Resources
Proteomics Databases
Metabolomics Databases
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Mass spectrometry is widely applied in modern scientific research, spanning biochemistry, environmental science, food safety, and medical diagnostics. In biochemistry, mass spectrometry plays a crucial role in proteomics research by enabling the identification and quantification of proteins, thereby helping scientists elucidate biological processes. In environmental science, mass spectrometry is instrumental in detecting environmental pollutants, such as heavy metals and volatile organic compounds, pr......
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Epitope mapping techniques systematically identify and characterize immune epitopes within proteins using high-resolution mass spectrometry and computational biology. Immune epitopes are protein regions that interact with the immune system to trigger an immune response, often serving as key antigen-antibody binding sites. The foundation of epitope mapping techniques lies in high-resolution mass spectrometry, which enables precise localization and characterization of immune epitopes. Compared to conv......
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Targeted mass spectrometry is a high-sensitivity, high-specificity approach in proteomics and metabolomics, primarily used for the precise quantification of specific proteins and metabolites. Compared to conventional untargeted mass spectrometry techniques, such as data-dependent acquisition (DDA) and data-independent acquisition (DIA), targeted mass spectrometry focuses on predefined analytes, enabling reproducible and high-precision quantification in complex biological matrices. Advantages and App......
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• Single-Cell Pathway Analysis
Single-cell pathway analysis is a powerful approach for elucidating intracellular molecular signaling and biological processes by leveraging high-throughput data from individual cells. Unlike traditional bulk-cell analysis, single-cell technology allows for an in-depth investigation of cellular heterogeneity, individual variability, and dynamic state transitions. This methodology is particularly advantageous for deciphering the regulatory mechanisms governing complex intracellular signaling pathways a......
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PSM mass spectrometry is a fundamental technique in proteomics, extensively employed for protein identification and quantification. This method operates by enzymatically digesting proteins into peptides, analyzing their masses using a mass spectrometer, and subsequently deducing the protein’s amino acid sequence. By comparing experimentally obtained peptide spectra with theoretical peptide data from protein databases, this approach enables accurate protein identification. With continuous advancement......
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Mass spec metabolomics involves applying mass spectrometry techniques for the comprehensive analysis and quantification of metabolites in biological systems, enabling the characterization of metabolic profiles under various physiological and pathological conditions. As an essential branch of systems biology, metabolomics investigates the composition, concentrations, and dynamic fluctuations of small-molecule metabolites, including carbohydrates, fatty acids, and amino acids. Mass spectrometry, a cor......
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• Solid-Phase Protein Synthesis
Solid-phase protein synthesis is a widely adopted technique that employs solid-phase supports for the controlled assembly of peptides and small proteins. Originally introduced in the 1960s by American chemist Robert Bruce Merrifield, this approach has undergone continuous refinements, establishing itself as a cornerstone of modern protein chemistry. The fundamental principle of solid-phase protein synthesis is to anchor the growing peptide chain onto an insoluble resin, enabling precise sequence ass......
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CPTAC proteomics is a pivotal approach in cancer research, enabling large-scale proteomic analyses to systematically investigate cancer-associated protein expression, post-translational modifications (PTMs), and interaction networks. Cancer is a highly heterogeneous disease governed by intricate regulatory layers, including genetic mutations, epigenetic modifications, and protein dysfunction. While traditional cancer genomics studies, such as those from The Cancer Genome Atlas (TCGA), have revealed ke......
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CD spectra analysis is a widely used spectroscopic technique for characterizing the structures of chiral molecules, particularly biomacromolecules. Chiral molecules exhibit differential absorption of left- and right-handed circularly polarized light, enabling CD spectra analysis to provide structural insights into proteins, nucleic acids, and carbohydrates. Since biomolecular functions are often dictated by their higher-order structures, CD spectra analysis plays a vital role in structural biology, dr......
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• De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
De novo mass spectrometry peptide sequencing with a transformer model is a computational approach that leverages advanced mathematical models to enhance peptide sequence identification in mass spectrometry data. Mass spectrometry is a fundamental tool in proteomics, enabling the determination of amino acid sequences from enzymatically digested peptide fragments. However, peptide fragmentation is highly complex, and fragment ion formation exhibits inherent variability, which can limit the accuracy of c......
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