Resources

Proteomics Databases



Metabolomics Databases

• • Common Challenges and Strategies for Disulfide Bond Analysis

  Disulfide bonds are critical chemical linkages within the higher-order structure of proteins, playing essential roles in protein folding, stability, and function. With the rapid advancement of biopharmaceuticals and proteomics, precise characterization of disulfide bonds has become a pivotal step in high-quality protein structural analysis. Nevertheless, disulfide bond analysis in practical experiments faces several technical challenges. The following summarizes these challenges and corresponding stra......

• • 4D-DIA vs 4D-PRM: Which 4D Quantitative Approach Suits Your Project Better?

  In contemporary proteomics, Data-Independent Acquisition (DIA) and Parallel Reaction Monitoring (PRM) have emerged as two principal strategies for non-targeted and targeted protein quantification, respectively. With the integration of Ion Mobility technology, 4D proteomics on the timsTOF Pro platform incorporates the mobility dimension into the analytical framework, substantially enhancing both separation and quantification performance. Within this technological context, 4D-DIA and 4D-PRM have become ......

• • Complete CUT&Tag Data Analysis Pipeline: From Sequencing to Interpretation

  CUT&Tag (Cleavage Under Targets and Tagmentation) is widely used in chromatin modification and transcription factor binding studies due to its high sensitivity, low background, and operational simplicity. While experimental procedures constitute the first step, robust downstream data analysis is essential for elucidating chromatin regulatory mechanisms. This article presents a systematic overview of the CUT&Tag data analysis workflow, aimed at facilitating efficient data interpretation and the constru......

• • Applications of TMT-Based Quantitative Proteomics in Drug Development and Biomarker Discovery

  With the advancement of precision medicine and biopharmaceuticals, proteomics has emerged as a core technology in both drug development and disease biomarker research. Among the various quantitative strategies, multiplexed mass spectrometry using Tandem Mass Tag (TMT) labeling has been widely applied in drug target screening, mechanistic studies, and biomarker discovery due to its high throughput, low batch variation, and high quantitative accuracy. This article systematically reviews the application ......

• • Mass Spectrometry-Based Host Cell Protein Analysis: Principles, Workflow, and Benefits

  In the biopharmaceutical field, recombinant protein therapeutics, such as monoclonal antibodies and fusion proteins, expressed and purified in mammalian cells, for example CHO cells, often contain a significant impurity: host cell proteins (HCPs). If HCPs are not thoroughly removed during downstream purification, they can induce immunogenic responses, compromise drug stability, and even pose safety risks to patients. Consequently, accurate identification and quantification of HCPs is a critical step i......

• • LC-MS/MS Workflow for Disulfide Bond Mapping Analysis

  Disulfide bonds are critical covalent linkages that maintain the stability of protein tertiary and quaternary structures, playing essential roles in protein structural characterization and biopharmaceutical development. In particular, in antibody therapeutics, recombinant proteins, and complex biopharmaceutical formulations, correct disulfide bond pairing directly influences protein folding conformation, biological activity, and safety. Consequently, LC-MS/MS-based disulfide bond mapping has emerged a......

• • Antibody Protein Sequencing: How Mass Spectrometry Reconstructs Antibody Variable-Region Sequences

  Antibody variable-region sequences define antigen recognition, yet many projects still lack a reliable genetic record for the antibody in hand. Hybridoma cells may be lost, expression plasmids may be incomplete, and legacy purified IgG may remain the only usable material. In these cases, researchers need primary structure evidence derived directly from the antibody protein rather than from amplifiable nucleic acids.

• • Planning an Antibody Protein Sequencing Project: Budget, Scope, and Vendor Deliverables

  Once a team decides to recover VH and VL sequence from purified IgG, the next questions are often practical rather than scientific. How much budget is realistic? What scope is required for recombinant handoff, publication, or QC documentation? Which deliverables separate a usable report from a partial sequence summary that cannot support the next decision?

• • Purified IgG or Hybridoma Cells? Selecting the Antibody Sequence Recovery Route for Your Project

  Antibody sequence recovery projects rarely fail because the binder is unknown. They fail because the team starts with the wrong material assumption. One project may have only an old IgG aliquot in the freezer. Another may still maintain a low-passage hybridoma culture with no sequence file. A third may hold a recombinant lot that must be verified before tech transfer. Each starting point supports a different recovery route.

• • Sparse VH/VL Coverage in Antibody Protein Sequencing: Digest, Purity, and LC-MS/MS Recovery Fixes

  A purified IgG sample can look acceptable on a Coomassie gel and still produce disappointing sequencing results. LC-MS/MS may run cleanly, yet variable-region coverage remains thin, CDR3 evidence is weak, or heavy-chain and light-chain assembly stops short of a usable VH/VL pair. For teams preparing recombinant expression, legacy clone rescue, or documentation submissions, sparse coverage creates immediate schedule risk.