Resources

Proteomics Databases



Metabolomics Databases

• • Workflow for TMT 16plex Quantitative Proteomics Analysis

  In systems biology research, accurate protein quantification is essential for characterizing the dynamic regulation of biological processes. Although traditional label-free approaches are relatively straightforward to implement, they often suffer from limitations in data consistency and control of batch effects. Owing to its high throughput, reduced inter-batch variability, and superior quantitative accuracy, Tandem Mass Tag (TMT) labeling has emerged as one of the most widely adopted strategies for m......

• • Step-by-Step Workflow for Quantitative Analysis of Protein Lactylation

  Protein lactylation is an emerging lysine post-translational modification that has recently gained significant attention in epigenetics, immunometabolism, and cancer biology. In contrast to well-established modifications such as acetylation and phosphorylation, analytical strategies for the detection and quantitative characterization of lactylation remain under active development. Consequently, researchers frequently encounter challenges related to experimental design, sample preparation, and data int......

• • Comprehensive Guide to Mass Spectrometry-Based Analysis of Histone PTMs

  In eukaryotic cells, DNA does not exist as a free molecule but is organized into nucleosomes by wrapping around histone octamers. Histone tails are enriched in lysine, arginine, and other residues that are subject to diverse post-translational modifications (PTMs), including acetylation, methylation, phosphorylation, and ubiquitination, catalyzed by specific enzymes. These PTMs finely modulate chromatin architecture and thereby regulate essential biological processes such as gene transcription, DNA re......

• • TMT-Based Biomarker Discovery

  With the rapid advancement of precision medicine, biomarkers have become essential for early disease detection, prediction of therapeutic response, and the development of targeted therapies. Although significant progress has been made in genomic biomarker research, proteins, as the direct effectors of biological function, undergo dynamic changes that more accurately reflect disease states. As a result, proteomics-based biomarker discovery has emerged as a major focus of contemporary biomedical researc......

• • How to Solubilize Hydrophobic Membrane Proteins for MS Analysis?

  Hydrophobic membrane proteins play indispensable roles in cellular physiology and are extensively involved in signal transduction, molecular transport, and cell-cell recognition. However, their highly hydrophobic transmembrane domains pose major challenges during sample preparation prior to mass spectrometry (MS) analysis. Conventional lysis buffers often fail to efficiently solubilize membrane proteins, resulting in poor extraction efficiency, protein aggregation and precipitation, and subsequent int......

• • How to Optimize Sample Preparation for Membrane Protein Identification?

  Optimization of sample preparation workflows for membrane proteins represents a critical prerequisite for achieving efficient and high-coverage proteomic analyses. Owing to their intrinsic properties, such as strong hydrophobicity, limited solubility, low abundance, and susceptibility to degradation, the extraction and enzymatic digestion of membrane proteins are considerably more challenging than those of soluble proteins. Consequently, the establishment of tailored and efficient pretreatment strateg......

• • How to Improve Reliability and Reproducibility of PPI Experimental Results?

  Protein-protein interactions (PPIs) play fundamental roles in cellular signaling, metabolic regulation, and disease pathogenesis. With the rapid advancement of omics technologies, PPI research has become a central focus in life science studies. However, due to the intrinsic complexity of experimental systems and pervasive non-specific interactions, PPI experiments frequently suffer from poor reproducibility and elevated false-positive rates. Enhancing experimental reliability and reproducibility has t......

• • How to Normalize Data in Label-Free Quantitative Proteomics?

  In label-free quantitative proteomics (LFQ), data normalization represents a fundamental step for ensuring inter-sample comparability and minimizing technical variability. In the absence of appropriate normalization, technical noise, such as differences in sample loading amounts and instrument performance drift, can obscure genuine biological variation, thereby introducing bias into the identification of differentially expressed proteins. Why Is Normalization Necessary for Label-Free Quantitative Pro......

• • How to Interpret Peptide Coverage and Protein Scores in Shotgun Data?

  Shotgun proteomics typically yields hundreds to thousands of identified proteins and peptide-spectrum matches (PSMs). However, determining which identifications are reliable, which proteins warrant downstream investigation, and which datasets are suitable for differential analysis or functional annotation remains a critical analytical challenge. Among the metrics used to assess identification confidence, peptide sequence coverage and protein-level scoring represent two key parameters that should be ev......

• • Critical Roles of Histone PTMs in Cancer Epigenetics

  Tumor initiation and progression are not solely driven by genetic mutations; instead, deeper layers of regulation frequently reside in epigenetic mechanisms. As fundamental structural components of chromatin, histones undergo diverse post-translational modifications (PTMs), including methylation, acetylation, and phosphorylation. Together, these modifications constitute a complex epigenetic code that precisely governs chromatin accessibility and transcriptional states. In cancer cells, histone PTMs ar......