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Proteomics01:33

Proteomics

7.2K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
7.2K
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

6.4K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
6.4K

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Related Experiment Video

Updated: May 30, 2025

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation
07:12

A Plasma Sample Preparation for Mass Spectrometry using an Automated Workstation

Published on: April 24, 2020

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A Technical Evaluation of Plasma Proteomics Technologies.

William F Beimers, Katherine A Overmyer, Pavel Sinitcyn

    Biorxiv : the Preprint Server for Biology
    |January 27, 2025
    PubMed
    Summary
    This summary is machine-generated.

    This study evaluated six plasma proteomic technologies for biomedical research. The Seer Proteograph XT method demonstrated superior proteomic depth and quantification capabilities compared to others, showing promise for cancer biomarker discovery.

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    Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification

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    Area of Science:

    • Biomedical Research
    • Proteomics
    • Analytical Chemistry

    Background:

    • Plasma proteomic technologies are crucial for biomedical research and diagnostics.
    • Rapid advancements necessitate rigorous technical evaluations of emerging platforms.

    Purpose of the Study:

    • To conduct a comprehensive technical comparison of six leading plasma proteomic technologies.
    • To evaluate methods based on proteomic depth, reproducibility, linearity, lipid interference, and limit of detection/quantification.
    • To assess the utility of these platforms for biomarker discovery in non-small cell lung cancer.

    Main Methods:

    • Six plasma proteomic technologies were evaluated: unenriched (Neat), Acid depletion, PreOmics ENRICHplus, Mag-Net, Seer Proteograph XT, and Olink Explore HT.
    • Methods were compared using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) and Olink Explore HT assays.
    • Performance metrics included proteomic depth, reproducibility, linearity, lipid interference tolerance, and limit of detection/quantification (LOD/LOQ).

    Main Results:

    • Seer Proteograph XT achieved the highest proteomic depth (~4,500 proteins), followed by Olink Explore HT (~2,600 proteins).
    • Neat, Mag-Net, Seer, and Olink demonstrated strong reproducibility, whereas PreOmics and Acid showed higher variability.
    • Seer exhibited superior LOD/LOQ, quantifying over 4,800 proteins, significantly more than other MS-based methods.

    Conclusions:

    • Seer Proteograph XT offers the greatest proteomic depth and quantification range among the evaluated methods.
    • The choice of plasma proteomic technology impacts achievable proteomic depth and reproducibility.
    • Further validation is needed to confirm the utility of these methods for non-small cell lung cancer biomarker discovery.