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Quantification Quality Control Emerges as A Crucial Factor to Enhance Single Cell Proteomics Data Analysis
Mol Cell Proteomics. 2024 Apr 13:100768. doi: 10.1016/j.mcpro.2024.100768. Online ahead of print.ABSTRACTMass spectrometry (MS)-based single-cell proteomics (SCP) provides us the opportunity to unbiasedly explore biological variability within cells without the limitation of antibody availability. This field is rapidly developed with the main focuses on instrument advancement, sample preparation refinement, and signal boosting methods; however, the optimal data processing and analysis are rarely investigated which holds an arduous challenge because of the high proportion of missing values and batch effect. Here, we introduc...
Source: Molecular and Cellular Proteomics : MCP - April 15, 2024 Category: Molecular Biology Authors: Sung-Huan Yu Shiau-Ching Chen Pei-Shan Wu Pei-I Kuo Ting-An Chen Hsiang-Ying Lee Miao-Hsia Lin Source Type: research

Replisome proximal protein associations and dynamic proteomic changes at stalled replication forks
Mol Cell Proteomics. 2024 Apr 12:100767. doi: 10.1016/j.mcpro.2024.100767. Online ahead of print.ABSTRACTDNA replication is a fundamental cellular process that ensures the transfer of genetic information during cell division. Genome duplication takes place in S phase and requires a dynamic and highly coordinated recruitment of multiple proteins at replication forks. Various genotoxic stressors lead to fork instability and collapse, hence the need for DNA repair pathways. By identifying the multitude of protein interactions implicated in those events we can better grasp the complex and dynamic molecular mechanisms that faci...
Source: Molecular and Cellular Proteomics : MCP - April 14, 2024 Category: Molecular Biology Authors: Carla-Marie Jurkovic Jennifer Raisch Stephanie Tran Hoang Dong Nguyen Dominique L évesque Michelle S Scott Eric I Campos Fran çois-Michel Boisvert Source Type: research

TIMAHAC: Streamlined Tandem IMAC-HILIC Workflow for Simultaneous and High-Throughput Plant Phosphoproteomics and N-glycoproteomics
Mol Cell Proteomics. 2024 Apr 10:100762. doi: 10.1016/j.mcpro.2024.100762. Online ahead of print.ABSTRACTProtein post-translational modifications (PTMs) are crucial in plant cellular processes, particularly in protein folding and signal transduction. N-glycosylation and phosphorylation are notably significant PTMs, playing essential roles in regulating plant responses to environmental stimuli. However, current sequential enrichment methods for simultaneous analysis of phosphoproteome and N-glycoproteome are labor-intensive and time-consuming, limiting their throughput. Addressing this challenge, this study introduces a nov...
Source: Molecular and Cellular Proteomics : MCP - April 12, 2024 Category: Molecular Biology Authors: Chin-Wen Chen Pei-Yi Lin Ying-Mi Lai Miao-Hsia Lin Shu-Yu Lin Chuan-Chih Hsu Source Type: research

Comprehensive proteomics analysis of polyhydroxyalkanoate (PHA) biology in Pseudomonas putida KT2440: the outer membrane lipoprotein OprL is a newly identified phasin
Mol Cell Proteomics. 2024 Apr 10:100765. doi: 10.1016/j.mcpro.2024.100765. Online ahead of print.ABSTRACTPseudomonas putida KT2440 is an important bioplastic-producing industrial microorganism capable of synthesizing the polymeric carbon-rich storage material, polyhydroxyalkanoate (PHA). PHA is sequestered in discrete PHA granules, or carbonosomes, and accumulates under conditions of stress, for example low levels of available nitrogen. The pha locus responsible for PHA metabolism encodes both anabolic and catabolic enzymes, a transcription factor, and carbonosome-localized proteins termed phasins. The functions of phasins...
Source: Molecular and Cellular Proteomics : MCP - April 12, 2024 Category: Molecular Biology Authors: Siobhan Kelly Jia-Lynn Tham Kate McKeever Eugene Dillon David O'Connell Dimitri Scholz Jeremy C Simpson Kevin O'Connor Tanja Narancic Gerard Cagney Source Type: research

Proteomics-derived biomarker panel facilitates distinguishing primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) from lung metastatic colorectal cancer (lmCRC)
This study aimed to explore the protein biomarkers that could distinguish between PAIM and lmCRC. To uncover differences between the two diseases, we used tandem mass tagging (TMT)-based shotgun proteomics to characterize proteomes of formalin-fixed paraffin-embedded (FFPE) tumor samples of PAIM (n = 22) and lmCRC (n = 17).Then three machine learning algorithms, namely support vector machine (SVM), random forest and the Least Absolute Shrinkage and Selection Operator (LASSO), were utilized to select protein features with diagnostic significance. These candidate proteins were further validated in an independent cohort (PAIM...
Source: Molecular and Cellular Proteomics : MCP - April 12, 2024 Category: Molecular Biology Authors: Jiaying Liu Xiaona Chang Liujia Qian Shuo Chen Zhangzhi Xue Junhua Wu Danju Luo Bo Huang Jun Fan Tiannan Guo Xiu Nie Source Type: research

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