A peptide sequence tag is a piece of information about a
peptide
Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides.
A ...
obtained by
tandem mass spectrometry that can be used to identify this peptide in a
protein database.
Mass spectrometry
In general, peptides can be identified by fragmenting them in a
mass spectrometer. For example, during
collision-induced dissociation peptides collide with a gas within the mass spectrometer and break into pieces at their
peptide bond
In organic chemistry, a peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide or protein cha ...
s. The resulting fragment
ion
An ion () is an atom or molecule with a net electrical charge.
The charge of an electron is considered to be negative by convention and this charge is equal and opposite to the charge of a proton, which is considered to be positive by conven ...
s (called
b-ions and
y-ions) have mass differences corresponding to the
residue
Residue may refer to:
Chemistry and biology
* An amino acid, within a peptide chain
* Crop residue, materials left after agricultural processes
* Pesticide residue, refers to the pesticides that may remain on or in food after they are applie ...
masses of the respective
amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
s. Thus, a
tandem mass spectrum contains partial information about the amino acid sequence of the peptide. The peptide sequence tag approach, developed by Matthias Wilm and
Matthias Mann
Matthias Mann (born 10 October 1959) is a scientist in the area of mass spectrometry and proteomics.
Early life and education
Born in Germany he studied mathematics and physics at the University of Göttingen. He received his Ph.D. in 1988 at Y ...
at the
EMBL
The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 and ...
,
uses this information to identify the peptide in a database. Briefly, a couple of masses are extracted from the spectrum in order to obtain the peptide sequence tag. This peptide sequence tag is a unique identifier of a specific peptide and can be used to find it in a database containing all possible peptide sequences.
Peptide fragment notation
A notation has been developed for indicating peptide fragments that arise from a tandem mass spectrum.
Peptide fragment ions are indicated by a, b, or c if the charge is retained on the
N-terminus
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the ami ...
and by x, y or z if the charge is maintained on the
C-terminus
The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is ...
. The subscript indicates the number of amino acid residues in the fragment.
Prime
A prime number (or a prime) is a natural number greater than 1 that is not a product of two smaller natural numbers. A natural number greater than 1 that is not prime is called a composite number. For example, 5 is prime because the only ways ...
symbols indicate the number of protons or hydrogens added to the fragment to form the observed ion. For example, y
'' denotes the singly charged ion analogous to a protonated peptide, (y
)
2+ is a doubly charged ion analogous to a doubly protonated peptide.
See also
*
Protein sequence
Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesi ...
*
Protein mass spectrometry
Protein mass spectrometry refers to the application of mass spectrometry to the study of proteins. Mass spectrometry is an important method for the accurate mass determination and characterization of proteins, and a variety of methods and instrume ...
References
{{reflist
External links
PeptideSearch ProgramSPIDER: Sequence Tag Based Search Tool
Mass spectrometry
Proteomic sequencing