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Chemical-Biology and Metabolomics Studies in Phage-Host Interactions
For many years, several studies have explored the molecular mechanisms involved in the infection of bacteria by their specific phages to understand...
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Sample Preparation in Microbial Metabolomics: Advances and Challenges
Microbial metabolomics has gained significant interest as it reflects the physiological state of microorganisms. Due to the great variability of...
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Microbial Metabolites Annotation by Mass Spectrometry-Based Metabolomics
Since the discovery of penicillin, microbial metabolites have been extensively investigated for drug discovery purposes. In the last decades,...
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Investigating the Warburg Effect in Renal Cell Carcinoma Using Spatial DYnamic MetabolOmics
This chapter focuses on the application of stable-isotope tracing in mass spectrometry imaging to unravel changes in the metabolic profile of renal...
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How to Extract Lipid Metabolites and Perform Lipid Analysis?
Lipids are complex metabolites and key components of physiology. They are ubiquitous and therefore of interest in various sample types. However, a...
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Identifying Sex-Specific Cancer Metabolites and Associations to Prognosis
In this chapter, we provide an overview of a bioinformatics workflow to identify sex-specific associations between metabolites and cancer prognosis...
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Using Quantitative Metabolomics and Data Enrichment to Interpret the Biochemistry of a Novel Disease
You will learn how to use quantitative metabolomics data and a variety of data enrichment techniques to diagnose a disease, to understand its...
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Quantification of Proteins in Blood by Absorptive Microtiter Plate-Based Affinity Purification Coupled to Liquid Chromatography-Mass Spectrometry
Liquid chromatography (LC) coupled to mass spectrometry (MS) is increasingly used for quantification of proteins in blood. This development is...
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The Small-Protein Enrichment Assay (SPEA) for Analysis of Low Abundance Peptide Hormones in Plasma
The analysis of low abundance peptide hormones such as insulin in blood plasma is difficult with unbiased mass spectrometry-based proteomics, as they...
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Glycomics-Assisted Glycoproteomics Enables Deep and Unbiased N-Glycoproteome Profiling of Complex Biological Specimens
Mass spectrometry-driven glycomics and glycoproteomics, the system-wide profiling of detached glycans and intact glycopeptides from biological...
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Multiplexed Bead-Based Peptide Immunoassays for the Detection of Antibody Reactivities
Antigenic peptides are commonly used in serological test settings such as enzyme-linked immunosorbent assays (ELISA) to determine reactive antibodies...
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Progress in Targeted Mass Spectrometry (Parallel Accumulation-Serial Fragmentation) and Its Application in Plasma/Serum Proteomics
Targeted mass spectrometry using multiple reaction monitoring (MRM) or parallel reaction monitoring (PRM) has been commonly used for protein...
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Array-Based Multiplex and High-Throughput Serology Assays
The detection of antibody responses using serological tests provides means to diagnose infections, follow disease transmission, and monitor...
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High-Throughput and In-Depth Proteomic Profiling of 5 μL Plasma and Serum Using TMTpro 16-Plex
High-throughput and in-depth proteomic analysis of plasma and serum samples remains challenging due to the presence of multiple high-abundance...
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Bioinformatics Tools and Knowledgebases to Assist Generating Targeted Assays for Plasma Proteomics
In targeted proteomics experiments, selecting the appropriate proteotypic peptides as surrogate for the target protein is a crucial pre-acquisition...
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High-Throughput Proteome Profiling of Plasma and Native Plasma Complexes Using Native Chromatography
We describe a high-throughput method for co-fractionation mass spectrometry (CF-MS) profiling for native plasma protein profiling. CF-MS allows the...
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Preparation of Cryoprecipitate and Cryo-depleted Plasma for Proteomic Research Analysis
When frozen plasma is slowly thawed in cold conditions (1–6 °C), high-molecular-weight plasma proteins precipitate forming a concentrate known as...
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Use of Longitudinal Serum Analysis and Machine Learning to Develop a Classifier for Cancer Early Detection
Early detection of solid tumors through a simple screening process, such as the proteomic analysis of biofluids, has the potential to significantly...
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Untargeted Metabolomics Based on Liquid Chromatography–Mass Spectrometry for the Analysis of Plasma and Erythrocyte Samples in Childhood Obesity
The circulating metabolome of human peripheral blood provides valuable information to investigate the molecular mechanisms underlying the development...