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.
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.
You can input your own crosslinker or use one of the examples.
- Only homo-bifunctional crosslinkers are covered by this
- The difference formula is the formula of the crosslinker
with the elements removed from the peptide subtracted. For
example, formaldehyde produces CH2 crosslinks.
However, in the reaction with two lysines, two H's are removed
from the amino groups. So the crosslinker difference formula
is just "C 1". That is the hydrogens cancel out.
- The Change in mass field will be filled in for you. You
don't need to calculate this value yourself. In fact, the
browser won't let you type in this field (on purpose).
Target ion m/z
The target ion m/z is used to display only those peptides
that are close to the chosen value. The target ion m/z
doesn't change the calculations in any way. The value
just controls which results are printed.
This part of the program will display the isotope peaks for
your peptide. The program allows stable isotope substitution
for one type of amino acid. If your peptide has a sulfur
containing amino acid, this calculation will take several
minutes ( sulfur has four naturally occuring isotopes).
- If you are using the isotope substitution option,
please note the following:
The isotope cluster of the unsubstituted "parent"
peptide will be displayed first. Be patient, because the
isotope cluster of the substituted peptide will then be calculated.
This calculation will take as long as the "parent" peptide.
Then the averaged isotope cluster will be displayed based
on the substituted amino acid composition that you enter.
- You can also specify isotope substitution for the
crosslinker. The crosslinker is listed as "=" in the amino
acids pull-down list.
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.
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
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.