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Impact of Local Air Pressure on Ion Mobilities and Data Consistency in diaPASEF-Based High Throughput Proteomics.
J Proteome Res
January 2025
Omics Technologies, Cellzome a GSK company, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
Data-independent acquisition (DIA) on ion mobility mass spectrometers enables deep proteome coverage and high data completeness in large-scale proteomics studies. For advanced acquisition schemes such as parallel accumulation serial fragmentation-based DIA (diaPASEF) stability of ion mobility (1/K) over time is crucial for consistent data quality. We found that minor changes in environmental air pressure systematically affect the vacuum pressure in the TIMS analyzer, causing ion mobility shifts.
View Article and Find Full Text PDFData from a multi-year targeted proteomics study of a longitudinal birth cohort of type 1 diabetes.
Sci Data
January 2025
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
The deployment of liquid chromatography-mass spectrometry-based plasma proteomics experiments in a large cohort is sparse, leading to a lack of data available for benchmarking, method development or validation. Comprised of 6,426 plasma analyses, The Environmental Determinants of Diabetes in the Young (TEDDY) proteomics validation study constitutes one of the largest targeted proteomics experiments in the literature to date. The proteomics data from this study were generated over the course of 2.
View Article and Find Full Text PDFSelected Ion Extraction of Peptides with Heavy Isotopes and Hydrogen Loss Reduces the Type II Error in Plasma Proteomics.
ACS Omega
January 2025
Department of Chemistry and Biology, Faculty of Science, Toronto Metropolitan University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada.
Naturally occurring peptides display a wide mass distribution after ionization due to the presence of heavy isotopes of C, H, N, O, and S and hydrogen loss. There is a crucial need for sensitive methods that collect as much information as possible about all plasma peptide forms. Statistical analysis of the delta mass distribution of peptide precursors from MS/MS spectra that were matched to 63,077 peptide sequences by X!TANDEM revealed Gaussian peaks representing heavy isotopes and hydrogen loss at integer delta mass values of -3, -2, -1, 0, +1, +2, +3, +4, and +5 Da.
View Article and Find Full Text PDFCorrecting mitochondrial loss mitigates NOTCH1-related aortopathy in mice.
Nat Cardiovasc Res
January 2025
Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
Loss-of-function mutations in NOTCH1 were previously linked to thoracic aortopathy, a condition for which non-surgical treatment options are limited. Based on clinical proteome analysis, we hypothesized that mitochondrial fusion and biogenesis in aortic smooth muscle cells (SMCs) are crucial for regulating the progression of NOTCH1-related aortopathy. Here we demonstrate that SMC-specific Notch1 knockout mice develop aortic pathology, including stiffening, dilation and focal dissection.
View Article and Find Full Text PDFImpaired hydrogen sulfide biosynthesis underlies eccentric contraction-induced force loss in dystrophin-deficient skeletal muscle.
J Clin Invest
January 2025
Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, United States of America.
Eccentric contraction- (ECC) induced force loss is a hallmark of murine dystrophin-deficient (mdx) skeletal muscle that is used to assess efficacy of potential therapies for Duchenne muscular dystrophy. While virtually all key proteins involved in muscle contraction have been implicated in ECC force loss, a unifying mechanism that orchestrates force loss across such diverse molecular targets has not been identified. We showed that correcting defective hydrogen sulfide (H2S) signaling in mdx muscle prevented ECC force loss.
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