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Related Concept Videos

Proteomics01:33

Proteomics

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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...
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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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Related Experiment Video

Updated: Jan 16, 2026

Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization
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Next-Generation Multiplexed Targeted Proteomics Quantifies Post-Translational Modifications, Compound-Protein

Steven R Shuken1, Geordon A Frere1, Charlotte R Beard2,3

  • 1Department of Cell Biology, Harvard Medical School, Boston, MA, USA.

Biorxiv : the Preprint Server for Biology
|September 26, 2025
PubMed
Summary
This summary is machine-generated.

GoDig 2.0 enhances targeted proteomics by increasing sample multiplexing and efficiency. This advanced platform enables high-throughput analysis of protein modifications, aiding in biomarker discovery for diseases like Alzheimer's.

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Area of Science:

  • Proteomics and Mass Spectrometry
  • Molecular Biology and Biochemistry
  • Biomarker Discovery

Background:

  • Targeted pathway proteomics is crucial for understanding cellular signaling.
  • Existing methods often require manual scheduling and synthetic standards, limiting throughput.
  • The GoDig platform was previously developed to address these limitations.

Purpose of the Study:

  • To present GoDig 2.0, an upgraded platform for sensitive, multiplexed targeted pathway proteomics.
  • To enhance sample multiplexing, time efficiency, and success rates compared to GoDig 1.0.
  • To enable flexible library generation and high-throughput analysis of protein modifications.

Main Methods:

  • GoDig 2.0 utilizes mass spectrometry for sensitive, multiplexed peptide quantification.
  • Increased sample multiplexing to 35-fold and reduced scan delays were implemented.
  • Spectral and elution libraries were generated from diverse mass spectrometry data types.
  • Libraries of human phosphorylation sites, diglycyl-lysine peptides, and reactive cysteines were compiled.

Main Results:

  • GoDig 2.0 quantifies >99% of 800 peptides in a single run, measuring 2.4× more targets than GoDig 1.0.
  • Kinase signaling differences were profiled across cell lines using a library of 23,989 human phosphorylation sites.
  • A hyperphosphorylated tau assay (including pTau127) was established in human brain tissue, identifying potential Alzheimer's disease biomarkers.
  • Diglycyl-lysine peptides and covalent compound-protein interactions were quantified.

Conclusions:

  • GoDig 2.0 significantly advances targeted proteomics capabilities.
  • The platform enables high-throughput, site-specific analysis of protein modifications in various biological contexts.
  • GoDig 2.0 facilitates biomarker discovery and the study of protein interactions and modifications.