Resources

Proteomics Databases



Metabolomics Databases

• • PTM Mass Spec

  PTM mass spec is an advanced technique used to examine the modifications proteins undergo after translation. PTMs are chemical changes occurring on specific amino acids during or after protein synthesis, through enzymatic or non-enzymatic processes. These modifications are vital for regulating protein function, stability, and cell signaling. PTMs include phosphorylation, acetylation, methylation, glycosylation, ubiquitination, and carboxylation, among others. By enhancing chemical diversity, PTMs modu......

• • Proteomics: Top-Down & Bottom-Up

  Proteomics top-down & bottom-up are two fundamental strategies in modern proteomics research and are widely applied in mass spectrometry-based analyses. Top-down proteomics directly analyzes intact protein molecules to determine their sequences and post-translational modifications (PTMs). In contrast, bottom-up proteomics involves enzymatic digestion of proteins into peptides, which are then analyzed via mass spectrometry to reconstruct protein sequences. This approach is particularly suitable for hig......

• • O-Link Proteomics

  O-Link Proteomics is a cutting-edge research methodology leveraging proximity extension assay (PEA) technology to conduct high-throughput and precise measurements of protein dynamics in biological processes. Developed by Olink, this PEA platform allows for the simultaneous quantification of multiple protein expressions. A hallmark of O-Link Proteomics is its high sensitivity and specificity. Traditional proteomics approaches often require large sample volumes and struggle with low detection limits and......

• • 6 Essential Native MS Strategies to Enhance Your Data Quality

  Native MS serves as a powerful tool for in situ characterization of complex biological assemblies, such as protein complexes and nucleic acid-protein interactions, by preserving their native conformation and non-covalent interactions. However, the sensitivity and reliability of native MS data heavily depend on the optimization of experimental conditions and analytical strategies. This article outlines 6 critical strategies covering the entire workflow—from sample preparation and instrumental settings ......

• • Experimental Design and Data Interpretation in Native Mass Spectrometry

  Native mass spectrometry is an analytical technique that investigates the structure and interactions of biomacromolecules (e.g., proteins, protein complexes, and nucleic acid-protein complexes) under conditions that closely mimic physiological environments. Unlike conventional denaturing mass spectrometry, this approach relies on gentle sample preparation and ionization conditions to preserve the native conformations and non-covalent interactions of biomolecules. Over the past decades, native mass spe......

• • Comparison and Advantages of Native Mass Spectrometry over Other MS Techniques

  Mass spectrometry has long been a fundamental analytical tool in modern life sciences and biomedical research, enabling the structural and functional characterization of biomolecules such as proteins and nucleic acids. Based on the preservation or disruption of biomolecular native states, mass spectrometry can be broadly classified into native mass spectrometry and denatured mass spectrometry. What distinguishes these two approaches? In what research contexts are they most suitable? This review provid......

• • De Novo Protein Sequencing: From Experimental Design to Data Interpretation

  De novo protein sequencing does not require a reference genome or database and directly determines the primary structure of proteins (amino acid sequence). Although significant progress has been made in recent years, several challenges persist, including the accuracy of sequence analysis, the difficulties associated with sequencing complex samples, the impact of post-translational modifications (PTMs), and computational complexity. This paper explores the primary challenges of de novo protein sequenci......

• • Key Techniques and Application Advances in De Novo Protein Sequencing

  De novo protein sequencing, as a core technology for determining the amino acid sequences of unknown proteins, has achieved significant breakthroughs in both methodology and application scenarios in recent years. Its primary advantage is that it does not rely on genomic or protein databases, enabling sequence reconstruction directly from mass spectrometry data. This approach is particularly useful for the study of proteins from newly discovered species, antibody therapeutics, and complex systems invol......

• • De Novo Protein Sequencing: Principles and Methods Overview

  De novo protein sequencing is a method for identifying the primary structure (amino acid sequence) of proteins without relying on genomic sequences or protein databases. This approach is essential for characterizing unknown proteins, advancing antibody drug development, conducting proteomic analyses of non-model organisms, and investigating post-translational modifications (PTMs). Traditional protein sequencing methods depend on genomic data or known protein databases for sequence alignment and identi......

• • Avoid Inaccurate Results with These Native MS Data Acquisition Tips

  Native mass spectrometry analysis is a powerful technique for investigating proteins and their complexes under near-physiological conditions, with broad applications in proteomics, structural biology, and drug discovery. However, due to the complexity of protein assemblies, the instability of the ionization process, and the variability of experimental conditions, native MS data are prone to inaccuracies and challenges in interpretation. These issues can compromise the scientific validity of studies an......