Resources

Proteomics Databases



Metabolomics Databases

• • Bottom-Up Proteomics Data Analysis Pipeline: From Sample Prep to Pathway Interpretation

  A standardized bottom-up proteomics data analysis pipeline from protein digestion and LC-MS/MS through identification, quantification, QC, and pathway enrichment.

• • Top 6 Tools for Bottom-Up Proteomics Data Analysis: MaxQuant, FragPipe, Proteome Discoverer, and More

  Compare six leading bottom-up proteomics data analysis tools for identification, quantification, PTM analysis, and targeted workflows.

• • Applications of Bottom-Up Proteomics in Clinical Research: Biomarkers, Subtyping, and Translational Workflows

  Explore how bottom-up proteomics supports clinical research through biomarker discovery, disease subtyping, drug mechanism studies, and QC-aware workflows for plasma, tissue, and biofluid samples.

• • Principles of Quantitative Ubiquitinomics: Enrichment, LC-MS/MS, and Quantification Strategies

  Learn the core principles of quantitative ubiquitinomics, including diGly peptide enrichment, TMT and SILAC quantification, LC-MS/MS site mapping, and analysis of ubiquitination dynamics.

• • How to Analyze Histone β-Hydroxybutyrylation by LC-MS/MS: Sample Prep, Enrichment, and Quantification

  A practical LC-MS/MS workflow for histone β-hydroxybutyrylation (Kbhb) analysis covering histone extraction, digestion, peptide enrichment, acquisition settings, site localization, and quantification.

• • Step-by-Step ABPP Experiment Protocol: Probe Design, Labeling, LC-MS/MS, and Activity Profiling

  A practical step-by-step ABPP protocol covering research objectives, activity-based probe selection, in vitro and in situ labeling, enrichment, LC-MS/MS acquisition, and activity profile analysis.

• • How ABPP Supports High-Throughput Compound Screening: Target Engagement, Off-Target Profiling, and Workflow Design

  A practical guide to how activity-based protein profiling (ABPP) supports high-throughput compound screening through competitive labeling, functional target validation, off-target profiling, and LC-MS/MS readouts.

• • SDS-PAGE Protein Detection Methods: Western Blot, Mass Spectrometry, and 2D-PAGE Beyond Gel Electrophoresis

  A practical guide to protein detection methods used with SDS-PAGE, including Western blot, mass spectrometry, 2D-PAGE, in-gel workflows, method selection, and common limitations.

• • Efficient and Accurate Protein Sequencing Methods: Mass Spectrometry, Edman Degradation, and Workflow Selection

  A practical guide to efficient and accurate protein sequencing methods, comparing mass spectrometry, Edman degradation, de novo interpretation, terminal analysis, and gene-based sequence inference for research and biopharma workflows.

• • Glycosylation Site Analysis in Protein Function Studies: LC-MS/MS Workflows, Site Occupancy, and Biological Interpretation

  A practical guide to glycosylation site analysis in protein function studies, covering N- and O-glycosylation, LC-MS/MS workflows, enrichment, site occupancy, glycoform interpretation, and disease or biopharma applications.