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Updated: Jan 25, 2026
Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis
Published on: May 8, 2021
Evaluation of Urinary Proteome Library Generation Methods on Data-Independent Acquisition MS Analysis and its
Mindi Zhao1, Xiang Liu2, Haidan Sun2
1Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Beijing, 100730, China.
Purpose:
As an important part of the data-independent acquisition-mass spectrometry (DIA-MS) analysis approach, spectral library generation is closely related to the final protein identification and quantitation.
Experimental Design:
In this study, an attempt is made to evaluate the influence of different sample separation methods (reversed-phase liquid chromatography (RPLC) linear gradient elution and spin column step gradient fractionation) and data acquisition modes (data-dependent acquisition (DDA) and DIA) on library generation of the human urine proteome.
Results:
The RPLC separation method provides more proteins for generating the library than the spin column; however, the spin column library leads to identification of more proteins when used for the urine proteome analysis. The DDA mode can provide a larger spectral library than the DIA mode and the DDA-library leads to more protein identifications in the study. Use of a combined urinary protein library provides the most complete protein and peptide information, and the DIA approach can provide accurate protein quantitative information even for low-abundance proteins.
Conclusions And Clinical Relevance:
When the combined library is used to analyze the normal individual urine proteome (18 males and 18 females), gender-related and age-related proteins are discovered and functionally analyzed. This strategy may benefit urine proteome DIA analysis.
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