This is the code repo for the paper Highly accurate and large-scale collision cross section prediction with graph neural network for compound identification. We developed a method named Structure included graph merging with adduct method for CCS prediction (SigmaCCS), and a dataset including 282 million CCS values for three different ion adducts ([M+H]+, [M+Na]+ and [M-H]-) of 94 million compounds. For each molecule, there are "Pubchem ID", "SMILES", "InChi", "Inchikey", "Molecular Weight", "Exact Mass", "Formula" and predicted CCS values of three adduct ion types.