Resources

Proteomics Databases



Metabolomics Databases

• • Cross-Linking Mass Spectrometry Sample Preparation

  Cross-linking mass spectrometry (XL-MS) is a powerful analytical tool for elucidating protein structures and interactions, with the sample preparation process being a crucial determinant of experimental success. The preparation protocol for XL-MS encompasses four main stages: protein extraction, purification, cross-linking, and preparation of cross-linked protein samples for mass spectrometry analysis.

• • Minimum Blood Volume for Proteomics Analysis

  Blood proteomics provides valuable insights into the biological functions of blood and its roles in various pathological conditions. In studies of blood proteomics, there is no universally defined minimum volume for blood collection. The required sample volume is determined by the specific research objectives and the analytical techniques employed. Typically, a collection of approximately 1–2 milliliters of blood is considered adequate. The following factors influence the determination of the minimum.......

• • Translate Protein Interactions Using IPMax

  Interacting proteins are defined as protein complexes formed through protein-protein interactions within cells, which are fundamental to key biological processes such as signal transduction, gene transcription and translation, and cell cycle regulation. IPMax leverages immunoprecipitation (IP), a widely used experimental technique for studying protein-protein interactions. This approach uses specific antibodies to isolate target proteins and their interacting partners, followed by protein mass spectrometry

• • COG Analysis of Proteomics

  COG (Clusters of Orthologous Groups of proteins) represents a systematic classification framework designed to categorize proteins in bacteria, archaea, and eukaryotes. COG analysis of protein profiles is primarily employed to assess the functional and evolutionary characteristics of protein sequences, grouping them into distinct categories based on orthology. The COG database is a comprehensive repository of protein profiles across multiple species, wherein protein sequences are grouped according to their..

• • Similarities and Differences Between Peptide Database Searching and Protein Database Searching

  The identification of polypeptides in databases is primarily performed by comparing the target polypeptide with entries in the database to ascertain its structural and functional characteristics. This approach relies on mass spectrometry, where the mass spectra of the polypeptides are analyzed, and candidates with matching molecular weights and charge states are identified. Peptide Mass Spectrometry-Based Identification Peptide mass spectrometry-based identification primarily involves aligning target.......

• • Which Samples Can Be Submitted for High-Throughput Proteomics Analysis

  Biological Fluid Samples These samples, which include blood, urine, cerebrospinal fluid, and saliva, contain proteins that serve as indicators of the body's health status. Tissue Samples Tissue samples encompass various human tissues such as liver, kidney, heart, lung, and brain, along with diverse tumor tissues. Analyzing proteins within these samples provides insights into tissue functionality and the underlying mechanisms of diseases.

• • Proteomics Measures Which Proteins

  Proteomics is a field dedicated to the comprehensive study of protein expression, modifications, interactions, and network formation within biological systems. The primary areas of focus include protein expression, structure, function, interactions, modifications, and quantitative protein analysis. The following provides an overview of protein types commonly examined in proteomics research:

• • Advantages of Spatial Proteomics

  Spatial proteomics is a cutting-edge method for examining protein localization within cells or tissues. By integrating proteomics and advanced microscopy techniques, it allows for a quantitative analysis of the spatial distribution and functionality of proteins. The benefits of spatial proteomics are outlined below.

• • Mass Spectrometry Tests the Primary Molecular Weight of Collagen Protein

  In biochemical research, mass spectrometry can be used to measure the size of molecules, determine their composition and even identify unknown substances. In this article, we will explore how to use mass spectrometry to test the primary molecular weight of collagen. Collagen is a macromolecular protein predominantly found within the muscle tissues of animals. Its primary structure comprises amino acids linked by peptide bonds, forming extended chain-like structures. The most critical amino acids for........

• • How to Determine Positive and Negative Peaks in Peptide Mass Spectrometry

  In mass spectrometry analysis, it is crucial to examine the spectrum to identify various peaks, which can manifest as either positive or negative, termed as positive and negative peaks. Positive peaks typically suggest a higher concentration of the substance or a larger ion mass, whereas negative peaks might indicate a lower concentration or smaller ion mass. However, these interpretations are not absolute, as peak values are influenced by numerous factors, including sample characteristics and analytical...