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Universal pretreatment development for low-input proteomics using lauryl maltose neopentyl glycol
In this study, we have developed a lauryl maltose neopentyl glycol (LMNG)-assisted sample preparation (LASP) method. This method effectively reduces protein and peptide loss in samples by incorporating LMNG, a surfactant, into the digestion solution and subsequently removing the LMNG simply via reversed phase solid-phase extraction. The advantage of removing LMNG during sample preparation for general proteomic analysis is the prevention of mass spectrometry (MS) contamination. When we applied the LASP method to the low-input SP3 method and on-bead digestion in co-immunoprecipitation-MS, we observed a significant improvemen...
Source: Molecular and Cellular Proteomics : MCP - March 6, 2024 Category: Molecular Biology Authors: Ryo Konno Masaki Ishikawa Daisuke Nakajima Yusuke Endo Osamu Ohara Yusuke Kawashima Source Type: research

Ribosome Profiling and Mass Spectrometry Reveal Widespread Mitochondrial Translation Defects in a Striatal Cell Model of Huntington Disease
Mol Cell Proteomics. 2024 Mar 4:100746. doi: 10.1016/j.mcpro.2024.100746. Online ahead of print.ABSTRACTHuntington disease (HD) is caused by an expanded polyglutamine mutation in huntingtin (mHTT) that promotes prominent atrophy in the striatum and subsequent psychiatric, cognitive, and choreiform movements. Multiple lines of evidence point to an association between HD and aberrant striatal mitochondrial functions; however, the present knowledge about whether (or how) mitochondrial mRNA translation is differentially regulated in HD remains unclear. We found that protein synthesis is diminished in HD mitochondria compared t...
Source: Molecular and Cellular Proteomics : MCP - March 6, 2024 Category: Molecular Biology Authors: Sunayana Dagar Manish Sharma George Tsaprailis Catherina Scharager Tapia Gogce Crynen Preksha Sandipkumar Joshi Neelam Shahani Srinivasa Subramaniam Source Type: research

Global interactome mapping reveals pro-tumorigenic interactions of NF- κB in breast cancer
This study describes a network of pro-tumorigenic protein interactions and their rearrangement upon NF-κB inhibition with potential therapeutic implications in tumors with high NF-κB activity.PMID:38417630 | DOI:10.1016/j.mcpro.2024.100744 (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - February 28, 2024 Category: Molecular Biology Authors: Petr Lapcik R Greg Stacey David Potesil Petr Kulhanek Leonard J Foster Pavel Bouchal Source Type: research

pXg: Comprehensive identification of noncanonical MHC-I-associated peptides from de novo peptide sequencing using RNA-Seq reads
Mol Cell Proteomics. 2024 Feb 23:100743. doi: 10.1016/j.mcpro.2024.100743. Online ahead of print.ABSTRACTDiscovering noncanonical peptides has been a common application of proteogenomics. Recent studies suggest that certain noncanonical peptides, known as ncMAPs (noncanonical MHC-I-associated peptides), that bind to major histocompatibility complex I may make good immunotherapeutic targets. De novo peptide sequencing is a great way to find ncMAPs since it can detect peptide sequences from their tandem mass spectra without using any sequence databases. However, this strategy hasn't been widely applied for ncMAP identificati...
Source: Molecular and Cellular Proteomics : MCP - February 25, 2024 Category: Molecular Biology Authors: Seunghyuk Choi Eunok Paek Source Type: research

Phosphorothioate RNA Analysis by NETD Tandem Mass Spectrometry
Mol Cell Proteomics. 2024 Feb 22:100742. doi: 10.1016/j.mcpro.2024.100742. Online ahead of print.ABSTRACTTherapeutic ribonucleic acids (RNAs) are routinely modified during their synthesis to ensure proper drug uptake, stability, and efficacy. Phosphorothioate (PS) RNA, molecules in which one or more backbone phosphates are modified with a sulfur atom in place of standard non-bridging oxygen, is one of the most common modifications due to ease of synthesis and pharmacokinetic benefits. Quality assessment of RNA synthesis, including modification incorporation, is essential for drug selectivity and performance, and the synthe...
Source: Molecular and Cellular Proteomics : MCP - February 24, 2024 Category: Molecular Biology Authors: Trenton M Peters-Clarke Qiuwen Quan Benton J Anderson William M McGee Emily Lohr Alexander S Hebert Michael S Westphall John E P Syka James L Stephenson Joshua J Coon Source Type: research