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Peptide Sequencing

Bioinformatic tools for Peptide Identification by Mass Spec

The Peptide sequence is the order of amino acid residues connected by peptide bonds. The peptide bond connects amino acids into a linear unbranched chain. The peptide bond is formed by a condensation reaction between the amino acid and the carboxyl group of another. The repeated amide N, C and carbonyl C atoms of each amino acid residue form the backbone of a protein molecule from which the various side-chain groups project. As a consequence of the peptide linkage, the backbone has polarity, since all the amino groups lie to the same side of the C atoms. Sequence databases have many peptide sequences. The peptide sequences in these databases use various notations to describe the sequence where the full names of the amino acids are rarely given and usually 3 or 1 letter abbreviations are used.Deductions can be made from the peptide sequence itself. For instance stretches of hydrophobic residues may indicate transmembrane helices in which these helices may indicate the peptide is a cell receptor. A beta sheet area can be also seen when certain residues are together. If the full length peptide sequence is known it is then possible to estimate the isoelectric point of the peptide. The peptide sequence can be determined from the following methods: DNA sequence, Edman degradation, and mass spectrometry.


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