Mass Spectrometry Analysis of Proteins in Hevea brasiliensis

The DEP spots were manually excised and in-gel digested with bovine trypsin as described (Wang et al., 2010 (link), 2015 (link)). Mass spectra of the peptides were acquired on an AB 5800 MALDI-TOF/TOF mass spectrometry (MS) instrument (AB SCIEX, Foster City, CA, United States) as described (Wang et al., 2015 (link)). The measured tryptic peptide masses were searched using ProteinPilot software (version 5.0) with an in-house MASCOT server against a self-constructed database derived from the original H. brasiliensis genome scaffolds (BioProject ID: PRJNA80191¹) and the draft genome (GenBank: AJJZ01000000) as described (Tang et al., 2016 (link)); this database included 46,718 sequences and 17,435,757 residues. Positively identification of protein spots was with scores higher than 65 (p < 0.001, the threshold with 95% confidence was 31), at least two matched peptides, and a minimum peptide coverage greater than 7%. Detailed identification information was provided in Supplementary Table S1 and Supplementary Figure S2.