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.