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Updated: Mar 9, 2026

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis

Published on: May 8, 2021

Quantitative Proteomics Based on Optimized Data-Independent Acquisition in Plasma Analysis.

Eslam N Nigjeh¹, Ru Chen¹, Randall E Brand²

¹Department of Medicine, University of Washington , Seattle, Washington 98195, United States.

Journal of Proteome Research

|December 21, 2016

Summary

This summary is machine-generated.

Data-independent acquisition (DIA) mass spectrometry offers powerful clinical biomarker discovery. This study optimized DIA for complex plasma samples, enhancing reproducibility and reliability for biomarker development.

Keywords:

data-independent acquisition (DIA)mass spectrometry pancreatic cancer plasma proteomics

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Area of Science:

Proteomics
Analytical Chemistry
Biomarker Discovery

Background:

High-resolution mass spectrometry enables data-independent acquisition (DIA) for large-scale studies.
DIA is suitable for clinical biomarker research but faces challenges with complex plasma samples.

Purpose of the Study:

To assess the utility of DIA methodology for clinical plasma biomarker detection.
To optimize DIA parameters for reliable quantification in complex biological matrices.

Main Methods:

Developed a reproducible sample preparation and LC-MS/MS analysis workflow.
Constructed a pancreatic cancer-relevant plasma spectral library (>14,000 peptides).
Optimized DIA parameters using a nonhuman protein internal standard.

Main Results:

Achieved higher analytical and biological reproducibility for specific tryptic peptides.
Established quantification reliability based on retention time and signal intensity.
Assessed linear dynamic range and lower limit of quantification, highlighting sample complexity impact.

Conclusions:

Optimized DIA methodology demonstrates robustness for targeted clinical plasma analysis.
The approach offers advantages for biomarker development in complex samples.
Successful validation in a clinical plasma cohort confirms assay utility.