Resources

Proteomics Databases



Metabolomics Databases

• • De Novo Protein Sequencing vs Database-Based Identification: How to Choose

  Introduction Protein sequencing projects often reach a decision point where two LC-MS/MS strategies appear equally plausible. Database-based identification matches experimental spectra to known protein entries and is efficient when the reference is reliable. De novo protein sequencing derives sequence information directly from peptide fragmentation data when the correct reference is missing, incomplete, or untrustworthy. The wrong choice can waste sample, delay cloning or QC decisions, and produce a r......

• • De Novo Protein Sequencing: Principles, Technical Challenges, and Research Applications

  Introduction Protein sequence is often treated as solved once a gene or construct sequence is available. In many research settings, that assumption breaks down. A purified band may not match any database entry. A recombinant product may differ from the intended construct. An antibody variable region may lack complete transcript data. A sample from a non-model organism may contain proteins with no reliable reference proteome. In these cases, researchers need sequence evidence derived from the protein i......

• • Monoclonal Antibody Sequencing: Principles, Workflow, and Service Planning Basics

  Technical guide for Monoclonal Antibody Sequencing: Principles, Workflow, and Service Planning Basics.

• • Common Failure Points in Monoclonal Antibody Sequencing Projects and How to Prevent Rework

  Technical guide for Common Failure Points in Monoclonal Antibody Sequencing Projects and How to Prevent Rework.

• • Monoclonal Antibody Sequencing for Legacy Antibody Redevelopment and Biosimilar Reference Work

  Technical guide for Monoclonal Antibody Sequencing for Legacy Antibody Redevelopment and Biosimilar Reference Work.

• • Co-IP Limitations & In-Cell Crosslinking MS for Weak Protein Interactions

  Introduction Co-immunoprecipitation, or Co-IP, is widely used to study protein-protein interactions because it can enrich a target protein and identify associated partners by Western blot or mass spectrometry. The method works well for stable complexes, especially when the bait protein, antibody, lysis buffer, and wash conditions are well optimized. However, many biologically important interactions are not stable. Signaling proteins, transcriptional regulators, membrane-associated complexes, kinase su......

• • How to Verify Heavy and Light Chain Pairing After Hybridoma Monoclonal Antibody Sequencing

  Technical guide to verifying heavy and light chain pairing after hybridoma monoclonal antibody sequencing using peptide evidence, mass checks, and reconstruction-focused decision criteria.

• • How to Evaluate De Novo Sequencing Services: Cost Drivers and Vendor Selection

  Introduction Once a research team decides that database-free sequence analysis is necessary, the next challenge is usually commercial rather than technical. How much should a database-free sequencing project cost? What deliverables justify the expense? Which vendor can produce data strong enough for publication, cloning, or QC release? These questions matter because the method is typically more resource-intensive than routine database-assisted identification. Project cost is shaped by more than sampl......

• • De Novo Sequencing When Database Search Fails: A Practical Troubleshooting Guide

  Introduction A failed database search is one of the most frustrating outcomes in a protein characterization project. The sample may be pure enough to detect clearly by SDS-PAGE or LC-MS, yet the search engine returns weak matches, low coverage, or multiple unrelated protein candidates. For a lab preparing a manuscript, validating a recombinant product, or documenting a proprietary protein, this result creates immediate uncertainty. Database-assisted protein identification works well when the correct ......

• • How to Interpret Monoclonal Antibody Sequencing Results Before Humanization or Engineering

  Technical guide for How to Interpret Monoclonal Antibody Sequencing Results Before Humanization or Engineering.