Resources

Proteomics Databases



Metabolomics Databases

• • PhIP-Seq: Methods, Applications and Challenges

  PhIP-Seq, also called phage immunoprecipitation sequencing, was developed for this type of discovery question. The method combines phage display peptide libraries, antibody capture, next- generation sequencing, and enrichment analysis. PhIP-Seq can help researchers identify antibody-reactive peptides, compare serological profiles across groups, and nominate candidate epitope regions.

• • Analyzing Data from PhIP-Seq Experiments

  PhIP-Seq data analysis can decide whether a broad antibody screening experiment becomes a clear candidate list or an ambiguous table of peptide read counts. A serum or plasma cohort may contain biologically meaningful antibody signals, but sequencing output alone does not identify disease-associated epitopes, exposure signatures, or biomarker candidates.

• • Applications of PhIP-Seq in Genomics

  PhIP-Seq, also called phage immunoprecipitation sequencing, can provide that bridge. The method uses DNA-encoded phage display peptide libraries to represent genomic, proteomic, pathogen-derived, or custom antigen spaces. Antibody-containing samples enrich the displayed peptides that antibodies recognize. Sequencing then identifies the peptide-encoding sequences. In genomics-oriented studies, the value comes from connecting sequence-defined libraries with antibody reactivity patterns.

• • How to Design a Pilot Study for Low-Abundance Endogenous Protein Interactions

  Low-abundance endogenous protein interactions are difficult to study because the signal can be lost at several points before mass spectrometry analysis begins. The bait protein may be weakly expressed, the interaction may be transient, and the antibody may enrich background proteins more efficiently than the true complex.

• • Can Crosslinking MS Prove a Direct Protein Interaction?

  Crosslinking MS is often used when researchers need interaction information beyond a protein list. A standard affinity purification experiment can show which proteins co-enrich with a bait, but it may not show which residues are close in space. Crosslinking mass spectrometry adds that spatial layer by chemically linking nearby amino acid residues and identifying crosslinked peptides by LC-MS/MS.

• • Protein Interaction Analysis in Native Cells vs Overexpression Systems

  Protein interaction analysis often begins with a practical decision: should the experiment use native cells or an overexpression system? The choice affects biological relevance, signal strength, background, and how confidently the final results can be interpreted. Native-cell analysis preserves endogenous protein levels and the natural cellular environment, but low-abundance proteins can be difficult to capture and detect.

• • Protein Sequencing Sample Problems and How to Avoid Failed Results

  Many protein sequencing problems begin before the mass spectrometer, Edman instrument, or terminal analysis workflow is used. A sample may look like a clean band on a gel, but still contain co-migrating proteins. A purified protein may have enough concentration on paper, yet the usable amount after cleanup may be low. A protein may have the correct molecular weight, but a blocked N-terminus can make direct N-terminal sequencing difficult.

• • Protein Sequencing Methods Compared: LC-MS/MS, Edman, N/C Terminal, and De Novo

  Choosing a protein sequencing method is rarely a simple technology preference. A researcher trying to identify an unknown gel band, a biologics team confirming primary structure, and a project manager recovering sequence information from a non-model organism all need sequence evidence. They do not need the same workflow.

• • Applications of Top-Down Proteomics for Cancer Biomarker Discovery

  Tumor biomarkers are critical molecular indicators for cancer diagnosis and therapeutic decision-making and have long been supported by proteomics technologies. However, cancer is a highly heterogeneous disease, and its key proteins often exist as diverse proteoforms characterized by extensive post-translational modifications (PTMs) and sequence variants. These subtle molecular features are frequently overlooked by Bottom-Up proteomics, thereby limiting both the depth and precision of biomarker discov......

• • Precise Identification of Protein Proteoforms: Applications and Advantages of Top-Down Mass Spectrometry

  In the investigation of proteome complexity, the comprehensive characterization of protein proteoforms remains a central challenge in biomedical research. Proteoforms, encoded by the same gene, exhibit substantial structural and functional heterogeneity arising from alternative splicing, post-translational modifications (PTMs), and point mutations. Accurate identification of these proteoforms is not only fundamental to elucidating disease mechanisms and facilitating targeted drug development, but also......