Resources

Proteomics Databases



Metabolomics Databases

• • Principles of PRM Quantitative Proteomics

  Parallel Reaction Monitoring (PRM) is a targeted quantitative proteomic approach that employs high-resolution mass spectrometry. It has become an essential tool for advanced quantitative analysis in life sciences. Compared with the conventional Selected Reaction Monitoring (SRM) technique, PRM utilizes Orbitrap or Time-of-Flight (TOF) mass spectrometers to perform comprehensive monitoring of fragment ions, thereby achieving superior selectivity, sensitivity, and reproducibility. Working Principles o......

• • Unveiling the Mechanisms of Protein Lactylation: From Metabolic Origin to Functional Implications

  In recent years, lysine lactylation (Kla) has emerged as a novel post-translational modification (PTM) with increasing relevance in epigenetic regulation and cellular metabolism, gaining attention as a promising frontier in the post-genomic era. The identification of protein lactylation has significantly broadened our understanding of the interplay between metabolic flux and transcriptional regulation, offering new perspectives for investigating cancer, immune responses, and metabolic disorders. This ......

• • SILAC-Based Strategies for Differential Protein Screening

  Variations in protein expression levels serve as crucial indicators for elucidating biological processes, disease mechanisms, and pharmacological effects. However, due to the intrinsic complexity of proteins and their broad dynamic expression range, achieving accurate and reproducible protein quantification remains a technical challenge in proteomics. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) has emerged to address this issue. SILAC-based differential protein screening incorporate......

• • How Does Lactylation Influence Protein–Molecule Interactions?

  Protein–molecule interactions represent fundamental biological processes that underlie essential cellular functions such as signal transduction, transcriptional regulation, substrate recognition, and macromolecular complex assembly. Post-translational modifications (PTMs), which covalently modify amino acid residues, play pivotal roles in modulating the three-dimensional conformation, chemical properties, and binding capacities of proteins. As a recently identified type of PTM, lysine lactylation (Kla......

• • How Does PRM Technology Facilitate the Analysis of Low-Abundance Proteins?

  In proteomics research and clinical translational applications, the quantitative detection of low-abundance proteins remains a major technical challenge. Although these proteins are expressed at very low levels, they often possess high biological significance, such as cytokines, transcription factors, inflammatory mediators, and early disease biomarkers. The conventional Data-Dependent Acquisition (DDA) approach is limited by acquisition depth and dynamic range, making it difficult to achieve consiste......

• • What Is Acylation Proteomics?

  Acylation proteomics refers to the systematic identification and quantification of protein acylation sites and their dynamic alterations in cells or tissues using high-throughput mass spectrometry. As an important branch of proteomics, it focuses on the comprehensive characterization of acyl-type post-translational modifications (PTMs). Definition of Protein Acylation Protein acylation is a class of post-translational modifications in which diverse acyl groups are covalently attached to specific resi......

• • What Is Co-Immunoprecipitation (Co-IP)?

  In routine laboratory research focused on protein function and signal transduction pathways, co-immunoprecipitation (Co-IP) is a fundamental technique encountered by nearly all life-science researchers. It is widely regarded as one of the gold-standard methods for validating protein–protein interactions and serves as an essential bridge linking immunology with modern proteomics and mass spectrometry technologies. Fundamental Principle of Co-Immunoprecipitation Co-immunoprecipitation is an immunoaffin......

• • How Can Peptidomic Liquid Biopsy Be Translated into Clinical Diagnosis?

  Liquid biopsy, owing to its non-invasive, real-time, and dynamic monitoring capabilities, has gradually become an important approach for tumor screening, disease early warning, and therapeutic evaluation. Currently, liquid biopsy mainly targets nucleic acid- or cell-level information, such as circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and exosomes. In contrast, peptidomic liquid biopsy offers a complementary approach with enhanced functional characterization. Analyzing bioactive pe......

• • How Can iTRAQ Labeling Technology Be Applied in Peptidomics Analysis?

  In peptidomics analysis, mass spectrometry (MS) is commonly employed to identify endogenous peptides naturally present in biological samples. However, information on peptide presence alone is insufficient to elucidate disease mechanisms or to discover reliable biomarkers. Quantitative analysis, particularly the comparative assessment of differential expression across multiple samples, is essential for understanding pathological processes and identifying potential therapeutic targets. iTRAQ Labeling Te......

• • Bottom-Up Proteomics Data Analysis Pipeline

  Bottom-up proteomics involves the enzymatic digestion of proteins into peptides, followed by identification and quantification through mass spectrometry, ultimately enabling the inference of protein identities and abundances. Owing to its high throughput, sensitivity, and adaptability, this approach is widely employed in biomarker discovery, disease mechanism elucidation, and drug development. Below is a standardized bottom-up proteomics data analysis pipeline. Sample Preparation and Protein Digestio......