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Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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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...
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Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
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A workflow for targeted proteomics assay development using a versatile linear ion trap.

Ariana E Shannon, Rachael N Teodorescu, Nojoon Soon

    Biorxiv : the Preprint Server for Biology
    |June 10, 2024
    PubMed
    Summary
    This summary is machine-generated.

    Hybrid quadrupole-linear ion trap instruments enable cost-effective targeted proteomics from global data-independent acquisition (DIA) measurements without high-mass accuracy. This approach allows for rapid assay development and consistent quantification even with limited sample input.

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    Area of Science:

    • Mass Spectrometry
    • Proteomics
    • Analytical Chemistry

    Background:

    • Single-cell proteomics requires high-mass accuracy instruments, limiting accessibility.
    • Triple quadrupoles are limited to targeted proteomics.
    • Linear ion traps (LITs) offer a cost-effective alternative for targeted and global proteomics.

    Purpose of the Study:

    • To demonstrate a workflow for developing targeted proteomics assays using a hybrid quadrupole-LIT instrument.
    • To enable targeted proteomics from global data-independent acquisition (DIA) without high-mass accuracy.
    • To assess the performance of this workflow for quantitative linearity and consistency.

    Main Methods:

    • Utilized a hybrid quadrupole-linear ion trap (LIT) mass spectrometer.
    • Employed gas-phase fraction-based data-independent acquisition (DIA) for target library generation.
    • Used EncyclopeDIA software for parallel reaction monitoring (PRM) assay scheduling and quantification.

    Main Results:

    • Achieved consistent quantification across three orders of magnitude of input material.
    • Demonstrated peptide quantitative linearity down to 25x dilution with only 1 ng proteome.
    • Showed consistency between flow cytometry immune cell populations and LIT-based proteomics immune markers at 1 ng total protein.

    Conclusions:

    • Hybrid quadrupole-LIT instruments provide an economic solution for targeted proteomics.
    • This workflow democratizes mass spectrometry for various laboratory settings.
    • Enables sensitive and quantitative proteomics without requiring stable isotope-labeled standards.