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Related Concept Videos

Proteomics01:33

Proteomics

9.2K
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...
9.2K

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Related Experiment Video

Updated: Jan 8, 2026

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples
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Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

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An Ultrasensitive Spatial Tissue Proteomics Workflow Exceeding 100 Proteomes Per Day.

Melissa Klingeberg1, Christoph Krisp2, Sonja Fritzsche1

  • 1Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany; MDC-Bruker Center of Excellence for Single Cell Omics, Berlin, Germany; Humboldt University of Berlin, Faculty of Life Science, Berlin, Germany.

Molecular & Cellular Proteomics : MCP
|December 19, 2025
PubMed
Summary

Optimized spatial tissue proteomics workflows enable high-resolution proteome analysis. This study details a cellenONE protocol and Evosep ONE Whisper Zoom gradients, achieving over 7,500 protein quantifications and supporting large-scale translational research.

Keywords:
Evosep ONEFFPEWhisper ZoomautomationcellenONEdiaPASEFliverspatial proteomicssquamous cell carcinomatimsUltratissue profilingtonsil

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A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
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A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Tissue Analysis

Background:

  • High-resolution spatial tissue proteomes require optimized sample processing, chromatography, and mass spectrometry (MS) acquisition.
  • Balancing these factors is crucial for comprehensive proteome coverage.

Purpose of the Study:

  • To present an advanced cellenONE protocol for loss-reduced tissue processing.
  • To compare Evosep ONE Whisper Zoom gradients and common DIA acquisition schemes on a timsUltra AIP mass spectrometer.
  • To evaluate the impact of tissue type, gradient length, and sample amount on proteome coverage.

Main Methods:

  • Utilized an advanced cellenONE protocol for tissue processing.
  • Employed Evosep ONE Whisper Zoom gradients (20, 40, 80, 120 samples per day).
  • Used three common data-independent acquisition (DIA) schemes on a timsUltra AIP mass spectrometer.

Main Results:

  • Tissue type, gradient length, and sample amount significantly influence proteome coverage.
  • Increased tissue sampling yielded diminishing returns for short gradients (120/80 SPD) but substantial gains for longer gradients (40/20 SPD).
  • Quantified over 7,500 proteins from 0.5 nL of tonsil T-cell niches using longer gradients and higher tissue amounts; 3,200 proteins were quantified from 0.04 nL with the 120 SPD method.

Conclusions:

  • The developed workflow enables the preparation and acquisition of over 100 high-quality spatial tissue proteomes daily.
  • This facilitates cohort-size spatial tissue proteomics for translational research.
  • Demonstrated application to oral cavity squamous cell carcinoma, revealing disease pathways and region-specific changes.