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Related Experiment Video

Updated: Jul 17, 2026

Digital Microfluidics for Automated Proteomic Processing

Digital Microfluidics for Automated Proteomic Processing

Published on: November 7, 2009

Fully automated online multi-dimensional protein profiling system for complex mixtures.

Kiyonaga Fujii¹, Tomoyo Nakano, Hiroshi Hike

¹Clinical Proteome Center, Tokyo Medical University, 2-6-1, Nishi-shinjuku Shinjuku-ku, Tokyo 163-0217, Japan.

Journal of Chromatography. A

|December 9, 2004

Summary

A new automated online system for multi-dimensional protein profiling using two-dimensional liquid chromatography and tandem mass spectrometry (2D-LC-MS-MS) significantly enhances proteome analysis. This high-throughput method doubles detected peptide fragments and protein coverage for complex mixtures.

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Last Updated: Jul 17, 2026

Digital Microfluidics for Automated Proteomic Processing

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Published on: November 7, 2009

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

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

Published on: November 15, 2017

Area of Science:

Proteomics
Analytical Chemistry
Biochemistry

Background:

High-throughput proteome analysis of complex protein mixtures is challenging.
Existing methods require extensive optimization and time.
Previous offline systems provided a foundation for automation.

Purpose of the Study:

To develop a fully automated online system for multi-dimensional protein profiling.
To improve the efficiency and depth of proteome analysis.
To enable high-throughput analysis of complex protein samples.

Main Methods:

Construction of a fully automated online two-dimensional liquid chromatography and tandem mass spectrometry (2D-LC-MS-MS) system.
Integration of strong cation-exchange (SCX) and reversed-phase (RP) chromatography.
Automated analysis within 4 hours, including six SCX fractionations and 40-minute 2D-RP chromatography.

Main Results:

The 2D-LC-MS-MS system more than doubled the number of detected peptide fragments and protein coverage compared to 1D-LC-MS-MS.
Analysis of human 26S proteasome identified 723 peptide fragments from 31 proteasome components.
Achieved an average of 63% sequence coverage, including N-terminal modifications.

Conclusions:

The developed online 2D-LC-MS-MS system is effective for high-throughput analysis of highly complex protein mixtures.
This automated system is suitable for dynamic proteomics applications.
The method significantly advances the capabilities of proteome profiling.