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Important Issues in Planning a Proteomics Experiment : Statistical Considerations of Quantitative Proteomic Data
Mass spectrometry is frequently used in quantitative proteomics to detect differentially regulated proteins. A very important but unfortunately...
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DIA-MSE to Study Microglial Function in Schizophrenia
Here, we describe a proteomic pipeline to use a human microglial cell line as a biological model to study schizophrenia. In order to maximize the...
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Silver Staining of 2D Electrophoresis Gels
Silver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels. It combines excellent sensitivity (in the low...
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Mass Spectrometry-Based Analysis of Mycobacterial Single-Colony Proteome
Mass spectrometry-based single-cell proteomic analysis has recently gained momentum and is now an emerging area with established protocols and...
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Protein Quantification Using the “Rapid Western Blot” Approach
For the quantification of certain proteins of interest within a complex sample, Western blot analysis is the most widely used method. It enables...
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Missing Value Monitoring to Address Missing Values in Quantitative Proteomics
Many classes of key functional proteins such as transcription factors or cell cycle proteins are present in the proteome at a very low concentration....
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Mining Protein Expression Databases Using Network Meta-Analysis
Public databases featuring original, raw data from “Omics” experiments enable researchers to perform meta-analyses by combining either the raw data...
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Quantitative MS Workflow for a High-Quality Secretome Analysis by a Quantitative Secretome-Proteome Comparison
Cells secrete proteins to communicate with their environment. Therefore, it is interesting to characterize the proteins which are released from cells...
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Application of Label-Free Proteomics for Quantitative Analysis of Urothelial Carcinoma and Cystitis Tissue
A label-free approach Label-free approaches based on a highly reproducible and stable workflow allows for quantitative...
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The Whereabouts of 2D Gels in Quantitative Proteomics
Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for...
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Isolation of Apoplastic Fluid from Woody Plant Leaves: Grapevine and Coffee as a Case Study
Proteomics is one of the key approaches to understand plant cell physiology involving the regulation of expression of many genes and metabolite...
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Quantitative Proteome Data Analysis of Tandem Mass Tags Labeled Samples
In mass spectrometry-based proteomics, relative quantitative approaches enable differential protein abundance analysis. Isobaric labeling strategies,...
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Automated Workflow for Peptide-Level Quantitation from DIA/ SWATH-MS Data
Data-independent acquisition (DIA) is a powerful method to acquire spectra from all ionized precursors of a sample. Considering the complexity of the...
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Serum Proteomic Profiling in Rheumatoid Arthritis by Antibody Suspension Bead Arrays
The versatility of protein microarrays provides researchers with a wide variety of possibilities to address proteomic studies. Therefore, protein...
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Mass Spectrometry-Based Proteomics for Analysis of Hydrophilic Phosphopeptides
Protein phosphorylation is a critical posttranslational modification (PTM), with cell signaling networks being tightly regulated by protein...
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Mesenchymal Stem Cell-Derived Extracellular Vesicle Isolation and Their Protein Cargo Characterization
In the present protocol, extracellular vesicles (EVs) released from a primary culture of human umbilical cord mesenchymal stem cells (MSCs) were...
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SWATH-MS Protocols in Human Diseases
Identification of molecular biomarkers for human diseases is one of the most important disciplines in translational science as it helps to elucidate...
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Quantification and Identification of Post-Translational Modifications Using Modern Proteomics Approaches
Post-translational modifications (PTMs) occur dynamically, allowing cells to quickly respond to changes in the environment. Lysine residues can be...
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Label-Free Proteomics of Quantity-Limited Samples Using Ion Mobility-Assisted Data-Independent Acquisition Mass Spectrometry
Over the past two decades, unbiased data-independent acquisition (DIA) approachesProteomicsapproaches have gained increasing popularity in the...
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Differential Proteome Analysis Using 2D-DIGE
Classical 2D-PAGE allows comparison and quantitation of proteomes by visualization of protein patterns using gel stains and comparative image...