Peptide sequence tag

A peptide sequence tag is a piece of information about a peptide obtained by tandem mass spectrometry that can be used to identify this peptide in a protein database.cite journal |author=Hardouin J |title=Protein sequence information by matrix-assisted laser desorption/ionization in-source decay mass spectrometry |journal=Mass spectrometry reviews |volume=26 |issue=5 |pages=672–82 |year=2007 |pmid=17492750 |doi=10.1002/mas.20142] cite journal |author=Shadforth I, Crowther D, Bessant C |title=Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines |journal=Proteomics |volume=5 |issue=16 |pages=4082–95 |year=2005 |pmid=16196103 |doi=10.1002/pmic.200402091] cite journal |author=Mørtz E, O'Connor PB, Roepstorff P, Kelleher NL, Wood TD, McLafferty FW, Mann M |title=Sequence tag identification of intact proteins by matching tanden mass spectral data against sequence data bases |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=93 |issue=16 |pages=8264–7 |year=1996 |pmid=8710858 |doi=]

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 bonds. The resulting fragment ions (called b-ions and y-ions) have mass differences corresponding to the residue masses of the respective amino acids. 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 at the EMBL,cite journal |author=Mann M, Wilm M |title=Error-tolerant identification of peptides in sequence databases by peptide sequence tags |journal=Anal. Chem. |volume=66 |issue=24 |pages=4390–9 |year=1994 |pmid=7847635 |doi=] uses this information to identify the peptide in a database. Briefly, a couple of masses is 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 and by x, y or z if the charge is maintained on the C-terminus. The subscript indicates the number of amino acid residues in the fragment.

ee also

*Protein sequence
*Protein mass spectrometry

References

External links

* [http://www.mann.embl-heidelberg.de/GroupPages/PageLink/peptidesearchpage.html PeptideSearch Program]
* [http://www.bioinfor.com/products/peaks/spider.php SPIDER: Sequence Tag Based Search Tool]
* [http://www.ionsource.com/tutorial/protID/peptidetag.htm Peptide sequence tag tutorial]