Boundaries around the model are set as the viscous absorbing boundary, and the bottom bedrock boundary is set as static boundary, serving as input boundary of the earthquake load and the dynamic input wave is applied as an acceleration record.
Cysteine carboxyamidomethlation was set as static modification and no other modification was checked.
Carbamidomethylation was set as static, and oxidation of methionine and phosphorylation of serine, threonine and tyrosine as dynamic modification respectively.
Carbamidomethylation of Cys was set as static modifications, phosphorylation of Ser/Thr/Tyr and oxidation of Met were set as variable modifications.
Search parameters included trypsin as the enzyme with 1 missed cleavage; oxidation of methionine was set as dynamic modification, while methylthio modification of cysteine and iTRAQ modification at N-terminus of the peptide and lysine were set as static modifications.
TMT tags on lysine residues and peptide N termini (229.162932 Da) and carbamidomethylation of cysteine residues (57.02146 Da) were set as static modifications, while oxidation of methionine residues (15.99492 Da) was set as a variable modification.
TMT tags on peptide N termini/lysine residues (+229.162932 Da) and carbamidomethylation of cysteine residues (+57.02146 Da) were set as static modifications, while methionine oxidation (+15.99492 Da) and serine, threonine, and tyrosine phosphorylation (+79.96633 Da) were set as variable modifications.
TMT tags on lysine residues and peptide N-termini (+ 229.162932 Da) and carbamidomethylation of cysteine residues (+ 57.02146 Da) were set as static modifications, while oxidation of methionine residues (+ 15.99492 Da) was treated as a variable modification.
Search parameters included trypsin as the enzyme with maximum 1 missed cleavage allowed; oxidation of methionine was set as a dynamic modification while alkylation at cysteine and iTRAQ modification at N-terminus of the peptide and lysine were set as static modifications.
Spectra were searched against the Arabidopsis thaliana entries in the nr-database with the following parameters: the peptide tolerance was set to 2 Da, MS/MS tolerance was set to 0.8 Da, carbamidomethylcysteine was set as a static modification, oxidation of Met as variable modification.
