Having fast, accurate, and broad spectrum methods for the identification of microorganisms is of paramount importance to public health, research, and safety. Bottom-up mass spectrometer-based proteomics has emerged as an effective tool for the accurate identification of microorganisms from microbial isolates. However, one major hurdle that limits the deployment of this tool for routine clinical diagnosis, and other areas of research such as culturomics, is the instrument time required for the mass spectrometer to analyze a single sample, which can take ∼1 h per sample, when using mass spectrometers that are presently used in most institutes. To address this issue, in this study, we employed, for the first time, tandem mass tags (TMTs) in multiplex identifications of microorganisms from multiple TMT-labeled samples in one MS/MS experiment. A difficulty encountered when using TMT labeling is the presence of interference in the measured intensities of TMT reporter ions. To correct for interference, we employed in the proposed method a modified version of the expectation maximization (EM) algorithm that redistributes the signal from ion interference back to the correct TMT-labeled samples. We have evaluated the sensitivity and specificity of the proposed method using 94 MS/MS experiments (covering a broad range of protein concentration ratios across TMT-labeled channels and experimental parameters), containing a total of 1931 true positive TMT-labeled channels and 317 true negative TMT-labeled channels. The results of the evaluation show that the proposed method has an identification sensitivity of 93-97% and a specificity of 100% at the species level. Furthermore, as a proof of concept, using an in-house-generated data set composed of some of the most common urinary tract pathogens, we demonstrated that by using the proposed method the mass spectrometer time required per sample, using a 1 h LC-MS/MS run, can be reduced to 10 and 6 min when samples are labeled with TMT-6 and TMT-10, respectively. The proposed method can also be used along with Orbitrap mass spectrometers that have faster MS/MS acquisition rates, like the recently released Orbitrap Astral mass spectrometer, to further reduce the mass spectrometer time required per sample.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11157548 | PMC |
http://dx.doi.org/10.1021/jasms.3c00445 | DOI Listing |
Clin Trials
January 2025
Department of Biostatistics, University of Washington, Seattle, WA, USA.
Background: N-of-1 trials compare two or more treatment options for a single participant. These trials have been used to study options for chronic conditions such as arthritis and attention deficit hyperactivity disorder. In addition, they have been suggested as a means to study interventions in rare populations that may not be tractable to include in standard clinical trials, such as treatment options for HIV-positive patients in need of organ transplant.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China.
With the advancement of high harmonic generation and X-ray free-electron lasers (XFELs) to the attosecond domain, the studies of the ultrafast electron and spin dynamics became possible. Yet, the methods for efficient control and measurement of the quantum state are to be further developed. In this publication, we propose using magnetic X-ray scattering (MXS) for resolving the molecular spin-state dynamics and establish a complete protocol to simulate MXS diffraction patterns in molecules with ab initio quantum chemistry based on the multiconfigurational method.
View Article and Find Full Text PDFIntroduction: Free radical-mediated oxidative renal tubular injury secondary to hyperoxaluria is a proposed mechanism in the formation of calcium oxalate stones. Vitamin E, an important physiologic antioxidant, has been shown in rat models to prevent calcium oxalate crystal deposition. Our objective was to determine if low dietary vitamin E intake was associated with a higher incidence of stones.
View Article and Find Full Text PDFIntroduction: Impella CP is a percutaneous left ventricle assist device used in selected patients undergoing high-risk percutaneous coronary interventions (HR-PCI). To improve outcomes after Impella-supported HR-PCI, institutional Impella programs have been developed.
Objectives: We evaluated the association between the standardized periprocedural management algorithm and outcomes of patients undergoing HR-PCI in the national IMPELLA-PL Registry.
Glob Chang Biol
January 2025
Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic.
Climate change poses an unprecedented threat to forest ecosystems, necessitating innovative adaptation strategies. Traditional assisted migration approaches, while promising, face challenges related to environmental constraints, forestry practices, phytosanitary risks, economic barriers, and legal constraints. This has sparked debate within the scientific community, with some advocating for the broader implementation of assisted migration despite these limitations, while others emphasize the importance of local adaptation, which may not keep pace with the rapid rate of climate change.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!