Peptide sequence or amino acid sequence is the order in which amino acid residues, connected by peptide bonds, lie in the chain. The sequence is generally reported from the N-terminal end containing free amino group to the C_terminal end containing free carboxyl group. Peptide sequence is often called protein sequence if it represent the primary structure of a protein.

Several deductions can be made from the sequence. Long stretches of hydrophobic residues may indicate transmembrane helices. Certain residues indicate a beta sheet area. If full-lenght protein sequence is available, it is possible to estimate the isoelectric point of the protein. Methods for determining the peptide sequence include deduction from DNA sequence, Edman degradation, and mass spectrometry.