PLMD (Protein Lysine Modifications Database) is an online data resource specifically designed for protein lysine modifications (PLMs). The PLMD 3.0 database was extended and adapted from our CPLA 1.0 (Compendium of Protein Lysine Acetylation) database (Liu et al., 2011) and CPLM 2.0 (Compendium of Protein Lysine Modifications) database (Liu et al., 2014), and the PLMD 3.0 release contains 284780 modification events in 53501 proteins for 20 types of PLMs, including Ne lysine acetylation (Yang et al., 2007; Shahbazian et al., 2007; Smith et al., 2009), ubiquitination (Gao, et al., 2013), methylation (Chen, et al., 2006), sumoylation (Ren, et al., 2009; Xue, et al., 2006), glycation (Priego Capote, et al., 2010), butyrylation (Chen, et al., 2007; Cheng, et al., 2009; Zhang, et al., 2009), crotonylation (Tan, et al., 2011), malonylation (Xie, et al., 2012), propionylation (Chen, et al., 2007; Cheng, et al., 2009; Zhang, et al., 2009), succinylation (Xie, et al., 2012; Zhang, et al., 2011), neddylation (Rabut, et al., 2014; Soucy, et al., 2010), glutarylation (Tan, et al., 2014; Hirschey, et al., 2015), hydroxylation (Uzawa, et al., 2003), biotinylation (Hassan, et al., 2008; Kuroishi, et al., 2011), 2 hydroxyisobutyrylation (Dai, et al., 2014), lipoylation (Posner, et al., 2013), formylation (Jiang, et al., 2007), carboxylation (Jimenez Morales, et al., 2014), phosphoglycerylation (Moellering, R. E. and B. F. Cravatt, 2013) and prokaryotic pupylation (Liu, et al., 2011).