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Proteomics

Proteomics

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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Related Experiment Video

Updated: May 31, 2025

Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier

Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier

Published on: December 9, 2022

Cell Storage Conditions Impact Single-Cell Proteomic Landscapes.

Bora Onat^1,2,3, Amanda Momenzadeh^1,2,3, Ali Haghani³

¹Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.

Journal of Proteome Research

|January 24, 2025

Summary

This summary is machine-generated.

Shipping cells for single-cell proteomics (SCP) requires understanding storage effects. Cold or frozen storage significantly alters cell size and proteome profiles, impacting SCP data quality.

Keywords:

HEK293T LC−MS SCP single cell proteomics storage conditions timsTOF-SCP

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Last Updated: May 31, 2025

Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier

Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier

Published on: December 9, 2022

Proteomic Analysis of Human Macrophage Polarization Under a Low Oxygen Environment

Proteomic Analysis of Human Macrophage Polarization Under a Low Oxygen Environment

Published on: January 7, 2019

Evaluation of the Storage Stability of Extracellular Vesicles

Evaluation of the Storage Stability of Extracellular Vesicles

Published on: May 22, 2019

Area of Science:

Proteomics
Cellular Biology
Mass Spectrometry

Background:

Single-cell transcriptomics (SCT) advanced cellular heterogeneity studies.
Single-cell proteomics (SCP) offers a more functional cellular dynamics perspective.
Logistical challenges in SCP necessitate remote sample processing, including shipping.

Purpose of the Study:

To investigate the impact of various cell storage conditions on single-cell proteomic analysis.
To evaluate how shipping and storage affect proteome composition and cellular morphology.

Main Methods:

Utilized Data-Independent Acquisition (DIA) with Parallel Accumulation Serial Fragmentation (diaPASEF).
Compared proteomic profiles of 293T cells stored at 37 °C (control), 4 °C overnight, and -196 °C (liquid nitrogen).
Analyzed changes in cell diameter, elongation, and proteome composition.

Main Results:

Both cold (4 °C) and frozen (-196 °C) storage conditions induced significant alterations in cell morphology (diameter, elongation).
Storage significantly impacted the proteome composition at the single-cell level.
Control conditions (37 °C) showed minimal alterations compared to cold and frozen storage.

Conclusions:

Cell storage conditions critically affect cellular morphology and proteome profiles.
Findings provide essential technical insights for optimizing SCP sample preparation and ensuring data integrity.
This study addresses a key technical gap for widespread adoption of remote SCP analysis.