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The Landscape and Perspectives of the Human Gut Metaproteomics
Mol Cell Proteomics. 2024 Apr 10:100763. doi: 10.1016/j.mcpro.2024.100763. Online ahead of print.ABSTRACTThe human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substant...
Source: Molecular and Cellular Proteomics : MCP - April 12, 2024 Category: Molecular Biology Authors: Zhongzhi Sun Zhibin Ning Daniel Figeys Source Type: research

Multi-omic analysis of Esophageal Adenocarcinoma uncovers candidate therapeutic targets and cancer-selective post-transcriptional regulation
CONCLUSIONS: By quantitative proteomic analysis we have identified GPA33 as an EAC-selective biomarker. Integrated analysis of proteome, transcriptome, and genome in EAC has revealed several genes with tumor-selective, post-transcriptional regulation of protein expression which may be an exploitable vulnerability.PMID:38604503 | DOI:10.1016/j.mcpro.2024.100764 (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - April 11, 2024 Category: Molecular Biology Authors: J Robert O'Neill Marcos Y ébenes Mayordomo Goran Mitulovi ć Sofian Al Shboul Georges Bedran Jakub Faktor Lenka Hernychova Lukas Uhrik Maria Gomez-Herranz Miko łaj Kocikowski Vicki Save Bo řivoj Vojtěšek Mark Arends OCCAMS consortium Ted Hupp Javier Source Type: research

Systematic investigation of the trafficking of glycoproteins on the cell surface
Mol Cell Proteomics. 2024 Apr 7:100761. doi: 10.1016/j.mcpro.2024.100761. Online ahead of print.ABSTRACTGlycoproteins located on the cell surface play a pivotal role in nearly every extracellular activity. N-glycosylation is one of the most common and important protein modifications in eukaryotic cells, and it often regulates protein folding and trafficking. Glycosylation of cell-surface proteins undergoes meticulous regulation by various enzymes in the endoplasmic reticulum (ER) and the Golgi, ensuring their proper folding and trafficking to the cell surface. However, the impacts of protein N-glycosylation, N-glycan matur...
Source: Molecular and Cellular Proteomics : MCP - April 9, 2024 Category: Molecular Biology Authors: Xing Xu Kejun Yin Ronghu Wu Source Type: research

The one hour human proteome
We describe deep analysis of the human proteome in less than one hour. We achieve this expedited proteome characterization by leveraging state-of-the-art sample preparation, chromatographic separations, data analysis tools, and by using the new Orbitrap Astral mass spectrometer equipped with a quadrupole mass filter, a high-field Orbitrap mass analyzer, and an asymmetric track lossless (Astral) mass analyzer. The system offers high MS/MS acquisition speed of 200 Hz and detects hundreds of peptide sequences per second within data independent- or data-dependent acquisition modes of operation. The fast-switching capabilities ...
Source: Molecular and Cellular Proteomics : MCP - April 5, 2024 Category: Molecular Biology Authors: Lia R Serrano Trenton M Peters-Clarke Tabiwang N Arrey Nicolaie E Damoc Margaret Lea Robinson Noah M Lancaster Evgenia Shishkova Corinne Moss Anna Pashkova Pavel Sinitcyn Dain R Brademan Scott T Quarmby Amelia C Peterson Martin Zeller Daniel Hermanson Ham Source Type: research

Fast and accurate disulfide bridge detection
Mol Cell Proteomics. 2024 Apr 2:100759. doi: 10.1016/j.mcpro.2024.100759. Online ahead of print.ABSTRACTRecombinant expression of proteins, propelled by therapeutic antibodies, has evolved into a multi-billion-dollar industry. Essential here is quality control assessment of critical attributes such as sequence fidelity, proper folding, and post-translational modifications (PTMs). Errors can lead to diminished bioactivity and, in the context of therapeutic proteins, an elevated risk for immunogenicity. Over the years, many techniques were developed and applied to validate proteins in a standardized and high-throughput fashi...
Source: Molecular and Cellular Proteomics : MCP - April 4, 2024 Category: Molecular Biology Authors: S øren Heissel Yi He Andris Jankevics Yuqi Shi Henrik Molina Rosa Viner Richard A Scheltema Source Type: research

Proteomics Impact on Cell Biology to Resolve Cell Structure and Function
Mol Cell Proteomics. 2024 Apr 2:100758. doi: 10.1016/j.mcpro.2024.100758. Online ahead of print.ABSTRACTThe acceleration of advances in proteomics has enabled integration with imaging at the EM and LM levels, cryo-electron microscopy of protein structures, and artificial intelligence (AI) with proteins comprehensively and accurately resolved for cell structures at nm to sub-nm resolution. Proteomics continues to outpace experimentally based structural imaging, but their ultimate integration is a path towards the goal of a compendium of all proteins to understand mechanistically cell structure and function.PMID:38574860 | D...
Source: Molecular and Cellular Proteomics : MCP - April 4, 2024 Category: Molecular Biology Authors: John J M Bergeron Source Type: research

Assessment of Kinome-wide Activity Remodeling Upon Picornavirus Infection
Mol Cell Proteomics. 2024 Mar 29:100757. doi: 10.1016/j.mcpro.2024.100757. Online ahead of print.ABSTRACTPicornaviridae represent a large family of single-stranded positive RNA viruses of which different members can infect both humans and animals. These include the enteroviruses (e.g., poliovirus, coxsackievirus, and rhinoviruses) as well as the cardioviruses (e.g., encephalomyocarditis virus (EMCV)). Picornaviruses have evolved to interact with, use, and/or evade cellular host systems to create the optimal environment for replication and spreading. It is known that viruses modify kinase activity during infection, but a pr...
Source: Molecular and Cellular Proteomics : MCP - March 31, 2024 Category: Molecular Biology Authors: Tim S Veth Lonneke V Nouwen Marleen Zwaagstra Heyrhyoung Lyoo Kathryn A Wierenga Bart Westendorp Maarten A F M Altelaar Celia Berkers Frank J M van Kuppeveld Albert J R Heck Source Type: research