Of the 96 differentially abundant proteins identified in the longitudinal analysis, YWHAH was significantly higher (p < 0.05, 2.4-fold) in VAP Baseline compared with control Baseline. Further comparison of VAP Baseline with other intubation time points in controls showed significant increase of PGK1 (p < 0.05, 2-fold) and NCL (p < 0.05, 2.2-fold) in the VAP Baseline. However, 26 proteins including YWHAH and NCL were not detected in VAP positive but were present in all Baseline (Fig. 3B, Table III). Here, PGK1 is linked to ventilator-associated pneumonia.