I've got a question for all you mass spec people out there.
We use PSD-spectra to identify proteins. Yesterday I was doing a
reflectron MALDI-MS analysis on a HPLC-fraction of a tryptic digest. At
first sight, the fraction contained two peptides with masses of 1399.14
and 1343.66 respectively. When I tried to select the peptide with a mass
of 1343.66, I didn't succeed. However, it appeared again when putting a
very small selection window on the 1399.14 peak. So it appears that the
smaller peptide is actually a fragment of the 1399.14 one, however it's
signal is around 50% higher! The rest of the PSD-spectrum is very bad
since only minor fragmentations occur.
Now, I was wondering if anybody has ever noticed a loss of around 55 u
when working with tryptic peptides is PSD-mode. If I remember correctly
there was a paper describing the loss of 60 u in reflectron mode when
arginine was the C-terminal amino acid. However, to my knowledge I did not
see anything on this 55 u loss. Also when looking at a list of possible
modifications I don't see anything with an increase of 55 u.
Has anybody out there seen this and can come up with an explanation?
Thanks in advance and greetings from a cold Belgium!
Kris Gevaert
Flanders Interuniversity Institute for Biotechnology (V.I.B.)
Department of Medical Protein Chemistry
Universiteit Gent
K.L. Ledeganckstraat 35
B-9000 Gent
Belgium
Telephone: -- 32 / 9 2 64 52 91
Fax: -- 32 / 9 2 64 52 93 or 53 37
e-mail: krgev@gengenp.rug.ac.be