database

Chem 638 – April 16, 2009– Database Exercise – Chemistry, room

A. C. Harms and M. M. Vestling

Goal: To learn how to use several public calculators and small molecule databases

1.) Find the elemental formula for the following peptide: KGSEQESVK

Mass Spectrometry deals with numbers, so it is important to have a way to translate letters to numbers at your computer. Most instruments have such translators, but one is not always at one's instrument.

2.) Your peptide with the sequence SLHTLFGDELCK has the unexpected mass of 1419.694. How is it modified? Hint: first calculate the mass of the unmodified peptide. Then go to the ABRF web site for Delta Mass. Be alert to what values each program is giving you: M+, [M+H]+, [M-H]-, monoisotopic, or average.

http://prospector.ucsf.edu [MS-Product]

http://www.ionsource.com/programs/pepcalc.htm

http://rna.rega.kuleuven.ac.be/masspec/pepcalc.htm

http://www.abrf.org/index.cfm/dm.home

3.) You think your peptide, KGSEQESVK, may be phosphorylated. Use the mass of the peptide plus Delta Mass to calculate what negative ion you should look for.

4.) Find vancomycin in PubChem. What information relevant to mass spectrometry is present? Does PubChem give the same mass for vancomycin as ChemCalc?

http://pubchem.ncbi.nlm.nih.gov

http://www.chemcalc.org

Another small molecule isotope pattern generator is Chemputer

http://winter.group.shef.ac.uk/chemputer/isotopes.html

5.) Say you don't have the name of the compound, but you believe its monoisotopic mass is 390.2770 based on a mass spectrum. How do you come up with ideas for the structure and formula for this compound? Notice how different databases will assign this compound to different classes of molecules.

http://webbook.nist.gov/chemistry [molecular weight]

http://metlin.scripps.edu/metabo_search.php

http://mmcd.nmrfam.wisc.edu/index.html

http://www.ch.ic.ac.uk/java/applets/f2m2f/

6.) If the monoisotopc mass is 390.2770, to use the example above, what ions should you look for in a) an electron impact mass spectrum? b) MALDI mass spectrum? c) electrospray ionization mass spectrum? Remember, mass spectrometry measures m/z, so compounds have to have some charge to be seen.

7.) A researcher walks into your mass spectrometry laboratory and wants to know if you can help find if cortisol and maybe some other related compounds in blood. What information can you gather from the following sites to start the conversation with the researcher?

http://www.genome.jp (GenomeNet--> KEGG) look at pathways and reactions

Do you see which enzyme converts cortisol to cortizone?

http://www.hmdb.ca (Human Metabolism Database in Canada)

Can you find the MS/MS data for this compound acquired on a triple quadrupole?