Resources

Proteomics Databases



Metabolomics Databases

• • Bottom-Up Proteomics Data Analysis Pipeline

  Bottom-up proteomics involves the enzymatic digestion of proteins into peptides, followed by identification and quantification through mass spectrometry, ultimately enabling the inference of protein identities and abundances. Owing to its high throughput, sensitivity, and adaptability, this approach is widely employed in biomarker discovery, disease mechanism elucidation, and drug development. Below is a standardized bottom-up proteomics data analysis pipeline. Sample Preparation and Protein Digestio......

• • Application of Bottom-Up Proteomics in Biomarker Discovery

  Biomarkers play a pivotal role in early disease screening, therapeutic efficacy evaluation, and precision medicine. However, the systematic and accurate identification of differentially expressed proteins within complex biological matrices remains a significant challenge. Owing to its high throughput, quantitative precision, and broad proteome coverage, bottom-up proteomics has emerged as a central tool for biomarker discovery. What Is Bottom-Up Proteomics? Bottom-up proteomics is an analytical appro......

• • Application of Bottom-Up Proteomics in Protein Quantification

  Bottom-up proteomics achieves precise identification and quantification of proteins by enzymatically digesting complex protein mixtures into peptides, which are subsequently analyzed using high-resolution mass spectrometry. This approach is particularly well-suited for qualitative and quantitative protein analyses. As life sciences continue to advance, bottom-up proteomics plays an increasingly critical role in biomarker discovery, signal transduction research, and drug development. What Is Bottom-Up......

• • Simultaneous Peptide Sequencing and Post-Translational Modification Profiling via Tandem Mass Spectrometry

  In proteomics, peptide sequencing and post-translational modification (PTM) profiling are essential for elucidating protein function, signaling pathways, and disease mechanisms. Recent advances in mass spectrometry, particularly tandem mass spectrometry (MS/MS), have enabled the concurrent acquisition of both peptide sequence and PTM data within a single experiment, substantially improving research efficiency and data utility. Tandem Mass Spectrometry: A Core Technique for Concurrent Sequence and PTM......

• • LC-MS/MS for Antibody Peptide Sequencing: Applications and Advantages

  Accurate determination of the primary structure of antibodies is critically important for drug development, functional characterization, and quality control. Liquid chromatography-tandem mass spectrometry (LC-MS/MS), due to its high sensitivity, broad dynamic range, and ability to detect post-translational modifications (PTMs), has become an essential platform for antibody peptide sequencing. It enables high-throughput and reproducible analysis, supporting comprehensive structural elucidation of antib......

• • How Does SILAC Contribute to Phosphorylation Research?

  Stable Isotope Labeling by Amino acids in Cell Culture (SILAC) has been widely applied as a metabolic labeling strategy in quantitative proteomics. Unlike chemical labeling methods such as iTRAQ and TMT, SILAC achieves isotope incorporation at the cellular level, thereby inherently minimizing biases introduced during sample preparation. This makes it a powerful approach for investigating protein post-translational modifications (PTMs), particularly phosphorylation. In this article, we provide an in-de......

• • How Does High-throughput Shotgun Proteomics Address the Challenges of Complex Sample Analysis?

  Proteomics has emerged as a critical tool for elucidating biological system functions, uncovering disease mechanisms, and identifying biomarkers. Nevertheless, complex samples, such as tissue sections, plasma, organoids, or host–pathogen co-culture systems, present formidable challenges in terms of protein diversity, abundance, and background interference. Obtaining comprehensive, accurate, and reproducible protein information from these samples remains a central issue in proteomics research. Owing to......

• • How Can Shotgun Proteomics Facilitate the Identification of Challenging Membrane Proteins?

  Membrane proteins are broadly distributed throughout cellular membrane systems, serving as essential mediators of signal transduction, molecular transport, and intercellular communication. Nevertheless, their high hydrophobicity, structural complexity, and generally low abundance often result in poor detection rates in conventional proteomics workflows. With the advancement of mass spectrometry technologies and sample preparation strategies, shotgun proteomics has emerged as a promising approach for m......

• • How Do iTRAQ/TMT Enhance Quantitative Performance in Shotgun Proteomics?

  In proteomics research, shotgun proteomics has been widely employed for complex sample analysis due to its broad proteome coverage and robust detection capability. Nevertheless, this approach encounters significant challenges in multi-sample quantitation, including poor reproducibility, limited throughput, and low analytical efficiency. Isobaric labeling strategies such as iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) and TMT (Tandem Mass Tags) have effectively addressed these limitatio......

• • How Can Mass Spectrometry Peptidomics Facilitate Biomarker Discovery?

  Biomarkers are molecular indicators that objectively reflect biological states, disease progression, or responses to treatment. They are widely applied in early disease screening, personalized therapy, and therapeutic efficacy evaluation. In recent years, with the advancement of multi-omics technologies, researchers have been shifting from a genetic level perspective to a protein functional level perspective. In this context, mass spectrometry peptidomics, with its high-resolution profiling of protein......