Re: Mass of protein and peptide standards

xiaohui chen (xhchen@biocserver.BIOC.CWRU.Edu)
Mon, 3 Aug 1998 14:55:58 -0400 (EDT)

At 12:42 PM 7/31/98 -0400, you wrote:
>To all of the mass spec. experts,
>
>I have a question regarding the correct mass of several proteins and
>peptides that I have been using for calibration standards.
>
>One of the standards I have been using is Bovine Insulin oxidized beta
>chain. Sigma lists the mass as 3495.9 Bruker's calibration list also lists
>the monoisotopic mass as 3494.65. But when I pull the amino acid sequence
>from swiss-prot and Do the calculations on both Rockefellers web site and
>EMBL's web site, I get a monoisotopic mass of 3397.674. What could account
>for this mass difference? Am I doing something wrong?
>
>The other standard is Horse heart cytochrome C. Sigma lists the mass as
>12384, Bruker lists the average mass as 12361.088 and I get an average
>calculated mass of 12374.02 including 1 Fe atom and 1 heme group with a mass
>of 616.6. Additionally, when I buy my standards from Sigma, for example,
>What modifications are on the cytochrome C. Swis-prot says cytochrome C has
>the following modifications
>
>Post translational modification: 1 ACETYLATION
>Binding site: 14 HEME (Covalent)
>Binding site: 17 HEME (Covalent)
>Binding site for metal ion: 18 IRON (Heme axial ligand)
>Binding site for metal ion: 80 IRON (Heme axial ligand)
>
>But the average mass with all of these modifications (calculated from
>Rockefeller's web site (www.proteimetrics.com)is 13088.50.
>
>Which mass is correct? and what am I actually getting from sigma?
>
>Thanks a lot in advance for the help
>
>
>__________________________________
>Brett Phinney
>North Carolina State University
>Department of Biochemistry
>Ph# 919-515-5786, Fax 919-515-2047
>ICQ# = 12442943
>
>

Brett,

I don't know about the modification of cytochrome C. For Bovine Insulin
oxidized beta chain, the MW you got from Swiss-prot is based on Cys side
chain -SH while that from Sigma is based on Cys side chain -SO3H. There are
two Cys in insulin beta chain, thus the average mass is 3399.93 (I got from
ExPAsy) + 6x16 = 3495.9 which is exactly the same as from Sigma.

Xiaohui Chen, Ph.D.
Department of Biochemistry
School of Medicine
Case Western Reserve University
2109 Adelbert Road
Cleveland, OH 44106
Ph: 216-368-3250
Fax: 216-368-3419
Email: xhchen@biochemistry.cwru.edu