Modified or Uncommon Amino Acids
- Homoserine, hsr: h
- Methionine sulfoxide, mso: m, is the oxidized form of
methionine. Use m to oxidize a particular M. Check "Oxidized
Methionine" to automatically oxidize all methionines.
- Ornithine, Orn: O, is an uncommon amino acid.
- Isoleucine or Leucine, Xle: X, isoleucine and leucine are
difficult to distinguish using mass spectrometry.
Post Translational Modifications
- One post-translational modification can be specified.
- Phosphorylated amino acids: s (serine), t (threonine),
and y (tyrosine). The phosphorylated amino acids are often given in
lower case, but not in this program.
Terminal Groups
Homoserine lactone: hsl, is produced on the N-terminus after
cleavage with CNBr. CNBr selectively cleaves after methionine. The
methionine is converted to homoserine lactone.
Substitutions
A given amino acid may be isotopically substituted. The
substituted amino acid is assumed to be 100% substituted.
Completely unsubstituted and completely substituted amino
acid can then be mixed in the specified percentage.
References:
Post-translational modifications:
PIR RESID Database
Rockefeller: PROWL Common Postranslational Modifications
ABRF: Delta Mass. A Database of Protein Post Translational Modifications
ExPASy: Accurate Mass & Pepetide Modification
ExPASy: FindMod tool
ExPASy: Find Mod Tool Masses
Wilkins M.R., Gasteiger E., Gooley A., Herbert B., Molloy M.P., Binz P.A., Ou K., Sanchez J.-C., Bairoch A., Williams K.L, Hochstrasser D.F.
High-throughput Mass Spectrometric Discovery of Protein Post-translational Modifications.
Journal of Molecular Biology, 289, p. 645-657 (1999).
Wilkins, M.R., Lindskog, I., Gasteiger, E., Bairoch, A., Sanchez, J.-C., Hochstrasser, D.F., and Appel, R.D. Detailed peptide characterisation using PEPTIDEMASS - a World-Wide Web accessible tool. Electrophoresis 18(3-4), 403-408 (1997)
Wilkins M.R., Gasteiger E., Bairoch A., Sanchez J.-C., Williams K.L., Appel R.D., Hochstrasser D.F.
Protein Identification and Analysis Tools in the ExPASy Server
in: 2-D Proteome Analysis Protocols (1998). Editor A.J. Link. Humana Press, New Jersey.
Some Search Engines that include post-translational modifications:
EMBL: Protein & Peptide Group PeptideSearch
UCSF: Protein Prospector
ExPASy: PeptideMass
Stable Isotope Substitution:
S. Sechi, B. T. Chait, "Modification of Cysteine Residues
by Alkylation. A Tool in Peptide Mapping and Protein Identification,"
Anal. Chem., 1998, 70, 5150-5158.
Xian Chen, Z. Fei, L. M. Smith, E. M. Bradbury, V. Majidi,
"Stable Isotope Assisted MALDI-TOF Mass Spectrometry for Accurate
Determination of Nucleotide Compositions of PCR Products,"
Anal. Chem., 1999, 71, 3118-3125.