Evaluation of Urinary Proteome Library Generation Methods on Data‐Independent Acquisition MS Analysis and its Application in Normal Urinary Proteome Analysis

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.