Identifying Sex-Specific Serum Patterns of Alzheimer's Mice through Deep TMT Profiling and a Concentration-Dependent Concatenation Strategy

• Published in: Journal of proteome research 2023-12, Vol.22 (12), p.3843-3853
• Main Authors: Dey, Kaushik Kumar, Yarbro, Jay M, Liu, Danting, Han, Xian, Wang, Zhen, Jiao, Yun, Wu, Zhiping, Yang, Shu, Lee, DongGeun, Dasgupta, Abhijit, Yuan, Zuo-Fei, Wang, Xusheng, Zhu, Liqin, Peng, Junmin
• Format: Article
• Language: English
• Subjects: Alzheimer Disease - metabolism; Animals; Chromatography, Reverse-Phase; Female; Humans; Male; Mice; Proteome - analysis; Reproducibility of Results; Tandem Mass Spectrometry - methods
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/acs.jproteome.3c00496

Alzheimer's disease (AD) is the most prevalent form of dementia, disproportionately affecting women in disease prevalence and progression. Comprehensive analysis of the serum proteome in a common AD mouse model offers potential in identifying possible AD pathology- and gender-associated biomarkers. Here, we introduce a multiplexed, nondepleted mouse serum proteome profiling via tandem mass-tag (TMTpro) labeling. The labeled sample was separated into 475 fractions using basic reversed-phase liquid chromatography (RPLC), which were categorized into low-, medium-, and high-concentration fractions for concatenation. This concentration-dependent concatenation strategy resulted in 128 fractions for acidic RPLC-tandem mass spectrometry (MS/MS) analysis, collecting ∼5 million MS/MS scans and identifying 3972 unique proteins (3413 genes) that cover a dynamic range spanning at least 6 orders of magnitude. The differential expression analysis between wild type and the commonly used AD model (5xFAD) mice exhibited minimal significant protein alterations. However, we detected 60 statistically significant (FDR < 0.05), sex-specific proteins, including complement components, serpins, carboxylesterases, major urinary proteins, cysteine-rich secretory protein 1, pregnancy-associated murine protein 1, prolactin, amyloid P component, epidermal growth factor receptor, fibrinogen-like protein 1, and hepcidin. The results suggest that our platform possesses the sensitivity and reproducibility required to detect sex-specific differentially expressed proteins in mouse serum samples.