In a bottom-up strategy, peptide sequences are first identified from MS/MS spectra, and the existence and abundance of the proteins are then inferred from the peptide information. At the same time, posttranslational modifications also play an important role in peptide matching. However, the protein inference step can produce errors and a loss of information. In addition, the genes and proteins are highly homologous in some species, such as human and mouse; if different species of proteins are mixed in one sample, it is difficult to find the difference from protein level alone. In this part, we try to demonstrate the importance of integrative analysis of peptide level and posttranslational modifications in proteomics by two examples.