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Proteomics Databases
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• TMT MS3 and SPS-MS3: How to Mitigate Ratio Compression and Enhance Quantitative Accuracy
In tandem mass tag (TMT)-based multiplexed proteomics, researchers frequently encounter a critical issue known as ratio compression. During MS1 acquisition, co-elution of homologous peptides from different samples and interference from co-isolated background ions often lead to dilution of reporter ion intensities, thereby underestimating the true abundance differences. To address this challenge, both instrument manufacturers and methodological researchers have developed TMT MS3 and Synchronous Precurs......
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Proteins are the fundamental effectors of biological processes, playing central roles in activities ranging from signal transduction to metabolic regulation. In basic research, the investigation of disease mechanisms and biomarker discovery, proteomics has become an indispensable and powerful analytical approach. However, mass spectrometry-based proteomics (e.g., DDA/DIA) still faces several challenges, including: (1) Limited Sensitivity: difficulty in detecting low-abundance cytokines or extracellula......
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• What Are the Best Software Tools for Shotgun Proteomics Analysis?
In shotgun proteomics, the large number of tandem mass spectra (MS/MS) generated by liquid chromatography–tandem mass spectrometry (LC–MS/MS) represent only the raw experimental data. Accurate protein identification, reliable quantification, and in-depth functional annotation and pathway analysis all depend on a scientifically rigorous and well-structured data analysis workflow. To achieve this, researchers rely on a suite of specialized bioinformatics tools and software platforms that span multiple a......
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• How to Enrich Membrane Proteins: What Are the Most Effective Methods?
Membrane proteins play a pivotal role as mediators linking intracellular and extracellular signaling pathways, representing over 30% of the human proteome and encompassing numerous pharmaceutical targets, including GPCRs, ion channels, and receptors. However, due to their high hydrophobicity, poor solubility, and generally low expression levels, membrane proteins are often underrepresented in proteomic analyses. Thus, the membrane protein enrichment is a crucial prerequisite for comprehensive and high......
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• How to Extract Membrane Proteins Using CNBr Cleavage Protocols?
Membrane proteins, characterized by strong hydrophobicity, complex three-dimensional conformations, and low abundance within cellular membranes, present substantial challenges in proteomic investigations. Conventional trypsin digestion often exhibits poor efficiency in membrane protein samples, resulting in low identification rates and poor reproducibility. In contrast, the cyanogen bromide (CNBr) cleavage method, owing to its specific recognition of methionine (Met) residues and cleavage at their C-t......
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• Top 5 Advantages of Tandem Mass Spectrometry in Peptide Sequence Analysis
In proteomics and structural biology, peptide sequence analysis serves as a foundational step for elucidating protein function, characterizing post-translational modifications (PTMs), and understanding their biological implications. Tandem mass spectrometry (MS/MS), renowned for its high-resolution structural elucidation and broad applicability, has become a widely adopted approach for peptide analysis. This article outlines the five key advantages of MS/MS in peptide sequencing, explores extended app......
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• Comprehensive Overview of Antibody Sequencing: From Peptide Identification to Full-Length Assembly
Antibody sequencing is a critical technique for determining the amino acid sequence of antibodies. It is extensively applied in antibody drug development, functional engineering, structural modeling, and intellectual property protection. Centered around high-resolution mass spectrometry, this approach reconstructs complete sequences of antibody light chains (LC) and heavy chains (HC) through enzymatic digestion and data-driven assembly. This article systematically outlines the core workflow, essential......
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High-throughput protein–protein interaction (PPI) detection represents a crucial approach for systematically elucidating cellular signaling pathways, deciphering protein functions, and understanding the architecture of biological networks. Among various PPI detection methods, Affinity Purification–Mass Spectrometry (AP-MS) is widely recognized as one of the most reliable and physiologically relevant techniques. It has been extensively applied across multiple biological systems, including mammalian cel......
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• How to Perform High-Sensitivity Membrane Protein Identification via Mass Spectrometry?
Membrane proteins constitute approximately 30% of the cellular proteome but account for more than 60% of all known drug targets. Members of this family include G protein–coupled receptors (GPCRs), ion channels, and receptor tyrosine kinases. Despite their biological importance, membrane proteins remain among the most challenging targets in proteomic research. Typically, membrane proteins exhibit the following characteristics: They contain highly hydrophobic transmembrane domains. Their cellular abund......
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• Common Mistakes in Peptide Sequencing and Their Solutions
Peptide sequencing plays a critical role in proteomics research, with widespread applications in protein identification, post-translational modification (PTM) localization, and quantitative analysis. Despite ongoing advancements in mass spectrometry (MS) platforms and computational algorithms, researchers continue to encounter various challenges throughout experimental workflows. This article systematically outlines common pitfalls in peptide sequencing and offers practical, actionable strategies for ......
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