Resources

Proteomics Databases



Metabolomics Databases

• • How to Handle Missing Values in Label-Free Quantitative Proteomics Data?

  In label-free quantitative proteomics, missing values constitute a non-negligible component of downstream data analysis. Missingness is frequently observed within raw mass spectrometry data, and inappropriate handling may compromise statistical inference and lead to biased or misleading biological interpretations. Consequently, rigorous identification and treatment of missing values are critical for ensuring data integrity and analytical reproducibility. Causes and Classification of Missing Values in......

• • What Is the Difference Between Targeted and Untargeted Metabolomics?

  As life science research continues to advance, metabolomics has emerged as an analytical discipline that directly profiles the downstream biochemical outputs of biological processes. Focusing on metabolites enables comprehensive characterization of the dynamic metabolic states of cells, tissues, or biofluids under defined physiological or pathological conditions. Benefiting from progress in high-resolution mass spectrometry, metabolomics has been widely applied in tumor metabolism research, drug metab......

• • How to Perform Label-Free Quantitative Proteomics Analysis Using Mass Spectrometry?

  Proteomics plays a central role in life science research by enabling systematic investigation of biological system functions, while quantitative analysis is essential for elucidating changes in protein expression, signaling pathway regulation, and disease mechanisms. Label-free quantitative proteomics (LFQ) has gained increasing attention due to its broad sample compatibility, streamlined experimental workflow, and reduced overall cost. With advances in high-resolution mass spectrometry, subtle variat......

• • Common Challenges in TMT Proteomics and How to Overcome Them

  Tandem Mass Tag (TMT) is a widely adopted labeling-based strategy for high-throughput quantitative proteomics. Owing to its multiplexing capacity, high quantitative accuracy, and ability to analyze multiple samples in parallel, TMT has become an essential approach in studies of disease mechanisms, biomarker discovery, and drug mode-of-action analysis. Nevertheless, despite its advantages, the practical implementation of TMT workflows is associated with multiple technical challenges. If not properly ad......

• • 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......