Resources

Proteomics Databases



Metabolomics Databases

• • DIA vs DDA Proteomics: Acquisition Strategy, Quantification, and Method Selection

  A practical comparison of DIA and DDA proteomics, including precursor selection, MS/MS complexity, reproducibility, missing values, spectral libraries, quantitative accuracy, and application scenarios.

• • Main Types of Protein Glycosylation: N-Linked, O-Linked, GPI Anchors, and Glycoproteomics

  A practical guide to the main types of protein glycosylation, including N-linked glycosylation, O-linked glycosylation, GPI anchors, C-mannosylation, glycation, site analysis, and LC-MS/MS glycoproteomics.

• • How to Identify Amino Acids and Modification Sites from a Mass Spectrum

  A practical guide to reading peptide mass spectra, using residue mass differences, b/y ions, neutral losses, database search, de novo sequencing, and PTM localization to identify amino acids and modification sites.

• • Activity-Based Protein Profiling in Drug Discovery: Target Identification, Selectivity, and Mechanism Studies

  A practical guide to activity-based protein profiling (ABPP) in drug discovery, including probe design, competitive ABPP, target identification, selectivity profiling, mechanism-of-action studies, and biomarker discovery.

• • Bottom-Up Proteomics in Single-Cell Proteomics: Challenges, Solutions, and Opportunities

  A practical guide to bottom-up single-cell proteomics, covering sample loss, microfluidics, TMT carrier channels, LC and CE separation, DIA acquisition, missing values, and data analysis.

• • Protein Expression Profiling: Quantitative Proteomics Workflow, Applications, and Method Selection

  A practical guide to protein expression profiling using LC-MS/MS quantitative proteomics, covering sample preparation, label-free and DIA workflows, data analysis, biomarkers, drug targets, and study design.

• • Glycoproteomics in Neuroscience: Mapping Neural Glycosylation, Biomarkers, and Drug Targets

  A practical guide to glycoproteomics in neuroscience, covering neural glycoproteins, glycopeptide enrichment, LC-MS/MS analysis, disease biomarkers, neurodevelopmental studies, and target discovery.

• • Protein Amino Acid Sequence Determination: Edman Degradation, MS Sequencing, and Method Selection

  A practical guide to protein amino acid sequence determination, including Edman degradation, LC-MS/MS protein sequencing, de novo sequencing, terminal sequencing, applications, limitations, and method selection.

• • 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......