Resources

Proteomics Databases



Metabolomics Databases

• • How to Deparaffinize FFPE Tissue Samples for LC-MS Proteomics?

  In clinical research and translational medicine, formalin-fixed paraffin-embedded (FFPE) tissue samples are highly valuable biological resources due to their long-term stability and comprehensive clinical information. However, before FFPE samples can be analyzed by LC-MS proteomics, a key technical challenge must be addressed: efficient and reproducible deparaffinization. Why Must FFPE Samples Be Deparaffinized? During FFPE sample preparation, tissues undergo formalin fixation and paraffin embedding.......

• • Workflow for TMT-labeled Quantitative Mass Spectrometry

  As life science research moves toward higher-resolution and large-scale, systems-level investigations, quantitative proteomics has become an essential approach for characterizing dynamic biological changes. In particular, mass spectrometry (MS)-based quantification has demonstrated substantial utility in studies of tumor heterogeneity, investigations of drug mechanisms of action, and discovery of disease biomarkers. Among available strategies, tandem mass tag (TMT) labeling is widely adopted for multi......

• • How to Improve LC-MS/MS Proteomics Data Quality: From Sample Preparation to Peptide Identification

  Learn how to improve LC-MS/MS proteomics data quality from sample preparation through peptide identification, including digestion control, acquisition depth, database setup, and PSM review.

• • How to Choose an LC-MS/MS Proteomics Service: Key Deliverables, Sample Requirements, and Cost Drivers

  How to choose an LC-MS/MS proteomics service: compare deliverables, sample fit, workflow capability, reporting quality, and project cost drivers.

• • Why Mass Spectrometry Proteomics Results Vary: Key Factors Behind Protein Coverage, Quantification, and Data Confidence

  Understand why proteomics results vary in coverage, quantitation, and confidence, and the sample prep, LC-MS/MS, and analysis factors involved.

• • What is mass spectrometry used for in proteomics?

  Learn what mass spectrometry is used for in proteomics: protein identification, quantitation, PTM mapping, biologics QC, and targeted monitoring.

• • What is LC-MS vs LC-MS/MS?

  Learn the difference between LC-MS and LC-MS/MS in proteomics, how each measures peptides, when to use each approach, and how terminology like MS/MS and tandem MS relates.

• • Scoping an MRM Quantitation Project: Transition Design, Sample Count, and Validation Deliverables

  MRM quantitation projects move faster when scope is defined before samples ship. Teams often request a large peptide panel and high sample count without confirming whether transitions are optimized in matrix, whether cycle time supports the panel size, or whether the final report must satisfy biomarker validation, biopharmaceutical QC, or internal research standards.

• • Multiple Reaction Monitoring or Discovery Proteomics? Matching MRM to Biomarker Validation and QC Needs

  Quantitative proteomics projects rarely fail because teams lack mass spectrometry capability. They fail because the selected workflow does not match the study stage or evidence standard required for the next decision. One team may need to survey thousands of proteins to generate biomarker hypotheses. Another may need to measure ten predefined peptides across five hundred clinical samples with tight reproducibility.

• • Weak or Missing MRM Peaks? Troubleshooting Transition Selection, Matrix Effects, and LC Separation

  An MRM assay can be fully configured yet fail to deliver usable quantitative data. Transitions may be defined, internal standards may be spiked, and the LC-MS run may complete without error, yet target peptides show weak peaks, missing transitions, poor linearity, or high variability across replicates.