Cerebrospinal fluid (CSF) Aβ42 and tau protein levels are established diagnostic biomarkers of Alzheimer's disease (AD). However, their inadequacy to represent clinical efficacy in drug trials indicates the need for new biomarkers. Sequential window acquisition of all theoretical fragment ion spectra (SWATH)-based mass spectrometry (MS) is an advanced proteomic tool for large-scale, high-quality quantification. In this study, SWATH-MS showed that VGF, chromogranin-A, secretogranin-1, and opioid-binding protein/cell adhesion molecule were significantly decreased in 42 AD patients compared to 39 controls, whereas 14-3-3ζ was increased (FDR < 0.05). In addition, 16 other proteins showed substantial changes (FDR < 0.2). The expressions of the top 21 analytes were closely interconnected, but were poorly correlated with CSF Aβ42, tTau, and pTau181 levels. Logistic regression analysis and data mining were used to establish the best algorithm for AD, which created novel biomarker panels with high diagnostic value (AUC = 0.889 and 0.924) and a strong correlation with clinical severity (all p < 0.001). Targeted proteomics was used to validate their usefulness in a different cohort (n = 36) that included patients with other brain disorders (all p < 0.05). This study provides a list of proteins (and combinations thereof) that could serve as new AD biomarkers. Cerebrospinal fluid (CSF) levels of Aβ1-42 (Aβ42), total Tau (tTau), and phosphorylated Tau181 (pTau181) are diagnostic markers of Alzheimer's disease (AD) 1,2. These biomarkers are currently used to confirm the core pathology of AD, i.e., Aβ and tau pathology, in deceased patients while they are alive 3 , and are also monitored in AD therapeutic trials 4. However, accumulating evidence has demonstrated a lack of utility of these markers after clinical onset of AD due to early concentration plateaus 5 and poor reflection of the clinical benefits of therapeutics that target them 6. CSF proteins related to synaptic function, neurodegeneration, inflammation, and Aβ metabolism have recently been suggested as supplementary biomarkers 7 ; however, they have not yet been clinically adopted.