hydrochloric acid and ultrasonication or high-pressure homogenization, achieving a 94% recovery rate. Further increases in the temperature or duration enhance hydrolysis, leading to a significant reduction in the nanofibril size. The increase in the number of acidic amino acids within the nanofibrils enhances electrostatic repulsion, promoting their dispersion under acidic conditions.
View Article and Find Full Text PDFPhys Chem Chem Phys
September 2025
Universiti Kuala Lumpur, Branch Campus Malaysian Institute of Chemical and Bioengineering Technology, Lot 1988, Kawasan Perindustrian Bandar Vendor, 78000 Alor Gajah, Melaka, Malaysia.
In this reply, we address the concerns raised regarding the theoretical consistency of the modeling approaches used in our original study on hydrogen sulfide adsorption onto ZSM-5. Specifically, the issues relate to the application of the Temkin isotherm, the Weber-Morris intraparticle diffusion model, and the use of a dimensional distribution coefficient in the thermodynamic analysis. We acknowledge that the simplified Temkin model was misapplied and does not strictly conform to theoretical requirements; however, it was used to represent mid-range adsorption behavior consistent with our experimental conditions.
View Article and Find Full Text PDFAnal Chem
September 2025
Laboratory for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland.
Phosphorothioate (PS) modifications in small interfering RNA (siRNA) moieties enhance stability and therapeutic efficacy, but introduce diastereomeric heterogeneity, complicating structural characterization. Conventional chromatographic methods, such as ion-pair reversed-phase liquid chromatography, provide limited resolution of complex stereoisomer systems, necessitating alternative analytical approaches. In this work, we systematically evaluate cyclic ion mobility spectrometry (cIMS) for the separation and identification of PS diastereomers by investigating oligonucleotide systems with varying chain length and PS linkage patterns that mimic the metabolic diversity in siRNA therapeutics.
View Article and Find Full Text PDFWorld J Microbiol Biotechnol
July 2025
Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.
Microbial methanation, which produces CH from H and CO (H/CO) using hydrogenotrophic methanogens, converts CO into a resource. The proposed system utilizes an isolated strain of hydrogenotrophic methanogen and an anaerobic microbial community from a deep aquifer where H and CO are produced via biodegradation of organic matter by fermentative bacteria, which CH is then produced from H and CO by hydrogenotrophic methanogens. The strain and microbial community were added separately to liquid medium in serum bottles.
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