Glutamine supplementation alleviated aortic atherosclerosis in mice model and in vitro
This study aimed to clarify the role of glutamine in atherosclerosis and its participating mechanism. Forty C57BL/6J mice were divided into wild control (wild Con), ApoE−/− control (ApoE−/− Con), glutamine + ApoE−/−control (Glut + ApoE−/− Con), ApoE−/− high fat diet (ApoE−/− HFD), and glutamine + ApoE−/− HFD (Glut + ApoE−/− HFD) groups. The degree of atherosclerosis, western blotting, and multiomics were detected at 18 weeks. An in vitro study was also performed. Glutamine treatment significantly decreased the degree of aortic atherosclerosis (p = 0.03).O-GlcNAcylation (O-Glc...
Source: Proteomics - September 8, 2023 Category: Biochemistry Authors: Hao Zhang,
Chunxiu Wang,
Haichen Sun,
Tian Zhou,
Chang Ma,
Xuexue Han,
Tianxing Zhang,
Jinggang Xia Tags: RESEARCH ARTICLE Source Type: research
HowDirty: An R package to evaluate molecular contaminants in LC ‐MS experiments
AbstractContaminants derived from consumables, reagents, and sample handling often negatively affect LC-MS data acquisition. In proteomics experiments, they can markedly reduce identification performance, reproducibility, and quantitative robustness. Here, we introduce a data analysis workflow combining MS1 feature extraction in Skyline with HowDirty, an R-markdown-based tool, that automatically generates an interactive report on the molecular contaminant level in LC-MS data sets. To facilitate the interpretation of the results, the HTML report is self-contained and self-explanatory, including plots that can be easily inte...
Source: Proteomics - September 8, 2023 Category: Biochemistry Authors: David Gomez ‐Zepeda,
Thomas Michna,
Tanja Ziesmann,
Ute Distler,
Stefan Tenzer Tags: TECHNICAL BRIEF Source Type: research
Oktoberfest: Open ‐source spectral library generation and rescoring pipeline based on Prosit
AbstractMachine learning (ML) and deep learning (DL) models for peptide property prediction such as Prosit have enabled the creation of high quality in silico reference libraries. These libraries are used in various applications, ranging from data-independent acquisition (DIA) data analysis to data-driven rescoring of search engine results. Here, we present Oktoberfest, an open source Python package of our spectral library generation and rescoring pipeline originally only available online via ProteomicsDB. Oktoberfest is largely search engine agnostic and provides access to online peptide property predictions, promoting th...
Source: Proteomics - September 7, 2023 Category: Biochemistry Authors: Mario Picciani,
Wassim Gabriel,
Victor ‐George Giurcoiu,
Omar Shouman,
Firas Hamood,
Ludwig Lautenbacher,
Cecilia Bang Jensen,
Julian Müller,
Mostafa Kalhor,
Armin Soleymaniniya,
Bernhard Kuster,
Matthew The,
Mathias Wilhelm Tags: TECHNICAL BRIEF Source Type: research
Proteomics elucidating physiological and pathological functions of TDP ‐43
AbstractTrans-activation response DNA binding protein of 43 kDa (TDP-43) regulates a great variety of cellular processes in the nucleus and cytosol. In addition, a defined subset of neurodegenerative diseases is characterized by nuclear depletion of TDP-43 as well as cytosolic mislocalization and aggregation. To perform its diverse functions TDP-43 can ass ociate with different ribonucleoprotein complexes. Combined with transcriptomics, MS interactome studies have unveiled associations between TDP-43 and the spliceosome machinery, polysomes and RNA granules. Moreover, the highly dynamic, low-valency interactions regulate...
Source: Proteomics - September 6, 2023 Category: Biochemistry Authors: Jorge Garc ía Morato,
Christian Johannes Gloeckner,
Philipp J. Kahle Tags: REVIEW Source Type: research
(Re ‐)use and (re‐)analysis of publicly available metabolomics data
AbstractMetabolomics, the systematic measurement of small molecules (<1000 Da) in a given biological sample, is a fast-growing field with many different applications. In contrast to transcriptomics and proteomics, sharing of data is not as widespread in metabolomics, though more scientists are sharing their data nowadays. However, to improve data analysis tools and devel op new data analytical approaches and to improve metabolite annotation and identification, sharing of reference data is crucial. Here, different possibilities to share (metabolomics) data are reviewed and some recent approaches and applications regard...
Source: Proteomics - September 6, 2023 Category: Biochemistry Authors: Michael Witting Tags: REVIEW Source Type: research
Front Cover
Cover Image © Wiley-VCH GmbH. The image is part of a figure in the article DOI:10.1002/pmic.201900203 by Lei Li, Yong Jiang et al. (Source: Proteomics)
Source: Proteomics - September 5, 2023 Category: Biochemistry Tags: FRONT COVER Source Type: research
Contents: Proteomics 17'23
(Source: Proteomics)
Source: Proteomics - September 5, 2023 Category: Biochemistry Tags: CONTENTS Source Type: research
Editorial Board: Proteomics 17'23
(Source: Proteomics)
Source: Proteomics - September 5, 2023 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research
Standard abbreviations
(Source: Proteomics)
Source: Proteomics - September 5, 2023 Category: Biochemistry Tags: STANDARD ABBREVIATIONS Source Type: research
Structural biology: The transformational era
(Source: Proteomics)
Source: Proteomics - September 5, 2023 Category: Biochemistry Authors: Shoshana J. Wodak,
Sameer Velankar Tags: EDITORIAL Source Type: research
