Resources

Proteomics Databases



Metabolomics Databases

• • Proteomics Data Quality Assessment Workflow: QC Metrics, Filtering, and Validation

  A practical guide to proteomics data quality assessment, covering preprocessing, filtering, normalization, statistical QC, missing values, batch effects, validation, and reporting.

• • How to Reduce Sample Degradation in FFPE Proteome Profiling?

  In clinical research and translational medicine, FFPE (Formalin-Fixed Paraffin-Embedded) samples are valuable resources for tumor research, elucidation of disease mechanisms, and biomarker discovery, owing to their long-term stability and comprehensive associated clinical data. Nevertheless, protein degradation and crosslinking modifications in FFPE samples remain critical challenges that limit the quality of proteomic analyses. Underlying Causes of Protein Degradation in FFPE Samples 1. Crosslinking......

• • How to Analyze Histone Butyrylation by LC-MS/MS?

  Histone modifications represent a fundamental aspect of epigenetic regulation. Among these, butyrylation, an emerging short-chain fatty acid-derived post-translational modification (PTM), has been increasingly recognized for its roles in gene regulation, metabolic homeostasis, and disease development. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) enables not only precise identification of modification sites but also quantitative comparison of butyrylation levels across different biological......

• • Antibody Peptide Mapping by LC-MS/MS: Workflow, Applications, and Quality Attributes

  A practical guide to antibody peptide mapping by LC-MS/MS, including digestion, peptide separation, sequence coverage, PTM identification, degradation monitoring, biosimilar comparability, and QC considerations.

• • What Is Label-Free Analysis? LFQ Principles, Workflow, Advantages, and Limitations

  A practical guide to label-free analysis and label-free quantification (LFQ), including MS1 intensity, spectral counting, LC-MS/MS workflow, normalization, missing values, batch effects, and comparison with labeling approaches.

• • Label Transfer in Protein Interaction Studies: Principle, Workflow, and Method Selection

  A practical guide to label transfer for protein interaction studies, including bait-prey labeling, activation, label transfer, MS detection, applications, controls, limitations, and method selection.

• • Top-Down Protein Sequencing Principle: Intact Protein MS, Fragmentation, and Proteoform Analysis

  A practical guide to top-down protein sequencing, including intact protein preparation, high-resolution MS, fragmentation, proteoform analysis, PTM preservation, applications, and limitations.

• • How Post-Translational Modifications Affect Protein Function?

  A practical guide to how post-translational modifications regulate protein activity, stability, localization, interactions, signaling, metabolism, disease mechanisms, and MS-based PTM analysis.

• • Glycan Profiling Methods vs Phosphoproteomics: Key Differences in Targets, Workflows, and Data

  A practical comparison of glycan profiling methods and phosphoproteomics, including analytical targets, sample preparation, LC-MS workflows, enrichment strategies, applications, limitations, and method selection.

• • Protein Analysis Mechanisms: How Extraction, Separation, Identification, and Quantification Work

  A practical guide to protein analysis mechanisms, including sample preparation, separation, LC-MS/MS identification, quantification, PTM analysis, structural methods, limitations, and method selection.