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LAFEM: A scoring model to evaluate functional landscape of lysine acetylome
Mol Cell Proteomics. 2023 Dec 15:100700. doi: 10.1016/j.mcpro.2023.100700. Online ahead of print.ABSTRACTProtein lysine acetylation is a critical post-translation modification (PTM) involved in a wide range of biological processes. To date, about 20,000 acetylation sites of Homo sapiens were identified through mass spectrometry-based proteomic technology but more than 95% of them have unclear functional annotations due to the lack of existing prioritization strategy to assess the functional importance of the acetylation sites on large-scale. Hence, we established a lysine acetylation functional evaluating model (LAFEM) by ...
Source: Molecular and Cellular Proteomics : MCP - December 17, 2023 Category: Molecular Biology Authors: Jun-Ze Liang De-Hua Li Yong-Chun Xiao Fu-Jin Shi Tairan Zhong Qian-Ying Liao Yang Wang Qing-Yu He Source Type: research

Dissecting ubiquitylation and DNA damage response pathways in the yeast Saccharomyces cerevisiae using a proteome-wide approach
Mol Cell Proteomics. 2023 Dec 13:100695. doi: 10.1016/j.mcpro.2023.100695. Online ahead of print.ABSTRACTIn response to genotoxic stress, cells evolved with a complex signaling network referred to as the DNA damage response (DDR). It is now well established that the DDR depends upon various post-translational modifications; among them, ubiquitylation plays a key regulatory role. Here, we profiled ubiquitylation in response to the DNA alkylating agent methyl methanesulfonate (MMS) in the budding yeast Saccharomyces cerevisiae using quantitative proteomics. To discover new proteins ubiquitylated upon DNA replication stress, ...
Source: Molecular and Cellular Proteomics : MCP - December 15, 2023 Category: Molecular Biology Authors: Ewa Blaszczak Emeline Pasquier Ga ëlle Le Dez Adrian Odrzywolski Natalia Lazarewicz Audrey Brossard Emilia Fornal Piotr Moskalek Robert Wysocki Gwena ël Rabut Source Type: research

Proteoform-resolved profiling of plasminogen activation reveals novel abundant phosphorylation site and primary N-terminal cleavage site
Mol Cell Proteomics. 2023 Dec 13:100696. doi: 10.1016/j.mcpro.2023.100696. Online ahead of print.ABSTRACTPlasminogen, the zymogen of plasmin, is a glycoprotein involved in fibrinolysis and a wide variety of other physiological processes. Plasminogen dysregulation has been implicated in a range of diseases. Classically, human plasminogen is categorized into two types, supposedly having different functional features, based on the presence (type I) or absence (type II) of a single N-linked glycan. Using high-resolution native mass spectrometry (native MS), we uncover that the proteoform profiles of human plasminogen (and plas...
Source: Molecular and Cellular Proteomics : MCP - December 15, 2023 Category: Molecular Biology Authors: Dario A T Cramer Victor Yin Tomislav Caval Vojtech Franc Dingyi Yu Guojie Wu Gordon Lloyd Christopher Langendorf James C Whisstock Ruby H P Law Albert J R Heck Source Type: research

A Causal Model of Ion Interference Enables Assessment and Correction of Ratio Compression in Multiplex Proteomics
In this study, we thoroughly characterized ion interference at the MS2 level using a defined two-proteome experimental system with known ground-truth. We discovered remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level of observed reporter ion interference in MS2-scans - a discrepancy that we found resolved by considering co-fragmentation of peptide ions hidden within the spectral "noise" of the MS1 isolation window. To address this issue, we developed a regression modeling strategy to accurately predict reporter ion interference in any dataset. Finally, we demonstrate...
Source: Molecular and Cellular Proteomics : MCP - December 14, 2023 Category: Molecular Biology Authors: Moritz Madern Wolfgang Reiter Florian Stanek Natascha Hartl Karl Mechtler Markus Hartl Source Type: research

iProPhos: a web-based interactive platform for integrated proteome and phosphoproteome analysis
We present two case studies to demonstrate that iProPhos can identify potential drug targets and upstream kinases contributing to site-specific phosphorylation. Ultimately, iProPhos allows end-users to leverage the value of big data in cancer proteomics more effectively and accelerates the discovery of novel therapeutic targets.PMID:38097182 | DOI:10.1016/j.mcpro.2023.100693 (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - December 14, 2023 Category: Molecular Biology Authors: Jing Zou Ziran Qin Ran Li Xiaohua Yan Huizhe Huang Bing Yang Fangfang Zhou Long Zhang Source Type: research

Secretome analysis: Reading cellular sign language to understand intercellular communication
Mol Cell Proteomics. 2023 Dec 9:100692. doi: 10.1016/j.mcpro.2023.100692. Online ahead of print.ABSTRACTA significant portion of mammalian proteomes is secreted to the extracellular space to fulfill crucial roles in cell-to-cell communication. To best recapitulate the intricate and multi-faceted crosstalk between cells in a live organism, there is an ever-increasing need for methods to study protein secretion in model systems that include multiple cell types. In addition, post-translational modifications further expand the complexity and versatility of cellular communication. This review aims to summarise recent strategies...
Source: Molecular and Cellular Proteomics : MCP - December 11, 2023 Category: Molecular Biology Authors: Wei Wu Jeroen Krijgsveld Source Type: research

Quantitative proteomics of tissue infiltrating T cells from CRC patients identified Lipocalin-2 induces T cell apoptosis and promotes tumor cell proliferation by iron efflux
In this study, we analyzed the protein expression pattern of the infiltrating T cells isolated from CRC patients using quantitative proteomics. CD4+ and CD8+ T cells were isolated from clinical samples and labeled by TMT reagents, and the DEPs were quantified by mass spectrometry. The T cell proteome profiling revealed dysfunctions in these tumor-infiltrating T cells. Specifically, anti-tumor immunity was suppressed due to differentially expressed metal ion transporters and immunity regulators. For the first time, Lipocalin-2 (LCN2) was shown to be significantly up-regulated in CD4+ T cells. Quantitative proteomic analysis...
Source: Molecular and Cellular Proteomics : MCP - December 10, 2023 Category: Molecular Biology Authors: Rui Che Qingsong Wang Minzhe Li Jian Shen Jianguo Ji Source Type: research