Robust, Precise, and Deep Proteome Profiling Using a Small Mass Range and Narrow Window Data-Independent-Acquisition...

Area of Science:

• Proteomics
• Mass Spectrometry
• Biochemistry

Background:

• Deep proteome profiling methods often require complex setups and exhibit limited quantitative precision.
• Existing data-independent acquisition (DIA) methods have limitations in proteome coverage and accuracy.

Purpose of the Study:

• To develop an easy-to-use, one-shot DIA method for high quantitative precision and proteome coverage.
• To improve the analysis of low-abundance proteins in samples with high dynamic range.

Main Methods:

• A novel DIA strategy focusing on a narrow mass range (430-670 m/z) with small, non-overlapping isolation windows.
• Application of the method to HEK cell lysates and mouse skeletal muscle proteome analysis.

Main Results:

• Quantification of over 9200 protein groups in HEK lysates with an average coefficient of variance of 3.2%.
• Doubled proteome coverage and significantly higher quantitative precision compared to standard data-dependent acquisition and a previous DIA method in mouse skeletal muscle.

Conclusions:

• The developed narrow mass range DIA method provides enhanced proteome coverage and quantitative precision.
• This method is particularly beneficial for quantifying low-abundance proteins in high-dynamic-range samples.